Re: [base] basedb-users Digest, Vol 70, Issue 1
On 2015-03-12 09:24, Jari Häkkinen wrote: One source for the problem is that the underlying RMAExpressConsole program doesn't handle ST arrays, or maybe treats ST arrays differently. I meant to say that problem may be with RMAExpressConsole but I don't know. Jari -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Anyone have a cloud-deployable image with BASE?
Hi, There is no cloud-deployable BASE available and there is no plans for one either. The demo server has moved and the redirect seems to be broken. I have sent a mail to the network administrator of the previous facilities asking them to restore the redirect. The demo server is located at https://base.onk.lu.se/demo/ but unfortunately it is empty and the plan is to populate it with some sample data. Cheers, Jari On 2014-11-06 22:24, Cornwell, Adam wrote: Hello, I have been interested in setting up BASE for a while now, and I think it’s about time to try it out. To facilitate this, I was wondering if anyone has a cloud-deployable (Amazon etc) image available, to avoid the usual boilerplate OS config and such? This would be quite useful given that the demo server has been down for a while. Thanks, Adam Cornwell Programmer/Analyst Center for Translational Neuromedicine -- ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- For a successful technology, reality must take precedence over public relations, for nature cannot be fooled. - Richard P. Feynman, Rogers Commission Report 1986 -- ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Base 3.2 installation on Mac OS 10.6 server
On 2013-09-12 16:47, Laurent TROXLER wrote: Yes, I can axes to Tomcat Home page and login as root. There I can see that base2 is uploaded. There isn't any obvious error on the web interface. To answer to Jari, I am working presently directly on the server to avoid any internet problem. Ok. What do you mean by work directory hierarchy ? Does it mean that each directory of the /Library/Tomcat/work/Catalina/localhost/base2 chain should be owned by www or it should be the case only for base2 ? At this time it is owned by root from the _appserveradm group (I guess setted by the system) On my machine all files and directories in /Library/Tomcat/work are owned by the tomcat user. Normally the ownership should be correct if you have not tampered with them. To decide the tomcat user do 'ps auxw | grep tomcat' and you should see the userid in the leftmost column in the listing (assuming that the program is called tomcat on your system). Another path is to look at the owner of the log files since these should be owned by the tomcat user on your system. Do 'ls -ls /Library/Tomcat/logs'. Change the ownership to match the owner of the log files with 'sudo chown -R userid:groupid /Library/Tomcat/work' Anyhow, I do not think the above is the problem. I was also wondering if my base.config file was well setted. Should the db.username be setted to base2user or to root ? Thanks again for your help. db.username should be set to the userid you used when you create the database in mysql, i.e., whatever you used as db_user in GRANT ALL ON base2.* TO db_user@localhost IDENTIFIED BY 'db_password'; The root userid is used in the web interface once you get the server running. (Assuming that you did not set it to something else during installation which I do myself.) going through the log files here is what I can get: system.log: repeating those two lines Sep 11 10:32:00 seridi java[85937]: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. Sep 11 10:32:02 seridi com.apple.launchd[1] (org.apache.tomcat): Throttling respawn: Will start in 8 seconds There is a short discussion on this issue at https://discussions.apple.com/thread/5270047?start=0tstart=0 maybe that can help you with the above issue? /Library/Tomcat/logs/catalina.2013-09-11.log : Sep 11, 2013 10:52:05 AM org.apache.catalina.startup.Bootstrap initClassLoaders SEVERE: Class loader creation threw exception java.lang.InternalError: Can't connect to window server - not enough permissions. at java.lang.ClassLoader$NativeLibrary.load(Native Method) at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1827) at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1724) at java.lang.Runtime.loadLibrary0(Runtime.java:823) at java.lang.System.loadLibrary(System.java:1045) at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50) at java.security.AccessController.doPrivileged(Native Method) at java.awt.Toolkit.loadLibraries(Toolkit.java:1605) at java.awt.Toolkit.clinit(Toolkit.java:1627) at sun.awt.AppContext$2.run(AppContext.java:240) at sun.awt.AppContext$2.run(AppContext.java:226) at java.security.AccessController.doPrivileged(Native Method) at sun.awt.AppContext.initMainAppContext(AppContext.java:226) at sun.awt.AppContext.access$200(AppContext.java:112) at sun.awt.AppContext$3.run(AppContext.java:306) at java.security.AccessController.doPrivileged(Native Method) at sun.awt.AppContext.getAppContext(AppContext.java:287) at com.sun.jmx.trace.Trace.out(Trace.java:180) at com.sun.jmx.trace.Trace.isSelected(Trace.java:88) Have you set the following parameters for the tomcat server? (See section Tomcat at the top in http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html CATALINA_OPTS=-Xmx1G -Dorg.apache.jasper.compiler.Parser.STRICT_QUOTE_ESCAPING=false -Dcom.sun.media.jai.disableMediaLib=true -Djava.awt.headless=true The last option is important, see http://stackoverflow.com/questions/11024555/elasticsearch-java-lang-internalerror-cant-connect-to-window-server since it will avoid the problem of connecting to the window server. If I remove the last option myself, I get a windowed application named org.apache.catalina.startup.Bootstrap that remains until I shutdown tomcat (cf. attached png). If I kill the window application then tomcat dies. If the headless option is true then the windowed application does not appear and tomcat runs fine. However, I do not know how I have managed to allow java to connect to my window server though. I have been running BASE for years now so may be it was something I had to fix long time ago? Cheers, Jari attachment: bootstrapApplication.ong.png-- How ServiceNow helps IT people transform IT departments: 1. Consolidate legacy IT systems to a single system of record for IT 2. Standardize and globalize service processes across IT 3.
Re: [base] Base 3.2 installation on Mac OS 10.6 server
On 2013-09-11 10:57, Laurent Troxler wrote: going through the log files here is what I can get: system.log: repeating those two lines Sep 11 10:32:00 seridi java[85937]: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. Sep 11 10:32:02 seridi com.apple.launchd[1] (org.apache.tomcat): Throttling respawn: Will start in 8 seconds /Library/Tomcat/logs/catalina.2013-09-11.log : Sep 11, 2013 10:52:05 AM org.apache.catalina.startup.Bootstrap initClassLoaders SEVERE: Class loader creation threw exception java.lang.InternalError: Can't connect to window server - not enough permissions. It seems like the tomcat process cannot connect to the window server. I have noticed that when I start (or stop) tomcat on my MacBook there is some interaction with the window server on my mac (i.e., the finder process). I have no idea why this happens but I think it is java that tries to connect to the window server. Are you sitting directly in the machine you try to run tomcat on? If you ssh into the machine you may be unable to connect to the window server since you must own the window server process. Try to log in directly to the mac server and start the services from a terminal. You may see some windows flash by during the start up phase. This experiment would be interesting. On my machine I allow Remote login (under the Sharing pane in System preferences) ... maybe that option resolves something. Can you connect to the tomcat server at all? As Nicklas points out, try connecting to http://hostname:8080 and you should see a Tomcat welcome page. Also, the tomcat server user should own the work directory hierarchy. On my machine this user is 'www'. I have a running BASE 3.2.3 server with Tomcat 6.0.35 and PostgreSQL 9.3.0. Non-Apple software I almost always install Macports packages (tomcat and Postgresql). I run on Mac OSX 10.7.5 non-server version. I think your issues are symptoms of a tomcat/java/mac window server clash. Cheers, Jari -- How ServiceNow helps IT people transform IT departments: 1. Consolidate legacy IT systems to a single system of record for IT 2. Standardize and globalize service processes across IT 3. Implement zero-touch automation to replace manual, redundant tasks http://pubads.g.doubleclick.net/gampad/clk?id=5127iu=/4140/ostg.clktrk ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] BASE database
We have realized that migration from BASE 1.2 to BASE 2/3 is only supported from a BASE 1.2 server running MySQL. We do think that adding support for other database engines is possible but we have not tested it and will not actively work on extending migration support beyond what can be found in BASE 2.15. I simply write this as information for interested users The path forward to add support for BASE 1.2 migration from a non-MySQL installation is to create a version of http://base.thep.lu.se/browser/tags/2.15/config/dist/mysql-migration-queries.sql for the database engine in use. Then change parameter queryStatementFile in migrate.properties to point to your new sql definition file. Some change in the migration code may be needed as well. We cannot estimate how much work is needed to be successful. Jari -- How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] BASE database
Hi, The procedure to upgrade from 1.2 to latest BASE is uncharted territory for us. We switched from 1.2 when BASE 2.6 was current. One path forward may be as outlined below. Each BASE 2 and newer distribution contains upgrade instructions. Please read them. Please report if you succeed and use the mailing list for further assistance so we can share this experience with the community. Good Luck, Jari 0) Backup your precious data. 1) Upgrade to latest 1.2.x version, i.e., version 1.2.17b available from http://base2.thep.lu.se/base1.2/ There are some notes regarding upgrading I found in the waybackmachine, http://web.archive.org/web/20070210105058/http://base1.thep.lu.se/ Update from 1.2.17: Fixed compilation errors with gcc 4.0. BASE 1.2.17: This release of BASE contains a number of minor fixes and some somewhat bigger changes. If you are upgrading from an older version, there are few things you need to do in addition to running the database migration script: - If you are using PHP 4.4.x, you have to make some changes to the files in include/local (reporter_columns.inc.php and raw_columns.inc.php) to get rid of warnings about assign-by-reference. If you haven't modified these files, simply remove them from where you have installed BASE before doing the 'make install', and they will be replaced by the newest version. If you have modified them, you should instead replace all occurences of = with a plain =. - The disk quota system has been extended to cover not only uploads but also experiments, raw data and other big things. For this to work the disk usage of existing users must be calculated and stored. Do this by running bin/refreshQuotaUsage.php before starting BASE after you've run dbmigrate_1.2_to_latest.php. There's more info in the new admin guide (in documentation/ and on the web site). - When exporting data for plugins, files in the 'normal' BASEfile format are now created from the serial format by an external program to reduce the time it takes. The program requires a valid BASEfile, with a header called 'section', and this could cause problems with some plugins whose definitions do not have a hidden parameter called 'section'. Such plugins need to be corrected. - It has been made easier to add new patterns for merging four 96-well plates into a 384-well plate. Changes to the PHP code are no longer necessary for this. The description of how to do it can be found in a couple of comments in plates.inc.php. * PHP 5.0 has not yet been fully tested with BASE although it might actually work. 2) Following the advice in http://base.thep.lu.se/chrome/site/2.17/html/admindoc/installation_upgrade/installation_upgrade.migration.html Upgrade then to BASE version 2.15.0 available for download from http://base.thep.lu.se/wiki/DownloadOld Read the migration program instructions carefully we haven't done that for several years ourselves. The migration may take long time. 3) Upgrade to latest BASE 2 version, 2.17.2 available from http://base.thep.lu.se/wiki/DownloadPage 4) Finally, upgrade to latest BASE 3 version 3.2.2 available at http://base.thep.lu.se/wiki/DownloadPage On 2013-05-07 09:42, Franck Samson wrote: Hello Sir, I'm looking for help on the BASEprogram, here is our situation we have a very old version of BASE (1.2 I think, the php version) and we would like to make it evolve to the latest version available, however the update tool run with this old version, Is there a way to make an update of our database to the latest version of BASE interface? Thank you for your help, Sincerely, -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Dealing wiht duplicate spots
On 2011-11-22 09.43, Nicklas Nordborg wrote: On 2011-11-21 21:32, Nantel Andre wrote: We don't have any regular users yet since we are still figuring out how it works. I am doing everything from my administrator account. Have you created a file format configuration for the files you are using? This is done in Administrate - Plug-ins Extensions - Plug-in configurations. Create a new configuration for the 'Raw data importer' plug-in and use the 'Test with file' function to get regular expressions, etc. correct. Anyway that's all the time I can give to this problem until later this week. This whole process has been much much more difficult than we expected. Please don't take this the wrong way but it might be a problem for your team as well if you ever hope to expand on your user base. It's not like we're new at this, we've been using microarrays since 1999 but I was getting tired of sending thousands of dollars to Agilent every year. Setting up a BASE server is not trivial. We have recently set up a new BASE installation for a project here and I guess we have spent several months just setting up lab procedures, data import procedures, and also made some customizations to BASE in order to further streamline the data entry. We don't have an explicit goal to get more users. We are primarily using BASE at our own site to solve our own problems. The Illumina extension package is an example of that. Unfortunately, we don't have the resources to develop things targeted for other platforms than what we are using ourselves. This doesn't mean that BASE can't be used with other platforms, but in order to get the most out of BASE one need to invest time and maybe also resources for customization. In may experience at least a week would be needed for initial testing and prototyping and then maybe a couple of months for setting up a production-ready server, formalizing lab and data handling procedures, developing custom plug-ins and extensions, etc. Two internal large scale uses are outlined in the BASE 3 document http://base.thep.lu.se/chrome/site/latest/html/why_base.html To get the most of BASE you need to dedicate resources to customize BASE to fit your needs and to learn what BASE can do for you. BASE use is a process, you start small and then extend your use of BASE as appropriate. In our lab (well some projects not all admittedly) we collect all important information collected during labwork in BASE. Therefore BASE is an integral part when setting up labprocesses where we make minor changes to lab work where needed and create customizations in BASE that fit our needs. The illumina extension was mentioned by Nicklas, but the reggie extension, http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie is the tool most appreciated by lab personnel. We track a lot of information about our samples and use the biomaterial LIMS extensively and reggie streamlines data input but also makes crosschecks and catches errors in data entry. Currently, we are working on defining our sequencing procedure in the lab and mirroring it in BASE. Our larger projects span over long time (years) and handles large sample sets. These projects use BASE to get organized, reduce errors, collect information that normally ends up in labbooks, to be able to share data, and as a analysis platform. And we have noticed improvements in labwork too :) Of course, our extensive BASE engagement is made easier because our PIs and funding agencies understand the benefits from organization and sharing of data/information. However, I want to emphasises, BASE is also usable for smaller groups and projects. One can ignore biomaterial and array LIMS, and directly create raw bioassays. Collect these into an experiment and head on to do analysis - The README for the affymetrix plug-in (http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix) outlines what needs to be done to get started with basically an empty BASE. The steps are general and can be adopted for other platforms. Cheers, Jari -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Error: GC overhead limit exceeded
Can the problem be that the jobagent does not get enough memory? CATALINA OPTS will only influence the BASE core server and if there are separate jobagent processed then these may need an increased memory setting? I may be completely off here but just a thought. Jari On 2011-05-23 08.27, Nicklas Nordborg wrote: It's difficult to say something about out of memory errors. 2GB should be more than enough. Have you verified in the Help - About - Configuration dialog that you really have 2GB? /Nicklas On 2011-05-23 04:03, Irina 264 wrote: Dear Team, I run Illumina plugin and had error: Java heap space. I have increased CATALINA OPTS=-Xmx2048m, however now I have the garbage collector problem: Error: GC overhead limit exceeded View job -- Run plugin: Illumina raw data importer java.lang.OutOfMemoryError: GC overhead limit exceeded at org.hibernate.engine.EntityEntry.getEntityKey(EntityEntry.java:182) at org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:198) at org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:898) at org.hibernate.loader.Loader.loadSingleRow(Loader.java:327) at org.hibernate.impl.ScrollableResultsImpl.prepareCurrentRow(ScrollableResultsImpl.java:254) at org.hibernate.impl.ScrollableResultsImpl.next(ScrollableResultsImpl.java:123) at net.sf.basedb.core.ScrollIterator.hasNext(ScrollIterator.java:66) at net.sf.basedb.core.RawDataBatcher.init(RawDataBatcher.java:263) at net.sf.basedb.core.RawDataBatcher.getNew(RawDataBatcher.java:104) at net.sf.basedb.core.RawBioAssay.getRawDataBatcher(RawBioAssay.java:1119) at net.sf.basedb.plugins.IlluminaRawDataImporter.beginData(IlluminaRawDataImporter.java:520) at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:691) at net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:468) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510) at java.lang.Thread.run(Thread.java:636) Did I gave too much memory? Regards, Irina -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Base 1.2 plugin - Virtual Array -1.1
Are you sure that all prerequisites are met? The plug-in configuration and the Base1PluginExecutor should be shared appropriately. Also, Virtual array works only on 2-channel data. Jari On 2011-03-10 17.25, Thomas Person wrote: Thanks! That change allows installation but once I atmpt to use the plugin, by clicking on the Run an Analysis Plugin icon when looking at an experiment under Bioassay set, the option select the the plugin in the drop down menu does not appear. Thanks again, Thomas From: Nicklas Nordborg [nick...@thep.lu.se] Sent: Wednesday, March 09, 2011 1:11 AM To: BASE ML Subject: Re: [base] Base 1.2 plugin - Virtual Array -1.1 On 2011-03-08 22:28, Thomas Person wrote: Howdy All, I'm attempting to install the Virtual Array 1.1 plugin on my Base 2.15 server. I get two sets of errors. ( I was able to install the Center-2.1 Plugin with no error). Thanks for the report. I can verify that the VirtualArray plug-in can't be installed as is. There seems to be a bug in BASE that is related to the 'descr' field in the 'pluginVirtualArray.base' file. This file has a space instead of a tab character between the 'descr' and the rest of the line. Please change the space to a tab and then re-try the installation. /Nicklas -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net UT Southwestern Medical Center The future of medicine, today. -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Error running RMAExpress plug-in
Have you followed the instructions in the README http://baseplugins.thep.lu.se/browser/plugins/base2/se.lu.thep.affymetrix/tags/0.7/README Do you have an CDF file attached to the design? Jari On 2010-12-06 07.56, Irina 264 wrote: I am trying to run the RMAExpress plug-in to import Affymetrix data, but I get the following error: net.sf.basedb.core.InvalidUseOfNullException: Invalid use of null. The 'design' value cannot be set to null. at net.sf.basedb.core.Affymetrix.getCdfFile(Affymetrix.java:126) at se.lu.thep.affymetrix.RMAExpress.runBinary(RMAExpress.java:131) at se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(AbstractExternalBinaryPlugin.java:262) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116) at net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.executeJob(ThreadJobExecutor.java:109) at net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.main(ThreadJobExecutor.java:202) I'm running BASE in a Linux Fedora11 with MySQL, tomcat6 Where is the problem? -- What happens now with your Lotus Notes apps - do you make another costly upgrade, or settle for being marooned without product support? Time to move off Lotus Notes and onto the cloud with Force.com, apps are easier to build, use, and manage than apps on traditional platforms. Sign up for the Lotus Notes Migration Kit to learn more. http://p.sf.net/sfu/salesforce-d2d ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Handling RNA-Seq and ChIP-Seq data
Hi, On 2010-10-18 20.35, Adam Halstead wrote: Thanks for your response Jari. I understand support for next generation sequencing data is currently being developed by the BASE developers - is there a beta version we can look at? Do you need help developing this functionality? What kind of effort would be involved here? There is no beta version. The sequencing support specification is still being drafted. That work is unfortunately currently halted due to other non-BASE related work. However, we expect to continue with specification work soon again. Hopefully we can present our ideas in the coming weeks. Then we will have an understanding of the effort involved and we happily accept help in developing the functionality. The first step would be input and feedback to the sequencing specifications when we release them. The current BASE development timeline is that we are finalizing the next 2.16 milestone. We were hoping to have what we call plate events in that release but it did not work out. The next milestone 2.17 will focus on solving/implementing plate events such that it supports our in-house needs for biomaterial tracking and processing. The milestone after 2.17 will be to introduce sequencing support in BASE. We expect this to happen during spring 2011. You may notice that I did not say 2.18 here since we will also look into having the sequencing support as an addon like the Illumina plugins package (http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina). However, I expect that we need changes to the BASE core even if we go for the addon option. For your in-house sequencing data, are you using BASE to manage it? Yes and no and we will. I'll start by explaining from the more negative no and finish with a positive yes. The no is related to that in the specific project we have not generated data as a part of the project. We are still developing and testing sequencing protocols and setting up new hardware for the project. We will store all sequencing data in BASE ... or at least information and references to where the raw sequencing data is stored. Our current thinking is that since we are already storing all sequencing raw (and processed) files in a file server serving our HiSeq we will not move these into the BASE file system. That said, I think this will be a use case for the sequencing specification. Yes, we are already using BASE to store and track biomaterial information related to the project. We are already doing laborative work on our material (currently more than 500 samples) and track the processing information about the material. When BASE supports sequencing data and we actually produce sequences we will add that information to BASE. Our time-line is that we need to build an omics data warehouse solution by year end . BASE will not support sequencing data as we want it to do before spring next year as outlined above. However, BASE can be used to store any data including sequencing data already today but you need to adapt to the microarray language and procedure. It is doable, we have done that as a excercise, but we prefer to add more sequencing specific support for our sequencing projects. Cheers, Jari -- Nokia and ATT present the 2010 Calling All Innovators-North America contest Create new apps games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Handling RNA-Seq and ChIP-Seq data
Hi, We are currently working on how to incorporate sequence data in BASE. We now have in-house sequencing capacity and need to manage all data generated. We have not formalized our ideas yet but we'll post whatever we will are planning to do in another mail/ticket in very near future. We welcome all ideas and feedback. Many improvements on BASE (such as file only raw data storage, file storage on external file servers) have been made during the last few months to accommodate seqdata. Jari On 2010-10-08 20.06, Adam Halstead wrote: I read with interest Bob MacCallum's post from Oct 2008: http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg01559.html Our group is looking into solutions with which to build a local data warehouse including the capability to store next-gen sequencing data (RNA-Seq, *ChIP*-*Seq*) and BASE looks to meet many of our other requirements. I also found that a ticket had been created (Ticket #1153 (new enhancement)) for the 2.x+ milestones. Any updates on this one? Thanks, Adam Programmer Analyst : Great Lakes Bioenergy Research Center : University of Wisconsin Madison -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] help
On 5/28/10 5:43 AM, Irina Maltseva wrote: I followed the installation instruction on http://base.thep.lu.se/chrome/site/doc/html/admindoc/installation_upgrade/installation_upgrade.html and change the user to ‘root’ in base.config file. I've created base2 and dynamic.base2 on mysql server using ./initdb.sh [root] root You probably read the following line in the documentation ./initdb.sh [base_root_login] base_root_password and used it too literally. The brackets [] are there to indicate that the parameter is optional. If you specify the parameter you should omit the brackets. In your case you should type ./initdb.sh strong_password where strong_password should be replaces with a good password. No need to specify the root account name if you want to use the default 'root'. Also, the password you used cannot be considered safe. So you need to recreate the database. You simply delete (drop) the base2 database and recreate it. Then you run the initdb.sh script and restart tomcat. Jari -- ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] base help
Hi, This question was asked the other day on the BASE user mailing list (http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg01954.html) and Nicklas responded to it. The problem is that user qouta is too low. Your BASE administrator must increase the quota or you must delete data to make room for other data. Remember deleting data will only move data to the trash and you must empty the trash before resources are released. How to change quota is described in the BASE manual available at http://base.thep.lu.se Please use the mailing list for support questions. More people may be able to help. Cheers, Jari On 4/29/10 4:39 PM, Youping Deng wrote: Dear Dr. Hakkinen, I am using base 2 for MA data management. But I am still new to base2. Using an old version: 2.4.3. When I tried to load data, i got an error massage: Permission denied: Quota has been exceeded. Could you help tell me the reason? I am not an database administrator, just a user. Thanks, Youping Deng, Ph. D. -- ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] FW: tab2mage and magetab
On 2/21/10 12:34 AM, alaa gaber wrote: 4-can base2 understand perl language Not directly, BASE is written in Java. You can write plug-ins using Perl or other languages. See plug-in developer documents for more details and browse plug-ins in http://baseplugins.thep.lu.se where several plug-ins are written in non-Java (using a Java wrapper that communicates with BASE). Jari -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] FW: tab2mage and magetab
Hi, Was this mail was intended for the mailing list? Jari On 2/21/10 12:34 AM, alaa gaber wrote: HI, I am asking 1-if the base2 uses a tab2mage format 2-i have a problem in converting tab2mage into mage-tab format 3-displaying both in base2 4-can base2 understand perl language my username:lola I am biomedical student THANKS IN ADVANCE I am looking for a reply Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Data truncation: Data too long
Hi, There is already a property Gene Symbol but maybe this won't cut it for you? Jari On 1/12/10 4:25 PM, flap...@free.fr wrote: Hello, I'm using the base-2.14.1 and I'm trying to import a genepix GAL file. I've add in the file named extended-properties.xml, this : property name=genename title=GeneName description=The identifier for the Gene name column=genename type=string length=300 / I was planning to have the gene name linked to the reporter. But i got this error : net.sf.basedb.core.BaseException: Data truncation: Data too long for column 'genename' at row 1 on line 4506 in file 'placenta_cto_sghm.gal': 6 11 4 IMAGE:1473... at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:731) at net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:468) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:110) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:506) at java.lang.Thread.run(Thread.java:619) Caused by: net.sf.basedb.core.BaseException: Data truncation: Data too long for column 'genename' at row 1 at net.sf.basedb.core.BasicBatcher.flushUpdate(BasicBatcher.java:453) at net.sf.basedb.core.BasicBatcher.update(BasicBatcher.java:352) at net.sf.basedb.plugins.ReporterFlatFileImporter.handleData(ReporterFlatFileImporter.java:656) at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:699) ... 4 more Caused by: java.sql.BatchUpdateException: Data truncation: Data too long for column 'genename' at row 1 at com.mysql.jdbc.ServerPreparedStatement.executeBatchSerially(ServerPreparedStatement.java:814) at com.mysql.jdbc.PreparedStatement.executeBatch(PreparedStatement.java:1452) at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeBatch(NewProxyPreparedStatement.java:1723) at net.sf.basedb.core.BasicBatcher.flushUpdate(BasicBatcher.java:445) ... 7 more the data for the column genename on line 4506 is almost the shorter of the GAL file ... I can delete/switch/mix the line, the import is stopping on this line every time. Where's the problem ? Thanks for the help, Flavien -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] MEV Launcher suggestions
tropy wrote: Nicklas Nordborg wrote: tr...@valdelsa.net wrote: 1. Log2 ratio transform MeV behaved (still behaves) inconsistently with data it read from TDMS with respect to logging data or not. In some cases MeV auto-logged data and in some other cases it did not. When we began to integrate MeV with BASE we could not find any written documentation on when to expect MeV to log or not. So, we decided to always export non-logged values because this makes it easy for the user to understand what is exported from BASE, and if we always do the same export, then the user does not need to hesitate over what data was exported. The export could be modified but as Nicklas says, it is trivial to log the data in MeV, so currently I would vote against a change to exporting log2 ratios. 2. Average on reporters (or by other Annotation Fields) Average on reporters might be possible, but I don't see how annotations should be used in this context. In any case, it may be better to have 'merge' functionality as a separate plug-in step. I am not aware of any BASE 2 plug-ins for merging but there is at least one BASE 1 plug-in that can merge on annotations. Yes, maybe the average on different annotations could be difficult to implement and should be computed by a specific plugin. But the average on reporters identifiers at least it's very important just to have the same results that you can get from the BASEexporter plugin. There is a BASE1 plug-in that does merge on reporters, http://baseplugins.thep.lu.se/wiki/se.lu.onk.VirtualArray but it only works for 2-channel data (maybe it is easy to add 1-channel support?). Running the plug-in before starting MeV would give you the same data in MeV and a BASEfile export (for the bioassay set resulting from the VirtualArray). The TDMS export and BASEfile export are two different exports coming from two different sources. The BASEfile export is a part of the core BASE functionality whereas TDMS export is a part of the MeV extension package. One may hope for similar functionality but since they have different origin there is no guarantee for getting the same functionality. (I'll admit that Nicklas has implemented both exports.) I would rather see the average on reporter removed from the BASEfile export than introducing it for the other exports. The reason for this is that I'd like plug-ins and functions to do well defined task. BASEfile export should export data, not calculate averages. What is missing is a general average on reporter plug-in that can be used before exporting data. (I'll add that to the wish list of plug-ins.) 3. Add the possibility to export raw data or formula columns also I don't think this is possible with the TDMS format, since there can only be one value (eg. the intensity) for each spot. Unless you mean that a formula should be selected *instead* of the regular intensity. This would then also solve 1). Frequently it's necessary to have the possibility to export not only ratios, but also different raw data columns or computed statistical quantities. The TDMS format supports additional columns to the left of the actual data matrix and one could add raw data columns and other formula based information there. However, I do not think BASE supports statistical quantities over bioassays trivially (as needed here). How would you use such extra columns in the TDMS file? Can MeV calulate the statistical quantities if raw data and formula based columns were added to the export? About this, if you're interested, I'll try to report to you (in a different thread / email) our experience about the transition from BASE1 to BASE2. I would be very interested since I get off-line questions regarding migration. Can you send it to the list for others to read and maybe find when they migrate. Which version of BASE2 did you migrate to? I have one facility that seems to have succesfully migrated to 2.12. Cheers, Jari -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] MEV Launcher suggestions
Jari Häkkinen wrote: MeV behaved (still behaves) inconsistently with data it read from TDMS The above line was meant to say MeV behaved (still behaves?) inconsistently with data it read from TDMS ... The question mark because I have not actually checked it. It may be that the issues in MeV has disappeared. Jari -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] File path derivations
Offord, Victoria wrote: I gather that the 2009 is the year and the 02 refers to the date the file was uploaded. How are the other numbers/values created as I wanted to add folders/directories from a program I am running which creates reults files for the data stored in BASE and wanted to keep them in line with the setup. Why not store the files in BASE? Manual transform creator (1( might help? Or using the same scheme as the MeV plug-in (2) that allows users to stores data in BASE from within MeV? (1)http://base.thep.lu.se/chrome/site/latest/html/appendix/appendix.coreplugins.html#coreplugins.analyze (2)http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev Jari -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Size limit of online file edit
Nicklas Nordborg wrote: I downloaded and installed Tomcat 6.0.16 and got the same problem. It works with Tomcat 6.0.20. And our production server runs 6.0.16. So, it is time to upgrade. Jari -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Size limit of online file edit
I can confirm Pawels problem. I run Firefox 3.5.3 on Mac OS X 10.6.1 (Snowleopard). My 63k file is now only 32k. Jari Nicklas Nordborg wrote: Pawel Sztromwasser wrote: I just tested it again (FF3.5.3). Here is how to reproduce: - upload a text file which is larger then 8kb - memorize file's size - edit file removing one character only - check the size again In my case removing one character from ~40kb file shrank the file to 24kb. Works fine with Firefox 3.5.3 on Windows when I test it. The test with Forefox 3.0 is on Linux. /Nicklas -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Size limit of online file edit
Jari Häkkinen wrote: I can confirm Pawels problem. I run Firefox 3.5.3 on Mac OS X 10.6.1 (Snowleopard). My 63k file is now only 32k. And redoing edit saves a 16k file, redoing the edit saves a 8k file, and another edit will not halve the size but a 7.99k file is saved. Jari -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Can't export data to Tmev
Nicklas Nordborg wrote: Daniel Octavio Palenzuela Gardon wrote: By other side, when we try to launch Mev in the Tools column when viewing bioassay sets of an experiment, there is a file with extension …TDMS.TXT that it`s suppose to be save in raw data, but when we do browse, there isn’t any file with this extension in raw data folder. Again... check your filters. And remember, the MeV generated file ends up in the directory you assigned for your experiment when the experiment was created. If you did not set a directory for your experiment, the files end up in your hone directory. Cheers, Jari -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Can't find getting started guide
Hi, The document you are looking for is obsolete, try the getting started section link at http://base.thep.lu.se instead. If you really want the outdated document you'll find it at http://base.thep.lu.se/browser/trunk/doc/historical/user/getting_started.html You'll need to download the file and then open it in your favourite browser. Where did you find the outdated link? Cheers, Jari Daniel Octavio Palenzuela Gardon wrote: Hi, Iam new in BASE and I wanted to start from getting_started guide that outlines the first steps with BASE 2. I tried next link http://base.thep.lu.se/chrome/site/doc/user/getting_started.html but unfortunately, this page is not found in the web. Can someone help me to find started guide for BASE2?. Many thanks Daniel -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Cloning a BASE instance
The steps I send covers my needs in that I do not use a secondary storage area, user files area is covered in my previous posting, and installed plug-ins are backed up by normal computer backups. But you are right, for a full clone you should also copy your complete BASE installation and the plug-ins. However, depending on which plug-ins you run you may need to install other external packages and may get binary compatibility issues (everything is not in Java). My needs are covered with the dumps in my previous posting since I use the BASE snapshot to recover from really stupid code that I sometimes write and wreck my BASE database. For me it is enough to restore base userfiles and the database. Plug-ins and base.config (and similar) are usually not harmed by poor SQL statements. Jari Olivier Lefevre wrote: The problem with zipping the BASE tree is that is no guarantee that all necessary files are under the BASE root. From looking at base.config there are at least three more roots to consider: * secondary storage area * plugins area * user files area Any others? -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Illumina plugin
Hi, Olivier Lefevre wrote: I am not having much luck installing that plugin. It wants you to run updatedb.sh. When I do that it says Building database, which is alarming in and of itself since that suggests it is rebuilding the db from scratch, which begs the question of whether it is possible to install that plugin on a live, already populated base instance: I don't want it to throw out all the existing data. The standard route to make changes to the database is to use the updatedb.sh script. You can run the updatedb.sh script as many times you like, it will only make changes if needed. If you follow the instructions that came with the Illumina package, i.e., http://baseplugins.thep.lu.se/browser/plugins/base2/net.sf.basedb.illumina/tags/1.3/INSTALL for the 1.3 release, it should install cleanly. Maybe the issue is to run the updatedb.sh script? You should simply run it like prompt cd /path/to/base/bin prompt ./updatedb.sh password This should finish cleanly with output similar to the listing below. If you have another root-userid than 'root' on your base installation you should run updatedb.sh like the below line. root-userid is the refering to BASE root-userid. prompt ./updatedb.sh root-userid password If I use the wrong userid or password I get a message indicating just that. Proper userid/password combination gives [0%]--System information- BASE : 2.12.1pre Database : jdbc:mysql://localhost/base2?characterEncoding=UTF-8useCursorFetch=truedefaultFetchSize=100useServerPrepStmts=true Dialect : org.hibernate.dialect.MySQLInnoDBDialect JDBC : com.mysql.jdbc.Driver; version 5.1 Java : Java(TM) SE Runtime Environment; 1.6.0_07-b06-153; Apple Inc. OS : Mac OS X; x86_64; 10.5.7 - [0%]Building database.. [30%] Database built successfully. [35%] Initialising database... [36%] --Creating quota types... [37%] --Creating quota... [38%] --Creating roles... [39%] --Creating users... [40%] --Creating groups... [41%] --Creating keys... [42%] --Creating units... [43%] --Creating protocol types... [44%] --Creating hardware types... [45%] --Creating hardware... [46%] --Creating software types... [47%] --Creating software... [48%] --Creating directories... [49%] --Creating file types... [50%] --Creating MIME types... [51%] --Creating plate geometries... [52%] --Creating plate mappings... [53%] --Creating labels... [54%] --Creating annotation types... [56%] --Creating clients... [57%] --Creating plugin definitions... [58%] --Creating example plugin configurations... [59%] --Creating formulas... [60%] --Creating job agents... [61%] --Creating data file types... [62%] --Creating platforms... [63%] --Creating news... [70%] Database initialised successfully. [75%] Updating database... [90%] Database updated successfully. [95%] Installing web application... [100%] Web application installed successfully. This was generated on a live installation (well tomcat is not running but otherwise a real live mysql database) But that's not the worst of of it. It immediately complains of APPARENT DEADLOCK!!! (twice) and also (many times) of Access denied for user 'base2user'@'localhost' (using password: YES), which is baffling since I supplied the correct uid and pwd at the command line when starting the script. Finally it gives up. Can anyone make a suggestion? Can you send the output of ./updatedb.sh Cheers, Jari -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Cloning a BASE instance
Before starting to clone BASE you could try to reset list settings with File - Reset list settings ... select memory and database in the pop-up. BASE stores uploaded or generated files as files in the filesystem. The database keep tracks of file locations. There is no information in files needed for having a consitent database, but of course removing files may upset BASE since a file will be missing somewhere. Cloning a BASE installation? Well there is no instruction for this. I simply do a sequence of commands on my macbook and hope the files generated will allow me to create a copy of my BASE server. It is a bit crude since I make a snapshot of all mysql dbs not only BASE dbs, but I only run BASE on my machine: #!/bin/sh BASE2TGZ=/tmp/base2.tgz MYSQL5TGZ=/tmp/mysql5.tgz echo Stopping tomcat tomcatstop mysqlctl stop echo Backing up basefiles at /path/to/base2 cd /path/to/base2 tar zcf $BASE2TGZ base2 echo Backing up /path/to/db/mysql5 cd /path/to/db sudo -u root tar zcf $MYSQL5TGZ mysql5 mysqlctl start echo Starting tomcat tomcatstart echo Done. Backup files are located in /tmp ls -lsh $BASE2TGZ $MYSQL5TGZ You of course need to keep a safe copy of base.config and other configuration files from your BASE installation. I haven't tested a restore in a long time ... haven't had the need. So you better test it before you trust it. Cheers, Jari Olivier Lefevre wrote: Are there instructions and/or scripts anywhere to assist with the cloning of a BASE2 instance or is it a use-your-brain-dude kind of thing? My problem is that I got a dump of a MySQL db but nothing else and there seem to be a lot of dangling links manifesting themselves in red-band error messages here and there, e.g., Item not found: RawDataType[id=blah]. That is not surprising since BASE seems to hold a lot of stuff in files on disk rather than in the db but it's unclear how to go about fixing that if you are not familiar with BASE. It would be nice if there was a fool-proof, automated procedure for cloning a BASE2 instance. -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Tab2Mage export
Hi, It is a while since Paulo asked the below question. I have added a ticket on this to the plug-in dev site, http://baseplugins.thep.lu.se/ticket/209 This means that we are going to look into creating a submission tool. It will probably target GEO submission since there are work done on ArrayExpress submission elsewhere. Can someone comment on the ArrayExpress progress? Cheers, Jari Paulo Almeida wrote: Hi, Does anyone have news on the plug-in that was being developed to export data in a format that is compatible with the ArrayExpress database? I know it has been asked before (by myself even), but I would like to have information on whether it is still planned, or will be released in the future, in order to make decisions about my system. Thanks, Paulo Almeida Instituto Gulbenkian de Ciência -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Crystal Reports #45; New Free Runtime and 30 Day Trial Check out the new simplified licensign option that enables unlimited royalty#45;free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] quantile normalization questions
Yannick Lippi wrote: __SECOND QUESTION: R/G quantile normalization Jari said: Obviously R-G quantile is not supported since the methods in net.sf.basedb.normalizers only work on ratios. - i am not expert on java developping.. but what does mean: methods in net.sf.basedb.normalizers only work on ratios Yes, the released normalizers work on ratios for 2-channel data. The normalizers work on 1-channel data also but obviously no on ratios in this case. The same is true for the new normalizers in development (to be relased in 1.1 due soon). - Do you mean it is not possible to implement plugins to perform R/G quantile normalizations? Of course, it is possible to implement such plug-ins. However, there is no plan from our side to do that. As always, we are happy to include contributions from other developers. - how could i pass through this problem? You need to create a plug-in that performs your specific normalization. It should be straightforward to add to the qQuantileNormalizer as options but unfortunately we cannot promise to do this work for you. I'll add R/G qQuantileNormalizations as wish list tickets to the plug-in dev site. Cheers, Jari -- Crystal Reports #45; New Free Runtime and 30 Day Trial Check out the new simplified licensign option that enables unlimited royalty#45;free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] normalization and ratios between 2 bioassays
YANNICK wrote: Hi BASE2 users! I am using BASE 2.11 and have some questions. I want to calculate Ratios from 2 bioassays organized as following: - 1st bioassay = control - 2nd = treatment Labellings are performed as following: Cy5= pool of all samples extracts. Same in all arrays (serves for normalizations between arrays) Cy3= experimental condition. Here are my questions: - is it possible to perform Rquantile normalization (cf normalizeBetweenArrays, R Bioconductors)? You should have a look at http://baseplugins.thep.lu.se/wiki/net.sf.basedb.normalizers and the associated milestone tickets for the next release of the package, http://baseplugins.thep.lu.se/query?milestone=net.sf.basedb.normalizers+1.1order=priority It provides a few more normalization methods of which quantile normalization is already available, and qQuantile normalization is planned for the next release of the package. You need to compare these normalizers to the ones provided by Bioconductor normalizeBetweenArrays. Obviously R-G quantile is not supported since the methods in net.sf.basedb.normalizers only work on ratios. The normalizer package discussed here does not target your issue with mixing ratios between assays ... contributions are welcome. Cheers, Jari - And how to calculate ratios for each reporter? we must calculate ratios of cy3 intensities between the two bioassays. (e.g. ch(2)[biaoassay1] / ch(2)[bioassay2]). Could someone help me? thanks! yannick lippi -- -- Equipe Interactions Plantes-Microorganismes UMR 5546 CNRS/Université P. Sabatier Pôle de Biotechnologies Végétales 24, chemin de Borde Rouge B.P. 17 Auzeville 31 326 CASTANET-TOLOSANFRANCE -- -- Stay on top of everything new and different, both inside and around Java (TM) technology - register by April 22, and save $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. 300 plus technical and hands-on sessions. Register today. Use priority code J9JMT32. http://p.sf.net/sfu/p ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Stay on top of everything new and different, both inside and around Java (TM) technology - register by April 22, and save $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. 300 plus technical and hands-on sessions. Register today. Use priority code J9JMT32. http://p.sf.net/sfu/p ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Item name when using batch importer
Hi Klemens, When using the batch importers you must create the names for all items yourself. We use a spreadsheet that follows the naming convention adopted in BASE. See the attached file that we use at our facility. Cheers, Jari Klemens Vierlinger wrote: Hi everyone, I quite like the way BASE names items by default when I enter the them by hand, i.e. sample1.e1.l2. However, I dont seem to be able to reproduce this nameing when I use the batch importers. Am I doing something wrong? Best Klemens -- This SF.net email is sponsored by: High Quality Requirements in a Collaborative Environment. Download a free trial of Rational Requirements Composer Now! http://p.sf.net/sfu/www-ibm-com ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net batch_upload_template.ods Description: Binary data -- This SF.net email is sponsored by: High Quality Requirements in a Collaborative Environment. Download a free trial of Rational Requirements Composer Now! http://p.sf.net/sfu/www-ibm-com___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] BASE and methylation data.
Hi Lavinia, I apologize the delayed response but I needed to check whether we anticipate this need for our own purposes. The good news is that our lab will be interested in getting methylation array support into BASE, the bad news is that we have no real time line for BASE methylation adaptation yet. In short, BASE cannot do methylation specific analysis today. We will add support on some level that needs to be defined. You can, as we do, store your methylation arrays in BASE down to the raw bioassay level. When we finally get, our someone contributes, methylation support into BASE you will be ready to go. For methylation data we currently just want to keep track of data produced at our university service facility and we also deliver data to the facility users through BASE. I have added methylation support to the wish list, http://baseplugins.thep.lu.se/ticket/196 Cheers, Jari Lavinia Gordon wrote: Dear all Is BASE capable of analysing Illumina HumanMethylation27 DNA Analysis BeadChip data? with thanks for your time, Lavinia Gordon. --- Bioinformatics Department Rm SW916, 9th Floor Murdoch Children's Research Institute Royal Children's Hospital Flemington Road, Parkville Victoria 3052 Australia Tel: (+613) 8341 6221 --- -- Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are powering Web 2.0 with engaging, cross-platform capabilities. Quickly and easily build your RIAs with Flex Builder, the Eclipse(TM)based development software that enables intelligent coding and step-through debugging. Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
[base] New version of MultiExperiment Viewer, MeV, extension for BASE released
A new version of the MeV extension for BASE was released yesterday and already improved today! The new extension is based on the latest MeV (4.3.02) and supports expression data analysis from BASE with simple clicks. MeV web page http://www.tm4.org/mev.html MeV BASE extension web page http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev BASE web site http://base.thep.lu.se Cheers, Jari -- ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] File types assigned when extracting an archive
I notice that I closed the ticket. Maybe we should reopen it and put it out BASE 3 milestone? Disclaimer: There is NO plans to start on a BASE 3 in the foreseeable future. Jari Nicklas Nordborg wrote: This was requested some time ago. There is a ticket at http://base.thep.lu.se/ticket/978 explaining why it can't be fixed. A workaround is to match file extensions to MIME types that are linked with file types. /Nicklas Pawel Sztromwasser wrote: Hi, Is it possible to assign file type to files uploaded in archive and extracted on the fly? The file type setting in upload window seems to affect only the archive file, not the extracted content. It would be useful for me and some of our users to have an option of automatic assigning type to files uploaded this way (since many plugins use file types to filter file view). Other option could be batch-changing of file type, similar to sharing many items at the same time. Would you consider including these changes in the road map? All the best, Pawel -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Affymetrix Power Tools Error
Hi, The problem seems to be in the apt-probeset-summarize program as you point out. Have you tried to run the same analysis outside of BASE? What is the outcome of that? Cheers, Jari philipp-1.kai...@novartis.com wrote: Hi, I am trying to get BASE 2.9.2 working with the APT 0.2 plugin on a Testserver. Envorinment Condition are as follows: Windows XP Prof SP2, Tomcat 6, Affymetrix Powertools Version: apt-1.10.1-20081103 In some cases the Conversion of .CEL files to Probeset Signal worked, but most of the time I get the following error Message: - Name Run plugin: APT Summarize plug-in Description Priority 5 (1 = highest, 10 = lowest) Status Error: Unexpected exit of APT sub-process: C:\Program Files\Tomcat 6.0\webapps\ROOT\plugins\APT\apt-probeset-summarize --cdf-file CHO2a520638F.CDF --cel-files inputfiles.txt --out-dir C:\Program Files\Tomcat 6.0\temp\APT Summarize plug-in\91 --analysis plier-mm Exit value: 1. Percent complete 100% java.io.IOException: Unexpected exit of APT sub-process: C:\Program Files\Tomcat 6.0\webapps\ROOT\plugins\APT\apt-probeset-summarize --cdf-file CHO2a520638F.CDF --cel-files inputfiles.txt --out-dir C:\Program Files\Tomcat 6.0\temp\APT Summarize plug-in\91 --analysis plier-mm Exit value: 1. at se.uu.lcb.APT.APTPlugin.runBinary(Unknown Source) at se.uu.lcb.APT.AbstractExternalBinaryPlugin.run(Unknown Source) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:106) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:504) at java.lang.Thread.run(Unknown Source) - As I understand the apt-probeset-summarize.exe just returns an error. Is there a possibility to further identify the problem? Thanks for your support folks! Philipp Kaiser -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Affymetrix Power Tools Error
The output from apt-probset-summarize indicates that the cel file is corrupt. Can you try to download the cel file from BASE and examine the size of the file. You should find the file when you view the details of a rawbioassay. Can you make windows to refuse to delete the files that are created by the plug-in (the temporary word directory). In this way you can examine the files exported from BASE for apt-probset-summarize. Jari philipp-1.kai...@novartis.com wrote: Dear Jari, indeed I tried to evaluate if the error occurs if doing the same procedure as BASE calls by hand. In all attempts I couldn't generate the same error. I also tried to permit the automatic deletion of files by BASE via access-policy in Windows to see the log file of apt-probset-summarize. The last lines of the log file are: 03/04/2009 15:54:00 Wrong number of cells: Expecting: 512656 and Testscan.CEL has: 0 03/04/2009 15:54:00 FATAL ERROR: Different chiptypes or probe counts found. Only first 10 errors printed, see log for rest. Thanks for your support. Philipp Kaiser Novartis Pharma AG, Werk Klybeck NBx PROCESS DEV. BIOINFORMATIC CHBS, WKL-681.1.10 Klybeckstrasse 141 CH-4057 Basel Switzerland Phone: +41 61 6962720 Fax: +41 61 6963373 Email : philipp-1.kai...@novartis.com Jari Häkkinen j...@thep.lu.se 04.03.2009 15:37 Please respond to BASE ML basedb-users@lists.sourceforge.net To BASE ML basedb-users@lists.sourceforge.net cc Subject Re: [base] Affymetrix Power Tools Error Hi, The problem seems to be in the apt-probeset-summarize program as you point out. Have you tried to run the same analysis outside of BASE? What is the outcome of that? Cheers, Jari philipp-1.kai...@novartis.com wrote: Hi, I am trying to get BASE 2.9.2 working with the APT 0.2 plugin on a Testserver. Envorinment Condition are as follows: Windows XP Prof SP2, Tomcat 6, Affymetrix Powertools Version: apt-1.10.1-20081103 In some cases the Conversion of .CEL files to Probeset Signal worked, but most of the time I get the following error Message: - Name Run plugin: APT Summarize plug-in Description Priority 5 (1 = highest, 10 = lowest) Status Error: Unexpected exit of APT sub-process: C:\Program Files\Tomcat 6.0\webapps\ROOT\plugins\APT\apt-probeset-summarize --cdf-file CHO2a520638F.CDF --cel-files inputfiles.txt --out-dir C:\Program Files\Tomcat 6.0\temp\APT Summarize plug-in\91 --analysis plier-mm Exit value: 1. Percent complete 100% java.io.IOException: Unexpected exit of APT sub-process: C:\Program Files\Tomcat 6.0\webapps\ROOT\plugins\APT\apt-probeset-summarize --cdf-file CHO2a520638F.CDF --cel-files inputfiles.txt --out-dir C:\Program Files\Tomcat 6.0\temp\APT Summarize plug-in\91 --analysis plier-mm Exit value: 1. at se.uu.lcb.APT.APTPlugin.runBinary(Unknown Source) at se.uu.lcb.APT.AbstractExternalBinaryPlugin.run(Unknown Source) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:106) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:504) at java.lang.Thread.run(Unknown Source) - As I understand the apt-probeset-summarize.exe just returns an error. Is there a possibility to further identify the problem? Thanks for your support folks! Philipp Kaiser -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] can you give spot images a css class?
Hi Chad,
The requested class will appear in BASE. We missed it for the 2.10
release but the request is now added to the ticketing system,
http://base.thep.lu.se/ticket/1242
Cheers,
Jari
Chad Matsalla wrote:
Greetings!
I'm using base-2.9.2 on tomcat 6.0.18 in Geronimo 2.1.3.
We use Combimatrix 90k arrays and the spot images are tiny (12px). I want to
use CSS to make them bigger. Can you give the spot images a class of
something like 'spotimage' so I can do that?
At the moment I'm using
#rawdata td.cell img { width: 30px; }
and it works but it feels ... wrong. I'd prefer
.spotimage { width: 30px; }
Thanks,
Chad Matsalla
Plant Biotechnology Institute
Saskatoon, Saskatchewan, Canada
--
Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM)
software. With Adobe AIR, Ajax developers can use existing skills and code to
build responsive, highly engaging applications that combine the power of local
resources and data with the reach of the web. Download the Adobe AIR SDK and
Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com
___
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject unsubscribe to
basedb-users-requ...@lists.sourceforge.net
--
Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
-Strategies to boost innovation and cut costs with open source participation
-Receive a $600 discount off the registration fee with the source code: SFAD
http://p.sf.net/sfu/XcvMzF8H
___
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject unsubscribe to
basedb-users-requ...@lists.sourceforge.net
Re: [base] Errors while creating bead summary Illumina data
Hi, As you describe it it seems like you have bead level data in your data files. The Illumina package for BASE expects bead summary data, i.e., the average for each bead type (together with some other numbers as described in http://baseplugins.thep.lu.se/browser/plugins/base2/net.sf.basedb.illumina/tags/1.2/README). If the above is correct there are two ways forward: 1) Create a small program that converts bead level data to bead summary data. This could be in line with Markus' contribution on how to convert Illumina BeadStudio data to IBS, see http://baseplugins.thep.lu.se/browser/plugins/base2/net.sf.basedb.illumina/trunk/contrib/README_beadstudio2ibs.txt 2) Add support for reading bead level data files to the Illumina package, i.e., perform what a converter in bullet 1 above would do. A plug-in could do the averageing and store IBS like data in the database. This of course requires that Code colun in Lucas sample is the same as Illumicode in IBS files (the same requirement is also true for a converter in 1 above). I am not sure if 2) is something we want to see, we opted out from this earlier since the data files are really large. Also, we did not see any benefit on storing the bead level data. Of course, in our discussions we opted out because we did not want to store bead level data in the database, but we would not do that in this scenario (only store large files). Any thoughts? Jari luca.beltr...@unifi.it wrote: Hello, I'm having trouble in creating bead summary files from bead level files on BASE 2.9.2 using the Illumina plugin package version 1.2. I created the array designs, imported the features and the reporters. Then I created a new raw bioassay and added two beadlevel files as they were supplied to me. When activating the bead summary importer, I get the following error (pasted from the log): Failed: Can't find start of data in file: File[id=386; name=4449817059_A_1.txt] on line 101 in file 4449817059_A_1.txt net.sf.basedb.core.BaseException: Can't find start of data in file: File[id=386; name=4449817059_A_1.txt] on line 101 in file 4449817059_A_1.txt at net.sf.basedb.illumina.plugins.BeadSummaryImporter.importScandata(BeadSummaryImporter.java:738) at net.sf.basedb.illumina.plugins.BeadSummaryImporter.run(BeadSummaryImporter.java:284) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:106) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:504) at java.lang.Thread.run(Thread.java:619) Caused by: net.sf.basedb.core.InvalidDataException: Can't find start of data in file: File[id=386; name=4449817059_A_1.txt] at net.sf.basedb.illumina.plugins.BeadSummaryImporter.importScandata(BeadSummaryImporter.java:677) ... 4 more I don't know why line 101, as it does not matter what it is on that line (I made a backup of the bead level file and removed the offending line just to make sure, since apparently setting skip as option in case of errors has no effect). I noticed that the header in my bead level data is different than what the README indicates, namely it is Code,Grn,GrnX,GrnY Also, the file is tab-separated, rather than comma-separated (but substituting tabs to commas does not fix the problem). Is there a way to work around this problem, is it a plugin limitation, or am I just doing things in the wrong way? Thanks in advance. Please CC me in replies, I'm not subscribed to this list. -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] BASE on 64-bit machine
I am running BASE on a 64-bit mac but my mysql server is a 32-bit binary (java is 64-bit). I have no problems to report related to the bitness but then again I am not completely in the 64-bit domain. Jari michael watson (IAH-C) wrote: Dear All Quick question with a quick answer I expect - our sys admin is recommending an upgrade to 64 bit version of Red Hat Enterprise 5. Are there are known problems with running BASE off a 64-bit server? Thanks Mick -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] JEP plugins
Hi Louise, Maybe you should look into the http://baseplugins.thep.lu.se/wiki/net.sf.basedb.normalizers package for inspiration on how to create a plug-in for your needs. Jari Nicklas Nordborg wrote: Louise Donnison wrote: Hi We have some raw bioassays in an experiment and I am trying to work out how to use the analysis plugins. We can run the Formula intensity calculator Mean FG - Mean BG to create a BioAssay set. We can run the Filter plugin to filter out flagged values and the JEP intensity transformer to set values. However, what I would like to do is if a spot is flagged (non 0), set its value to the mean of that spots reporters (flagged 0) across the whole experiment. Calculate a mean of the channel 1 and channel2 values for each reporter for non flagged reporters. Is that possible? I have been looking at the JEP extra value calculator plugin but I am not sure how I can create such a mean using that plugin The JEP plug-ins are very simple and doesn't support means or other aggregated values. They can only work with the data for a single spot at a time. /Nicklas -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Experiment overview loads very slowly
Hi all, The 2.11 release will target performance issues. The next release is 2.10 but we have not set a dead line for the 2.10 release yet. However, a hopefully performance boosted BASE 2.11 should be out during the spring, until then we have to live with some slow BASE clicks. I agree with Pawel that the Experiment overview is way too slow. The BASE team is aware of several performance issues but we have so far not prioritized them. Please contribute with performances issues to be examined and also ideas on how to resolve them. Jari - Change we believe in ... an even better BASE. Pawel Sztromwasser wrote: Hi Nicklas, I agree that the query is rather complex and has to take some time to execute, but over 200ms? Besides, the effect that it is causing (extremely long experiment overview loading) is really annoying. I had a look at db server logs and found the query: select distinct annotation0_.id as id1_0_0_, annotation6_.id as id1_6_1_, annotation0_.version as version2_0_0_, ... fields from annotation0_ and annotation6_ tables... annotation6_.projectkey_id as projectkey19_6_1_, annotation6_.owner as owner20_6_1_ from Annotations annotation0_ left outer join InheritedAnnotations inheriting1_ on annotation0_.id=inheriting1_.annotation_id left outer join AnnotationSets annotation2_ on inheriting1_.annotationset_id=annotation2_.id left outer join AnnotationSets annotation3_ on annotation0_.annotationset_id=annotation3_.id left outer join InheritedAnnotationSets inheriting4_ on annotation3_.id=inheriting4_.inherited_id left outer join AnnotationSets annotation5_ on inheriting4_.annotationset_id=annotation5_.id inner join AnnotationTypes annotation6_ on annotation0_.annotationtype_id=annotation6_.id where annotation2_.id=$1 or annotation5_.id=$1 order by annotation6_.name ASC It contains 3 joins with no reason (adding AnnotationSets table 3 times, never using fields exclusively belonging to it). When I removed the 3 joins (and fixed dependencies) the FROM-WHERE part looks like: from Annotations annotation0_ left outer join InheritedAnnotations inheriting1_ on annotation0_.id=inheriting1_.annotation_id left outer join InheritedAnnotationSets inheriting4_ on annotation0_.annotationset_id=inheriting4_.inherited_id inner join AnnotationTypes annotation6_ on annotation0_.annotationtype_id=annotation6_.id where inheriting1_.annotationset_id=$1 or inheriting4_.annotationset_id=$1 order by annotation6_.name ASC New query executes in ~5ms, so much faster. I am not sure how easy it is to apply the fix on the java-code level, but I guess it should be possible. Another way for quick and easy fix is to perform two queries and merge results: one query for directly inherited annotations (WHERE inheriting1_.annotationset_id=$1) and the other for indirectly inherited (WHERE inheriting4_.annotationset_id=$1). Each of these queries runs ~2.5ms and merging to lists in java shouldn't take too long either. The only problem I see could be duplicate elements on the merged list, but as long as annotation can't be inherited directly and indirectly by the same annotation set, the fix should work. Will you consider applying the fix to one of the next releases? Pawel Nicklas Nordborg wrote: Pawel Sztromwasser wrote: Hello, We have noticed that Experiment overview is very slow for large experiments (40 raw bioassays) with many items annotated (mainly samples). I takes over a minute for some of the experiments to load overview (or re-validate). I narrowed the issue down to this line: ListAnnotation inherited = annotationQuery.list(dc); in addAnnotations(..) method (ExperimentOverview.java). The list(dc) method takes ~200ms to complete. It is not much, but multiplied by number of items on the way from rawbioassay down to biosource (annotations are checked for each of them) and by number of rawbioassays... it causes most of the delay. Does anybody see similar problem? It is probably just a non-optimal postgres query, if experiment overview works fine on mysql dbs. Annotations are rather expensive in terms of database access. Each value usually needs 2 separate queries to retrieve. In other words, it is not unusual that it takes a lot of time. /Nicklas -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net -- This
[base] Changing default permission setting for a project
The default project permission for items created with an active projects is 'RUWD'. Can I change this default to a simple 'R'? It is of course possible to restrict all project members credential to 'R' individually, but I would prefer to set the project credentials for new items to 'R'. Cheers, Jari -- Check out the new SourceForge.net Marketplace. It is the best place to buy or sell services for just about anything Open Source. http://p.sf.net/sfu/Xq1LFB ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] Getting Internal File Name
There is an ftp-server extension for BASE, http://baseplugins.thep.lu.se/wiki/net.sf.basedb.ftp Maybe this can help? It should be possible to get Perl to download files using ftp. And the names are the native names, i.e. no translation is needed to the internal name. Jari Offord, Victoria wrote: I'm trying to transfer the files held in a project into an external system but I require the location the file is stored so that it can be passed into a Perl script which will copy the file. I am unable to get the location of the file held within the Java 'File' class because the method getInternalName is private and therefore is inaccessible from the jsp, is there a way of accessing this value from the jsp? -Original Message- From: Nicklas Nordborg [mailto:[EMAIL PROTECTED] Sent: 25 November 2008 19:22 To: BASE ML Subject: Re: [base] Adding a new button to the submenu Offord, Victoria wrote: Its ok, have figured it out now thank you though for replying. Would you know what the numbering system of the folders means when files are uploaded. For example I have 2008-48/25-21/file.txt It is based on the date and time of the file upload to prevent that too many files ends up in the same folder. /Nicklas - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] problem attaching files to raw bioassays using the batch importer -- BASE 2.8.4
Are the raw data files visible to the plug-in? If you upload the files with ftp they are not automatically assigned to a project. You need to set the parameter defining how the plug-in should find existing items referenced in the file. If this is not the problem, can you try to only map the file and nothing else. Jari Micha Bayer wrote: Hello again, I can't get the raw bioassay batch importer to attach actual file objects to the raw bioassays I am importing. I have - provided a data column with file names in my data batch import file - mapped this column to the File property in the import config - provided a path to the data directory in the import config - put the actual raw data files into that directory The import works without errors but when it is done there are no files attached to my raw bioassays (even after a refresh). Under File in the detail view of the RBAs it just says -none-. Has anyone else seen this behaviour? I don't want the raw data imported into the db, I just want files to be associated with the RBA. Cheers Micha == Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.ac.uk/staff/michabayer == __ SCRI, Invergowrie, Dundee, DD2 5DA. The Scottish Crop Research Institute is a charitable company limited by guarantee. Registered in Scotland No: SC 29367. Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [EMAIL PROTECTED] quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). __ - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] problem attaching files to raw bioassays using the batch importer -- BASE 2.8.4
I have not encountered any problems with attaching files earlier. I decided to play around with partially filled import files. I succeeded in creating a file that fails to attach files even though the importer reports success. BASE 2.8.4 and my 2.9pre test version both fails but the resolution of the problem is only tested on my 2.9pre test machine. Lets go, I am simply using three columns NamePlatformFile A affymetrix A.cel B affymetrix B.cel with the CEL files properly uploaded. A and B raw bioassays are successfully created as Affymetrix data. The file type is set to 'CEL file' but no file was attached. Note, I did not specify type, but when a Data file type column was added NamePlatformFileData file type A affymetrix A.cel CEL file B affymetrix B.cel CEL file things work. Rerunning the import ... voila the raw bioassays where updated with assigned files. I decided to start from scratch with a file like NamePlatformFileData file type C affymetrix A.cel CEL file D affymetrix B.cel CEL file and two raw bioassays were succesfully created with file attached! I hope this helps! I suppose the above should be reported as a ticket. The ticketing work will be left for Monday because the ale next to my keyboard has been flirting with me for a while now. Cheers! Jari Micha Bayer wrote: No, still no joy. Are the raw data files visible to the plug-in? If you upload the files with ftp they are not automatically assigned to a project. I uploaded them with HTTP, and they have definitely been assigned to the project. You need to set the parameter defining how the plug-in should find existing items referenced in the file. I have tried with this parameter set to Name, ID and Name/ID. If this is not the problem, can you try to only map the file and nothing else. I have tried this too, and in conjunction with all three of the above parameters settings for item identification. The import/update seems to go ok and the plugin tells me at the end that it has updated all items but it hasn't actually done so. Is this functionality working for you? Cheers Micha == Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.ac.uk/staff/michabayer == __ SCRI, Invergowrie, Dundee, DD2 5DA. The Scottish Crop Research Institute is a charitable company limited by guarantee. Registered in Scotland No: SC 29367. Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [EMAIL PROTECTED] quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). __ - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject
Re: [base] batchimport example spreadsheet seems corrupted
Micha Bayer wrote: Hi, I have been trying to look at the example file for the batch import but it seems corrupted. I am trying to open it in OpenOffice 2.3.0 and the file does load but then Calc instantly hangs. The file is created with OpenOffice 2.4 and works. I downloaded it and could successfully open the file. Has anyone else had the same problem? More to the point, has anyone got a version that works, or better still, an Excel version of it? Generating an excel version from my OpenOffice creates a non-fully working sheet. You can browse the Google docs version linked from http://base.thep.lu.se/wiki/DocBookSupport There is no real need to use the sample directly simply create a file using your data following the sample. Jari - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] high-throughput transcriptome sequencing data
Hi Bob, Sorry for not commenting your thoughs on storing sequencing data in BASE. We have discussed it here and will be looking into it later. This will become an issue for us also since we have sequencing equipment generating huge quantities of data. So far we are only getting friendly with the new machine. I think we should add your thoughts to a ticket for further discussions. I hope we can be more active on this issue later this autumn. How urgent is this issue for you? Regarding SNP-data and other arrays with huge quantities of information. We have decided to avoid storing this sort of data in the database tables, it would probably cripple BASE. We have prepared BASE during the last releases for storing raw data in files instead of the raw tables, and also to store data in files also when analysing the data, i.e. in the analysis tree. However, there is no plug-ins that take advantages of these new features but they will appear. We are not currenlty working with Affymetrix SNP data wrt BASE. However, we now have the Affymetrix platform available at our department and may soon face the challenges of getting that data into BASE (it has not been decided to store that data in BASE yet). Maybe the Uppsala people has something on this, http://madr.lcb.uu.se/ ? On our side we are interested in getting Illumina SNP data into BASE and have slow progress towards realising it but we expect that to appear during the winter. We are supposed to write a specification on how we want to see this in BASE but there is very little written so far. If you are getting confused when I talk about experimental equipment at our department it is natural. I am at the Dept. of Oncology now but I am still using my old mailing address in this list. Cheers, Jari Bob MacCallum wrote: Hi again. Any thoughts on this (see below) at all? Please reply off-list if you are feeling shy. I'd also like to raise some general questions about scalability. 1. Is anyone working on an Affymetrix SNP plugin? 2. Is anyone doing anything with tiling arrays? I realise that archiving the .CEL files is no problem. Using BASE to run analysis programs on those files is possible through plugins. But storing per-feature data in the analysis tables is going to break, when you have millions of features, right? cheers, Bob. Bob MacCallum writes: I'm just thinking out loud about how to incorporate high throughput transcriptome sequencing data into BASE. It's some way off, but I'm assuming that it will be cheap and quantitative enough to replace arrays at some point during the renewal period of our project (2009-2014). 1. Create an array design with all genes of interest (ideally this would be the largest set possible, e.g. known genes + predicted genes of all qualities, perhaps even predicted genes from the new sequence data). The layout would be fictitious, of course (what's the minimum one can get away with?). 2. Create a rawbioassay to correspond to each sequencing run. Then *one* of 3a/b/c for each sequencing run/rawbioassay: 3a. Outside BASE, align the new sequences to genome or transcript sequences and calculate intensities for each gene on the array design and dump into a tab delimited raw data file. Attach that file to the rawbioassay and import numeric data as usual. 3b. Upload the text file of sequences to the raw bioassay's data file. Create a BASE plugin to do the the alignment and quantification as in 3a, and load the numeric data into the database. 3c. Similar to 3b, but calculate the intensities at the create root bioassay step, similar to the Affymetrix RMA plugin. 4. continue with analysis as normal. biosources, samples etc can be linked to the bioassay too, of course. I guess a new raw data type (for Generic platform) would have to be created for 3a (and 3b?) but that's not difficult. Is it possible to go with 3a, but also attach the sequence file to the raw bioassay (or scan?) - something like keeping tiff files for scans? Just for documentation purposes. Any thoughts from the community or developers? cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ The BASE general discussion mailing list
Re: [base] How to connect to FTP server
Hi, In ftp/config.xml the nio-listener tag there is a port property set to 2121. I think this sets the port number. See http://baseplugins.thep.lu.se/browser/extensions/net.sf.basedb.ftp/trunk/ftp-config.xml#L29 Jari Pawel Sztromwasser wrote: Hi all, I have just upgraded to the latest BASE 2.8.2 and installed the base-FTP server. Everything went smoothly, but I have one, little silly question: how do I connect to the server? what is the address? I have tried various combinations of the host name where BASE is installed (with and without port number) and haven't managed to connect. I couldn't find anything in the ftp-config.xml and docs either. What am I missing? All the best, Pawel - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] BASE 2.7.2 released. Important bug fix included!
Hi all, We have released BASE 2.7.2. The release includes important bug fixes in the LOWESS plug-in shipped as a part of the BASE package. Some other improvement are also included in the release. It is highly recommended at all BASE installations where LOWESS is used as a part of their analysis in BASE are upgraded to this release. More details on the LOWESS problem is given below. Note, we have not found any problems with the BASE1 lowess implementation and analysis made with BASE1 lowess in BASE1 or BASE2 are still valid. More information about the changes in 2.7.2: http://base.thep.lu.se/query?milestone=BASE+2.7.2group=resolution Download from: http://base.thep.lu.se/wiki/DownloadPage We regret any inconvenience that the LOWESS bug may have caused, The Lund BASE team Text copied from the installation/upgrade chapter of the BASE documentation, http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.upgrade.html Bug in the LOWESS plug-in affecting BASE version 2.0 -- 2.7.1 This release fixes a serious bug in the LOWESS plug-in shipped as a part of the BASE package. The bug is found in all BASE versions between 2.0 and 2.7.1, and has caused incorrect normalization values to be calculated. All data that has been normalized with the BASE2 LOWESS plug-in prior to BASE 2.7.2 should be considered invalid and needs to be re-normalized with the fixed version. Downstream analysis steps that has used the incorrectly normalized data also needs to be redone. For more information about the bug see http://base.thep.lu.se/ticket/1077 BASE 2.7.2 includes a utility for finding all experiments/bioassay sets that includes data normalized with the LOWESS plug-in. An administrator can use this utility to extract a list of all experiments/bioassay sets that needs to be fixed. The utility can also tag the name of the found experiments/bioassay sets with FIX LOWESS to make it easier to find data that needs to be fixed. The utility can't see any difference between data normalized with the old version and the fixed version. It will simply report all data that has been normalized with the LOWESS plug-in. Only use the utility a single time right after the upgrade to BASE 2.7.2. The utility is a command line program that should be executed on the BASE application (web) server. cd base-dir/bin ./onetimefix.sh lowess_warn -u login -p password -f We recommend running the utility as the root user. The -f option is optional. If it is included the found experiments/bioassay sets are tagged with FIX LOWESS, otherwise only a list with the information is generated. - Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] lowess normalisation
The problem is now being fixed, http://base.thep.lu.se/ticket/1077. Unfortunately this problem affects all versions of BASE2 and everyone are recommended to upgrade to the future 2.7.2 (or later). The problem is localized and 2.7.2 will be released later today or at latest tomorrow. More details on the issue will follow in the announcement of the new release. Cheers, Jari Bob MacCallum wrote: Has anyone had problems with the Lowess analysis plugin? To me it looks like it is overcorrecting. Where a M/A plot is largely below the zero line before normalisation, it ends up largely above it afterwards. I'm using default values (including 0 for block group size). Default values were always fine in BASE1. You can look for yourself with the guest login at http://fungen.vectorbase.org/base2 Experiment Male vs. female (Koutsos et al., 2007) is a good small example. I don't see a recent ticket on this (I have not upgraded in a few months). cheers, Bob. - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Luminex data
There is support for Illumina using the Illumina plug-in package, http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina. Illumina is bead-based and maybe a similar package can be created for Luminex? So, BASE supports bead based data but luminex is currently not directly supported. Jari david vilanova wrote: Hello, Are there any plans to support luminex expression data based on beads ? The overall workflow for tracking the samples is the same, the only think that change is that instead of usign arrays, it would be beads. If not , do you knwo of any available lims system for beads ? - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Which import plugins are available in BASE?
Good Morning All, I have a lot of Affymetrix array data that I would like to analyze together. The zip that contains these files is very big and I can't upload it to BASE to use Batch Data Importer to import it into my experiment. There is a known issue with files larger than 2GB, http://base.thep.lu.se/ticket/841 Is your file larger than 2GB? There is a thread related to this issue, http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg01464.html The resolution in this thread did not help the original poster but it might help you. It would be beautiful if were possible to add to an experiment raw bioassays that uses the same Array Design used by existing raw bioassays. Are there any plans to implement such a feature? There is the batch data importer, http://baseplugins.thep.lu.se/wiki/uk.ac.scri.batchimporter, that you already refer to above. Also, there is the tab2mage importer, http://baseplugins.thep.lu.se/wiki/uk.ac.ebi.Tab2MageImporter, but I think it is still immature. We may have a look at the batch data importer in the future to see if we can improve and customize it for our core facility needs. However, I cannot give any time projections for this work. In principle the current batch data importer should be usable even if smaller than 2GB files are used for data upload. Split the zip-file to reasonable size, use the plug-in. This will create a lot of raw bioassays and assign them to the experiment you selected to import from. Jari - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] BASE2 backups
Hi, We are working on a backup scheme here in Lund. We'll send a note when we have something that at least works. Then we can all improve our backup strategy ;-) Why use svn? Do you need to track changes to files? For the userfiles directory a simple rsync should be fine, it is incremental (transfers only changes). Cheers, Jari Bob MacCallum skrev: Hi all, Does anyone have any genius solutions for backing up BASE2? We're trying to get a major production server online and obviously backups would be quite useful. I can do what we already do for BASE1: periodic full mysqldump and rsync of BASE's filestore to an off-site location. That approach only allows me to restore to the latest full dump (to keep db and files in sync). I wonder if subversion could be used to manage the userfiles directory in BASE2? (i.e. commit new files to svn at the same time as a mysqldump was done). I suspect this is a heavier workload than svn was designed for. A more incremental approach to backing up the db would be useful when we are in the tens/hundreds of gigs. Maybe a slave mysql server? Could that work reliably between two distant sites? Any ideas? cheers, Bob. - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] APT version 0.2 released
Nice work. I've successfully tested the apt-summarize plug-in. I do not have any genotype data so I have to leave that for someone else to test. I miss a short description of the two plug-ins. How to use them and what to expect from them. Specifically the genotyoe plug-in requires some additional files (or one file). Is the chrx file alwasy the same for a given .cdf (array design in BASE speak)? If yes, maybe we should extend array design to also store the chrx file for seamless use. Also, should there be more than one Affy raw data type, one for expression and another for snp? Jim Collet made an inquiry about support for 'apt-cel-extract' to the mailing list in the beginning of this year. How do we proceed to get this algorithm (and others) into the APT plug-in set? Cheers, Jari Robin Andersson skrev: Hi all, A plugin package for execution of the Affymetrix Power Tools apt-probeset-summarize and apt-probeset-geneotype are available for download from: http://madr.lcb.uu.se/browser/plugins/se/uu/lcb/APT/tags/0.2 From this repository you can download a precompiled jar file or the source code. See the INSTALL file for instructions. This package is a suggested replacement of the affymetrix package including the Plier and RMAExpress plugins. Robin - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] BASE 2.5.1 released
A new version of BASE is available for download at http://base.thep.lu.se/wiki/DownloadPage Fixed issues are listed at http://base.thep.lu.se/query?status=closedmilestone=BASE+2.5.1 The Lund BASE team - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] BASE 2.5 released
Hi all, We are happy to announce the release of BASE 2.5. The packages are added to the download area, http://base.thep.lu.se/wiki/DownloadPage Please send feedback through the mailing lists. Happy BASEing The Lund BASE team - SF.Net email is sponsored by: Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Java memory error
We cannot recreate this problem. We have used the CDF importer on BASE 2.5.0beta and 2.4.5 with no problems. One difference may be that we use jobagents (i.e., running jobs in a different thread than the core BASE application) but we did not experience any failures prior to switching to jobagents. We even tried to give the jobagent 2GBs of memory to play with without any problems. So ... we have no clue on what is going on. Are you able to do anything with your BASE? You are running a pure non-tampered BASE installed according to the installation instructions? Can you please send us the information from the about button, configuration tab. Jari matthew lange wrote: The cdf file mentioned in my original post is called HG-U133_Plus_2.cdf, and is downloadable from Affymetrix. It is 97 MB. Here is the Stack trace provided through the BASE CDF ProbeSet Importer (not using the custom reporter importer here, just the generic one that comes with base), accessible from the array design page, as verify Reporters link. Thanks a bunch for your help. Let me know if I can be more specific. Kind Regards, matthew java.lang.OutOfMemoryError: Java heap space at java.lang.String.substring(String.java:1770) at java.lang.String.subSequence(String.java:1803) at java.util.regex.Pattern.split(Pattern.java:993) at java.lang.String.split(String.java:2103) at java.lang.String.split(String.java:2145) at affymetrix.gcos.cdf.CDFFileData.readTextProbeSets(Unknown Source) at affymetrix.gcos.cdf.CDFFileData.readTextFormat(Unknown Source) at affymetrix.gcos.cdf.CDFFileData.open(Unknown Source) at affymetrix.gcos.cdf.CDFFileData.read(Unknown Source) at affymetrix.fusion.cdf.FusionCDFData.read(Unknown Source) at net.sf.basedb.core.Affymetrix.checkIfReportersExists(Affymetrix.java:416) at net.sf.basedb.plugins.CdfFileReporterImporter.importFromCdf(CdfFileReporterImporter.java:460) at net.sf.basedb.plugins.CdfFileReporterImporter.run(CdfFileReporterImporter.java:183) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:89) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:421) at java.lang.Thread.run(Thread.java:595) On Dec 3, 2007 11:02 PM , *Nicklas Nordborg* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: -- Forwarded message -- From: *Nicklas Nordborg* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Date: Dec 3, 2007 11:02 PM Subject: Re: [base] Java memory error To: BASE ML basedb-users@lists.sourceforge.net mailto:basedb-users@lists.sourceforge.net Cc: Joseph Fass [EMAIL PROTECTED] mailto:[EMAIL PROTECTED], [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Matthew Lange wrote: I am using the latest Base, and trying to load an initial data set. My initial effort was to modify the reporter importer to load some affy Why have you modified the reporter importer? What modifications have you made? The regular reporter importer can import Affymetrix csv files without problems. The hard part may be to come up with regular expressions that works. Sample configurations can be downloaded from http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html probes from a csv file. This worked fine for a small list, but as the list approached 500 individuals, I started receiving out of memory What do you mean with individuals? We regularly test with importing 5+ reporters/probesets. It works fine with 500MB memory with room to spare. errors from the Java Heap...and even brought Tomcat to its knees on a couple of occassions. As a workaround, I uploaded the an 80ish MB CDF file from Affy, which contains the array design. This went in fine. Then I tried to use the feature that allows me to import reporters from the CDF file--again Java OOM errors, and tomcat whining. We use the Affymetrix Fusion SDK for reading CDF files. I don't know about the memory requirements. I think the binary format uses less memory since data is read from the file at demand. If the file is in text format everything is parses and stored in memory. The biggest test file we have is ~40MB text format. Memory usage stays below 100MB while parsing that file. We have given Tomcat 2GB to play with, and this seems like it should be more than enough. Are there known issues with this utility that I should be aware of, or is there a rule-of-thumb to follow when allocating memory to tomcat, based on the size of files that need to be parsed? Or maybe another memory setting somewhere that I must have overlooked? Are you really sure that you have given
Re: [base] Getting started with BASE2.4
Are you logged in as with administrator privileges? Only users with administrator privileges are allowed to use the Reporter map importer and thus configure it. There is no need to create this plug-in it comes with pre-installed with BASE. Jari Diana Bernal wrote: Dear BASE staff, I am strating to set up BASE 2.4. I have followed the BASE 2.1 - User documentation: Getting started. I was able to configure the /Reporter importer/ , now I should configure the /Reporter map importer/ . However I can't find it. Shoul I create a new plug-in for the /Reporter map importer/, if so how do I create a new plug-in?. Thankyou very much. Diana Bernal - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] regular expression and wildcards
I moved it to the BASE core ticketing system as http://base.thep.lu.se/ticket/811 Jari Nicklas Nordborg wrote: vegard nygaard wrote: Thanks for quick answers. I would like column mappings to support wildcards or regular expressions. Not a big thing, but I took the liberty to add it as a ticket. Implement it if it is cheap and when you have time. You added it to the wrong site. It is a BASE core issue. It has nothing to with the plug-ins on the BASE plug-ins site. /Nicklas - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] regular expression and wildcards
Nicklas Nordborg wrote: vegard nygaard wrote: F633 Median not working but giving a funny error message: Error: For input string: F633 MEdian on line..., (The E's in the input has been uppercased!) That is because string like '1.23e-2' are not recognised as numbers unless the 'e' is first converted to a capital 'E'. That is, Java cannot handle scientific notation properly (cf. http://base.thep.lu.se/changeset/3703) Jari - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] BASE 2.4.5 available for download
A new version of BASE is available for download at http://base.thep.lu.se/wiki/DownloadPage This release contains one fix removing a debug sleep statement. Server performance is improved when upgrading to this release. The Lund BASE team - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] migration from 1.2.16 to 2.3.2
Select 'Download BASE' at http://base1.thep.lu.se/ and download version 1.2.17b. Follow the instructions in the package to upgrade from 1.2.16 to 1.2.17b The 1.2.20/21 is a reference to the underlying database schema version and not the BASE application version. It is a little bit confusing. Jari Spollen, William G. wrote: We installed and used BASE 1.2.16 a few years ago and now want to migrate the data to BASE 2.3.2 on another machine. The migration script we found on the web did not work. After looking around it appears I am to upgrade first to version 1.2.20 or 21, but we cannot find any such version at SourceForge. Where can I find this version? Thanks Bill - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Tab2Mage Importer has problemsfinding AnnotationTypeCvImporter
However, given the performance improvement you should go for 2.4.4 Jari Nicklas Nordborg wrote: vegard nygaard wrote: When I briefly inspected what was created in BASE it looked OK despite the error messages in the log. The overview tab for the experiment crashed though, but it has done that for me a lot and may not be caused by the tab2mage importer. Anyways here is the error message java.lang.NullPointerException This has been fixed in the 2.4.4 release. See http://base.thep.lu.se/ticket/803 for a manual workaround if you don't want to upgrade. /Nicklas - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Problems running Tab2Mage Importer, NOT sufficient Disk Space
Just for your information: Dominic Oyeniran wrote: This is a known issue and has been documented here: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt. Please scroll to the usage section right after the installation section. We prefer to use links to the more generic http://baseplugins.thep.lu.se since lev is merely the current host of the baseplugins (and base) and it may changes in the future. That is the above link should be a more archive safe http://baseplugins.thep.lu.se/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] 2.4.2 = 2.4.3 - any database schema change?
There is no need to delete the database between upgrade in a stable release of BASE. Please read http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.upgrade.html for upgrading instructions. Jari Dave Hau wrote: 2.4.3 release followed closely after 2.4.2 release. I would like to upgrade from 2.4.2 to 2.4.3, but was just wondering if I could keep my database and just copy the entire 2.4.3 www directory to my tomcat server. Preferably I would like to not have to nuke the entire database this time around for the upgrade. Is there a database script in the base package I can do a diff on to see if there's been any schema change? I did a quick search and didn't find any. Thanks and best regards, Dave Hau - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Error: Run Plugin: RMAExpress plug-in
Hi, jesse paquette wrote: Hello, I'm still trying to get through the 2.1 getting started document (http://base.thep.lu.se/chrome/site/doc/user/getting_started.html). Moving on to section 2d, Analysing an experiment step I. I'm getting an error when I try to run the RMAExpress plug-in job. The stack trace is below. I'm curious as to why the plug-in is looking for the RMAExpressConsole application in the Tomcat temp directory. I think I've configured everything properly so far. The RMAExpressConsole application file is located in the same directory as the plug-in's affymetrix.jar library. What is the name of the RMAExpressConsole file. Is it with or without .exe extension. If it is without the extension can you please try to add the extension, and the other way around if it is with the extension. I've got about 100 raw .CEL files to load. How's the batch import functionality coming along? Take a look at http://baseplugins.thep.lu.se/wiki/uk.ac.ebi.Tab2MageImporter I think this should solve your batch import problem. Cheers, Jari - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Base1PluginExecuter parameter xml
Why not use the clustering in the MeV plugin shipped with BASE? Jari Johan Enell wrote: Hj Bob, The clustering from Base1 will not work in Base2. Or more precisely, you will be able to run the plugin but you wont be able to se the result. The visualization page in Base1 was a specific php page for that plugin and we didn't want a solution like that in Base2. When you configure Base1 plugins you should always start of from a base1 plugin configuration file. From the plugin page in Base1 you will find an export link with each plugin. Use that file to configure the Base1PluginExecuter. /Johan 11 sep 2007 kl. 16.58 skrev Bob MacCallum: Hi, I was trying to find out if base1's hierarchical clustering would run under base2 - and got to the point where I need to provide parameter settings as XML. I could spend an hour figuring this out by hand (e.g. from the examples on the BASE2 demo server) but I'm convinced there's an easier way. I've searched the plugin site for documentation. Could someone help please? Since the hierarchical clustering isn't on the BASE2 demo server, does that mean it doesn't work? We know that there won't be any display tools available in BASE2 for this, but we can work with the PNGs and assorted text files. many thanks, Bob. - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] BASE 2.4 released
Hi all, We are happy to announce BASE 2.4. The packages are added to the download area, http://base.thep.lu.se/wiki/DownloadPage Please send feedback through the mailing lists. Happy BASEing The Lund BASE team - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] import of affymetrix data - which approach
Hi, The plier and rmaexpress plug-ins calculates the probeset expression values using information from the cel/cdf files. The plugins are presented on the BASE plugin site http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix How the expression values are calculated is presented elsewhere (please follow links from the plugin website). The raw data for Affymetrix is stored in the original cel files and is not stored in database tables like GenePix and other data. Affymetrix related expression data is not stored in the database tables until the creation of the first root bioassay set. You do not need to create another affymetrix plugin if you are happy with the algorithms provided by plier and rmaexpress. However, if you need something else then you may need to write your own plugin (or help us improve the current affymetrix plugin). You may want to change the extended-properties.xml, some information on this is available here, http://base.thep.lu.se/chrome/site/doc/admin/extended-properties.html The problem with using CDFs in your array design is most likely related to missing reporters (probesets). Have you imported the reporters associated with the design (CDF)? Please read the information provided in the plugin site and http://base.thep.lu.se/chrome/site/doc/user/getting_started.html (nice example on the workflow in BASE with references to Affymetrix data). And, of course, you can also use the mailing list. Cheers, Jari Reha Yildirimman wrote: Hello, like some other people I am trying to import data from affymetrix CEL files. Searching the archive I have read that people use the RMAExpress and PLIER plugins. As far as I understood the plug-in extracts/calculates the intensities but where are those data stored, since the associated raw data type for affymetrix has no database table definition? Furthermore, are those intensities the stated MEAN values inside the CEL file and are extracted intensities for each coordinate/probe or only for probe sets ? I have another approach and if that seems ineffective to you please drop me a line! My approach is to change the affymetrix data type inside the raw-data-type.xml from a simple file-definition to a database-definition like the other data-types defined inside the xml. I added properties for the values: MEAN (float), STDV (float), NPIXELS (float) To be able to import data via a base-plugin from a CEL file each data line has to have an association to a reporter - thus I added a column holding the ProbeSet ID for each CEL file. My problem is that when I associate a CDF file to an array design - which I need for reference purpose - it states under Properties: Features: Yes(0) This makes the raw data importer fail with: Item not found: Feature[row=null, column=null, block=null, metaGridX=null, metaGridY=null] on line 2 If I take out the connection to the CDF - thus turning the Feature property to No - the raw data importer works. How can I get around the problem without having to add to each line inside the CEL file fake numbers for the features row, column, block, ... Thanks alot in advance. Best, Reha - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Hakkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Solvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Unable to import root bioassay
Hi, You have probably not imported all probeset into the reporter table. Please make sure that ALL reporters are imported, that is check that the number of imported and updated reporters match the number of probesets in the affychip you use. Cheers, Jari [EMAIL PROTECTED] wrote: Dear All: I have some trouble to launch my experiment analysis thus I send you the error message which appears Name Run plugin: RMAExpress plug-in Description Priority 5 (1 = highest, 10 = lowest) StatusError: Unable to import root bioassay. Percent complete 100% Created 2007-06-15 15:20:53 Started 2007-06-15 15:21:26 Ended 2007-06-15 15:21:42 Serverbiobase.crs4.org PluginRMAExpress plug-in Configuration - none - net.sf.basedb.core.BaseException: Unable to import root bioassay. at se.lu.thep.affymetrix.RMAExpress.storeResult(RMAExpress.java:424) at se.lu.thep.affymetrix.RMAExpress.run(RMAExpress.java:307) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:88) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420) at java.lang.Thread.run(Thread.java:595) Could somebody say me what is wrong? I am using BASE 2.2.2 and mysql Ver 14.12 Distrib 5.0.27, for redhat-linux-gnu (i686) using readline 5.0 thanks This message was sent using IMP, the Internet Messaging Program. - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Hakkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Solvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] BASE 2.3.1 released
Hi all, Our best BASE so far is available for download at http://base.thep.lu.se/wiki/DownloadPage Happy BASEing, The Lund BASE team -- Jari Hakkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Solvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Base and webservices
Hi, there is sample code available at http://baseplugins.thep.lu.se/wiki/se.lu.thep.webservices_clients that runs against the demo server. The code is written in Perl and R. The Perl can be used as a script or used to get BASE/R connectivity from an R environment. Jari Nicklas Nordborg wrote: Emmanuel Courcelle wrote: Hello Just to have some information about the future: Are there any plans to use some or all functionalities of BASE through some web service ? Do you have some documentation about this, is there anything already running (even experimental) ? We have been experimenting with this in a separate branch. http://base.thep.lu.se/browser/branches/webservices It is possible to login and list your Affymetrix experiments and download the CEL and CDF files associated with each raw bioassay. There is no documentation about this exception what you can get from reading the source code. I don't think the entire BASE API will be exposed through webservices. Webservices require a coarser API to make it usable. Right now we are waiting for more use cases in order to be able to start working on that API. /Nicklas - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Hakkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Solvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Add new plates
A list of all core plug-ins with sample configuration files (also for plate importer) is available at http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html Jari Nicklas Nordborg wrote: Audrey Bihouee wrote: Hi everybody, A little question in BASE 2 : I'm very suprised because I can't find anywhere where you can add a new plate de novo. In the plate page, only Merge is available. But how could you merge plates if you don't have any plates at all ? In the plate type page, I can add a new plate type but I can't add associated plates. You have to use the Import function to import plates. You will need a file that contains the reporter ID for each well coordinate. The file may contain multiple plates. For an example see the test file that we use: http://base.thep.lu.se/browser/trunk/src/test/data/test.plate96.import.txt?format=raw If you don't have an Import button on the Array LIMS-Plates page you must first define a file format(=plugin configuration) from the Administrate - Plugins - Configurations page. See the Getting started documentation (http://base.thep.lu.se/chrome/site/doc/user/getting_started.html) for more information about how to create plugin configurations. /Nicklas Thanks for help. Audrey - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Hakkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Solvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] walk thru
Hi, There is a getting started document available at http://base.thep.lu.se/chrome/site/doc/user/index.html Jari Gabe Dagani wrote: Greetings, Has anyone created a simple walkthru for setting up a simple experiment, uploading GPR, GPS, TIFF files into a project and doing some analysis? I am just a beginner and the manual is outdated for base 2.0. thanks - Gabe -- Jari Hakkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Solvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Offline files
Yes, there is a problem with spammers of trac environments. We have changed the ticket reporting system to require authentication (details on the baseplugins wiki). For BASE and Proteios this has fixed the problem of ticket spam (at least for now), so hopefully the ticketing system will stay clean. Jari Micha Bayer wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:basedb-users- [EMAIL PROTECTED] On Behalf Of Jari Häkkinen Sent: 30 November 2006 15:42 To: BASE ML Subject: Re: [base] Offline files There is a possibility to get access to the subversion repository and trac environment just for this kind of stuff. Check out http://baseplugins.thep.lu.se Trac environment allows for discussions about the importer through the ticketing system. I just looked at the ticketing system on the plugins page and it looks like it's been majorly vandalized by spammers. Is this email based? Someone might want to take a look at this. Cheers Micha _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [EMAIL PROTECTED] quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] BASE 2.1.1 released
A new minor release is available for download at http://base.thep.lu.se/wiki/DownloadPage A list of fixed item is available here http://base.thep.lu.se/query?status=closedmilestone=BASE+2.1.1order=id Jari -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Offline files
with some kind of spreadsheet (each one in a different format of course), so the leap to MAGE-TAB is not so great. Ok, enough from me... Micha Bayer writes: -Original Message- From: [EMAIL PROTECTED] [mailto:basedb- users- [EMAIL PROTECTED] On Behalf Of Nicklas Nordborg Sent: 29 November 2006 14:40 To: BASE ML Subject: Re: [base] Offline files Jari Häkkinen wrote: Hi all, Just a thought, I think the best choice to trigger a large import like this is to create a plug-in instead of adding extra tabs to the file browser. The plug-in should start by requesting the zip file/directory to import. If the zip file is not already uploaded the user will have an opportunity to upload it. After choosing the zip file/directory the plug-in could start its import and creation of necessary items. The above is fairly straightforward already today and the new code would start at import/creation of necessary items. This will yield very little (or no) changes to the core and the plug-in should probably be started from the experiment listing page. This will of course change the experiment list jsp (a import tab is needed). No change is needed to the jsp. The new plugin will be detected and an Import button will appear. /Nicklas So what interface would I have to implement for this to happen, if I were to turn my code into a plugin? If it's not too much work I might consider doing this, that would be much better. Cheers Micha == Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.sari.ac.uk/MichaBayer.htm = _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [EMAIL PROTECTED] quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). --- -- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department
Re: [base] Offline files
a dye swap for one biological replicate, the bulk loader will label each extract with both dyes for *all* replicates (leaving you with unused labelled extracts after linking to the hybs). One quite low cost way to define your experiment for a bulk loader is Tab2MAGE (soon to be MAGE-TAB, see http://www.biomedcentral.com/1471-2105/7/489/abstract ) - although it feels strange to say this because I have been *exporting* Tab2MAGE from BASE 1.2 rather than importing it. The input files for our bulk loader are specified here: http://wiki.vectorbase.org/vectorbase/index.php/MicroarrayExperiments (look for the example file links) but note that the BASE-specific parameters (protocols, raw file parsers, array designs, etc) are configured by the user in an interactive process before the upload. Our bulk loader is also 2-channel only... I have a feeling that the Tab2MAGE parser could be adapted into a BASE 2 bulk loader somehow, although I think all Tab2MAGE code is Perl. I think MAGE-TAB is something we could get the average bench scientist to provide (with a little help MGEDifying the annotations). So far every experiment I have loaded has come with some kind of spreadsheet (each one in a different format of course), so the leap to MAGE-TAB is not so great. Ok, enough from me... Micha Bayer writes: -Original Message- From: [EMAIL PROTECTED] [mailto:basedb- users- [EMAIL PROTECTED] On Behalf Of Nicklas Nordborg Sent: 29 November 2006 14:40 To: BASE ML Subject: Re: [base] Offline files Jari Häkkinen wrote: Hi all, Just a thought, I think the best choice to trigger a large import like this is to create a plug-in instead of adding extra tabs to the file browser. The plug-in should start by requesting the zip file/directory to import. If the zip file is not already uploaded the user will have an opportunity to upload it. After choosing the zip file/directory the plug-in could start its import and creation of necessary items. The above is fairly straightforward already today and the new code would start at import/creation of necessary items. This will yield very little (or no) changes to the core and the plug-in should probably be started from the experiment listing page. This will of course change the experiment list jsp (a import tab is needed). No change is needed to the jsp. The new plugin will be detected and an Import button will appear. /Nicklas So what interface would I have to implement for this to happen, if I were to turn my code into a plugin? If it's not too much work I might consider doing this, that would be much better. Cheers Micha == Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.sari.ac.uk/MichaBayer.htm = _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [EMAIL PROTECTED] quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). --- -- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV
Re: [base] Offline files
The zip up-loader is meant to be used for uploading bulks of files, and is working well. For retrieving files from the server there is no batch support. Jari Bob MacCallum wrote: Nicklas Nordborg writes: Giovanni Coppola wrote: Hi everybody, I have two questions: 1) is there a way to download images or raw data files in batches? No. yes but there is a zip file unpacker (in BASE 2) I haven't used it, but doesn't this cut down on the GUI clicking if you want to upload a lot of files? At some point, someone will come up with a bulk loader which will batch/bulk/mass upload files *and* create/annotate/link the data objects (I'm not volunteering, yet...) 2) while I was trying that (to download more than one file at once), in the 'Files and Directories' tree, I accidentally moved Offline some files, and now I don't seem able to download them anymore. Is there a way to restore them in the Primary position? They have been deleted from the server. You have to upload them again. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Offline files
Hi all, Just a thought, I think the best choice to trigger a large import like this is to create a plug-in instead of adding extra tabs to the file browser. The plug-in should start by requesting the zip file/directory to import. If the zip file is not already uploaded the user will have an opportunity to upload it. After choosing the zip file/directory the plug-in could start its import and creation of necessary items. The above is fairly straightforward already today and the new code would start at import/creation of necessary items. This will yield very little (or no) changes to the core and the plug-in should probably be started from the experiment listing page. This will of course change the experiment list jsp (a import tab is needed). In my naive view this will only affect a jsp and a new plug-in is needed. Jari dominic oyeniran wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Micha Bayer Hi Micha, I have just finished writing one. The user uploads a zip file, a new directory is created in the user's raw data directory (with the same name as the zip file) and the files are then unzipped in there. They are then imported one by one as new RawBioAssay objects and at the end a new Experiment is created that has all these hanging off it. At the moment it only works for non-Affy data though. To do this I had to hack the BASE source (plugin wasn't possible as far as I can tell), and I am always reluctant to do that sort of thing because of versioning/upgrade issues (i.e. having to repeat this every time a new version is out). I have modified the JSP page that controls the menus and inserted a new item there, and added a couple of JSP pages myself that provide the UI for all this. I did some more detailed testing yesterday and things worked fine but it's all still pretty raw and probably full of bugs. I am happy to share the code with others though, or even make it a full contribution to BASE if people are happy with it (perhaps after it has been gone over by some of the BASE team). I also think the exception handling needs more work probably. Base 2 has plans to have tab2mage import (importing experiments and associated files) see Ticket #338 on base2 trac http://base.thep.lu.se/ticket/338 system, and your zip file loader would certaily help to in importing experiments from repositories and doing other interesting stuff. We have this on our do list and would certainly appreciate if you can share the code with us to help in this process. Also, do you have plans to extend the functionality to non-affy data too? Thanks and hope to read from you. Dominic - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Offline files
Ah, even better ;-) Nicklas Nordborg wrote: Jari Häkkinen wrote: Hi all, Just a thought, I think the best choice to trigger a large import like this is to create a plug-in instead of adding extra tabs to the file browser. The plug-in should start by requesting the zip file/directory to import. If the zip file is not already uploaded the user will have an opportunity to upload it. After choosing the zip file/directory the plug-in could start its import and creation of necessary items. The above is fairly straightforward already today and the new code would start at import/creation of necessary items. This will yield very little (or no) changes to the core and the plug-in should probably be started from the experiment listing page. This will of course change the experiment list jsp (a import tab is needed). No change is needed to the jsp. The new plugin will be detected and an Import button will appear. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Offline files
Micha Bayer wrote: Hi Jari, That sounds perfectly reasonable when you put it like this, but I was put off going down that route by a post to the list from Nicklas (http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg00228.html) where he says that it is best to not use a plugin to do this because of interface issues (whatever they are). I think Nicklas was thinking about very interactive plug-ins. Personally, I think a plugin would be far better than what I have done -- if I was to persist with my solution I would have to modify the BASE source every time a new version comes out. Our belief is that basically no modification to BASE is needed if one creates a import plug-in that creates all needed items automatically (using information from files of course). Trouble starts when communication is needed from the user after plug-in start. The plug-in system allows for communication just before a plug-in is started (at least was design like this, I suppose one can tweak user interaction with the plug-in but thats out of this topic). I also think that batch import *is* a high priority thing for most users, whether they have a pile of legacy data or not. Most biologists I know would probably rather spend a solid period doing labwork, and then process a whole bunch of experiments in a oner. I also think it is a nonsense to have a human doing boring, repetitive stuff -- computers are there to do that. Why waste your time on something that a for loop can do. So perhaps the dev team should reconsider this. I agree, I think it is an important issue as well. However, we think that we work on many other important issues already. We are mainly working on core stuff and hoping that others contribute with things that can be written as plug-ins. You are already doing this, and unfortunately you were pushed in the wrong direction. I am just talking to my boss about code ownership issues but I can probably offer up my stuff one way or another, and people can then either cannibalise it and turn it into a plugin, or adopt it (or a modified version) into the core etc etc -- happy with any solution that makes others benefit from my blood sweat and tears shed . :-) Dominic would probably benefit from your code and through him the code will probably end up in the BASE repository. Contributions are welcome and we consider all of them for inclusion the the BASE code base. Cheers Micha Cheers, Jari - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] long term future and support for BASE2
Hi, This is a fair question. We are four people involved in the BASE project as programmer in more or lesser degree (Nicklas and Martin are full time employed to work on BASE). We also have a close collaboration with the Oncology Department here in Lund and they also put effort in BASE (1 and 2) progress. The software part of BASE crew is funded until the end of 2009. BASE is an essential part of the core service at the microarray facility here at Lund University so we expect to be supporting BASE at least during this time. What happens beyond 2010 depends on so many things... So, jump on to BASE and help us make the software better. Cheers, Jari Micha Bayer wrote: Hi, This is a non-technical question, for a change. We are about to make a fairly long-term commitment to BASE as our microarray platform and were wondering what the future looks like for BASE, in terms of support and funding (we're talking the next few years rather than months here). This is obviously an issue with all open source projects, and I 'm sure BASE is no exception. I guess many other users may be in the same boat -- no-one wants the support for their system to suddenly dry up, and then to have to migrate their data to something else. It would be good if someone could shed some light on this. Thanks Micha == Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.sari.ac.uk/MichaBayer.htm = _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [EMAIL PROTECTED] quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] Browser compatibility
Hi all, We have previously decided to only support Firefox and Internet Explorer due to lack of resources. If someone is prepared to perform Safari testing we could add reasonable fixes into BASE to resolve Safari issues. Is there someone out there who is willing to become a Safari/BASE tester. The list of BASE team supported browsers is short: Firefox production releases 2 or later. Internet Explorer 7 or later. Jari -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] how to import reporters ?
The reporter import button does appear because there is no plug-in configured for import of reporters. You need to create a configuration for the Reporter importer plug-in. We have compiled a getting started document that outlines the first steps with BASE 2, http://base.thep.lu.se/chrome/site/doc/user/getting_started.html Jari Emmanuel Courcelle wrote: As I wrote in the previous mail: The columns are numbered from 0 so the file we have been testing on the Rgn R² column should be column number 32 and the mapping to use \32\. I counted twice, but of course you should check that it is correct. Sorry, you're right You have to import reporters before you can import raw data. The error message means that there is no reporter with external ID=SMa1894 in the database. OK Sorry for the probably stupid question, but how do I import reporters ? I tried the Reporters screen, but I found only buttons labelled New Delete New reporterl list Export, there is no import button... - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] 2 questions about Plugin configuration
Nicklas Nordborg wrote: Emmanuel Courcelle wrote: Hello Now using Base 2.1... I am trying to configure the Raw Data importer plugin, to upload and parse genepix-type files. 1/ Pb configuring this plugin -- I click Plugin/Configuration/New -configuration name: bla bla -Raw DataType: Genepix -Next -Test with file/Select some uploaded file/Parse the file Then I get an error: Start of data couldn't be found. Please try again with different settings. In the window with the data file, I search the line marked Block Column Raw a.s.o., (it is the nb 30 for me), I have a box marked 'Unknown': I choose in the list Data header, I click and this fills up the field Data header regexp I then click again on Parse the File, this produces THE SAME error: I tried with some other (simpler) regular expressions, same behaviour: am I doing anything wrong ? I don't think so. It seems strange that it can't find the data the second time you click on Parse the file button. I really don't know why that is happening. Most of our test data files are Genepix files and we have not had any problems with them. I am thinking that maybe something gets trunkated or there is a problem with different types of linebreaks. Can you send me a few lines from a file with this problem? If should be enough with one line of data. If your headers have sensitive information please remove them as well. I noticed a similar problem as Emmanuel. I choose a data header line and tried to parse the file. It did not work so I only used the first part of the regexp created by the wizzard. This solved the problem for me and the wizzard could parse the file. I'll try to see if I can reproduce this problem and report back later. Cheers, Jari - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] BASE2 and affymetrix
Yesterday, I checked in a compilation of discussions regarding Affymetrix in BASE 2.0, http://lev.thep.lu.se/trac/base/browser/trunk/doc/affymetrix.txt, to the subversion repository. The development of the Affy support follows the plan outlined in this document. If you have any thoughts you'd line to share with us, please use the mailing lists or add comments through http://lev.thep.lu.se/trac/base/ticket/150 Cheers, Jari -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Anybody install BASE under Tomcat?
Hi, There is no way to install BASE 1.2.17 (NOTE version number) since 1.x is based on PHP. However, BASE 2.0 is a complete rewrite in Java an runs with Tomcat. So, to run BASE in Tomcat you must switch to BASE 2.0. BASE 2.0 inherently supports Affymetrix but the import plug-in for Ayffymetrix data is still to be written. This plug-in will appear as a part of the next milestone for BASE 2.0 (http://lev.thep.lu.se/trac/base/roadmap). More information on BASE 2.0 is available at http://base.thep.lu.se/base2/ Jari Longfei Yu wrote: Hi, I am wondering if anybody tried to install BASE system under Tomcat? I have done more implementation based on the BASE2.17, and it will support the Affymetrix experiment. I have added some more tables in the original database, so that the new system can extract the data from EXP, CEL, CHP file, and the user also can download all of them and DAT files for their experiment. However, the new implementation is based on Java technology, and I run the Affymetrix part under Tomcat, and the original BASE under apache. But, I want to merge them together, and put them all under Tomcat. I want to know if anybody did that successfully? If I want to run BASE2.17 under tomcat, what I need to do? Reinstall the BASE, or just copy the corresponding folds to Tomcat? Any suggestions will be appreciated. Thanks a lot! Best Regards, Longfei -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] MAGE-ML for ArrayExpress update, plug-ins
Yes ... but probably after release. We have already assigned enough for us all to do, but this wil be added asap after Feb 23. There are more R related stuff to be implemented during the spring. Jari charles girardot wrote: Hi Jari, Could you make sure that the R dispatcher (AROMA BASE, by Henrik Bengtsson from Lund) continues to work in BASE 2.0 Thanks Charles On 16 janv. 06, at 13:40, Jari Häkkinen wrote: Hi Angela, BASE plug-ins ... we are slowly working on getting the web page up again. Meanwhile we urge those of you who have plug-ins to send them to us through http://lev.thep.lu.se/trac/baseplugins Jari Angela Burr wrote: Hi, Our group has been using BASE for over a year and we have been eagerly awaiting the completion of MAGE-ML creation corrections (so that MAGE-ML files created by BASE are acceptable for ArrayExpress submission). We have data in BASE that we need to submit to ArrayExpress. Would you please give an update on the progress and possibly a timeline for when these changes will be incorporated into BASE 1.2.x? We really appreciate all the work on this project, adding this function in BASE will be very helpful. Also, when will more plug-ins be added to the new BASE plug-in development site? Our group is interested in adding more analysis plug-ins to our BASE installation and I'm sure that many BASE plugins have already been written. We would prefer not replicate the work if others have already written similar plug-ins. Thank you for the updates in advance. Angela Burr Center for Genomics and Bioinformatics Indiana University, Bloomington --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_idv37alloc_id865op=click ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
