Re: [base] Base2 install errors

Sam Hunter wrote: Hi, I'm new to Base, and am trying to set it up for testing. I am install on Ubuntu with base-2.0RC1. I downloaded and install the Java SDK, (jdk-1_5_0_06-nb-5_0-linux.bin), and mysql seems to be working fine. When I get to the "./initdb.sh password" stage of the install, I g

Re: [base] Base2 install errors

+--+ > 1 row in set (0.00 sec) > > So I know that the database is working, and that the base2user has > access to it, but yeah, I think something is going wrong with the java > mysql drivers as you suggest. > > thanks, > > Sam > > > On Fri, 2006-04-07 at 07:57 +0200

Re: [base] BASE 2 migrate and bulk upload questions

Bob MacCallum wrote: Hi BASE team/users, Just two quick questions about BASE 2: Is there/will there be a bulk upload facility? (ideally it would handle everything: samples, annotations, experimental factors, extracts, hybs, scans, raw data) - I can't find anything on the web about this. No, w

Re: [base] base-2.0RC1.2220

David Zhao wrote: Hi there, I was able to build base2, initialize database, and deploy base2 to tomcat 5.5.15. However, when I tried to access base2 for the first time through http://mytomcatserer:8080/base2 , I've got this error: Have you done an 'ant dist'

Re: [base] base2 reporter import error

David Zhao wrote: Hi there, I've just installed base2, and had it up and running. I tried to import agilent chip reporter data into base2, I've got an error showed at the bottom. Apparently the reporter format is not recoginzed, how do I setup one? or get one? Go to Administrate -> Plugins

Re: [base] base2 reporter import error

David Zhao wrote: > Hi Nicklas, > > > Thanks for your reply, actually the tomcat setup was correct, I do get > error report page for other error, instead of HTTP500 generic error page. > BTW, how do I stop BASE2 writing to the mysqld.log file, 'cause when I > perform a raw data upload, the log

Re: [base] base2 raw data import error

David Zhao wrote: > Acutally, I've figured out what I did wrong, if anybody is interested, > please see comments below: > > for raw data import (also reporter files), dataHeaderRegexp should the > regular expression respresentation of the header line, dataSplitter > should be: \t for tab-delimi

[base] BASE 2.0 RC2 released

Hello all, I am happy to announce that BASE 2.0 RC 2 is now available for download: http://lev.thep.lu.se/trac/base/wiki/DownloadPage Installation instructions are available at the BASE2 home page: http://lev.thep.lu.se/trac/base/wiki /Nicklas ___

[base] BASE2 and affymetrix

Yesterday, Jari 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 l

Re: [base] BASE2 demo server

Lepp, Dion wrote: > Hi all, > > > > I’m trying to test out the BASE2 demo server and have hit a few > stumbling blocks. Hopefully someone here can help me out with the > following questions. > > > How would one: > > > > 1) add well information to a plate? > > 2) import fea

Re: [base] Loading sample data

David Waring wrote: > I have installed the latest version of Base2. Everything seems to be > running fine. I would like to load the sample data. I cannot find > instructions. Any help? Go to View -> Samples. Add samples by clicking on the New button in the toolbar. /Nicklas _

Re: [base] (no subject)

David Waring wrote: > I have installed Base2 with PostgreSQL and am in the process of testing > things out. I have been able to add reporters, plates, arrays, extracts > hybridizations raw data and experiments. I am trying to analyse an > experiment so I chose new bioassay set, chose the formula

Re: [base] Defining a new raw data type for Illumina

Reha Yildirimman wrote: > Hello, > > using Base2 we are trying to implement the Illumina Chip design. In order > to use the raw data files describing coordinates and intensities of probes > there is a need to define a new raw data type besides the given ones > (affymetrix,agilent,spotfinder

Re: [base] link to base2 pages without relogin from anther web application

David Zhao wrote: > Hi there, > > I'd like to able to link to specific base2 pages from another web > application, how can I do this? Thanks in advance! The URL must must contain the ID parameter that is assigned when you log in. For example: http://lev.thep.lu.se/base2demo/my_base/index.jsp?I

Re: [base] link to base2 pages without relogin from antherweb application

MacCallum, Bob wrote: > This is something we are interested in too. > > Currently we link to pages in BASE 1 doing the following: > > 1. modify nologin.phtml to fill in a guest username and password by default > 2. guest account has very few priviliges and can't even change its own >password

Re: [base] Batch import

Ana Conesa wrote: > Dear list > > We are setting up BASE2 for storage of our microarray data. We have > finally managed to create plug-ins for reporters, arrays and raw data > and we would like now to have a way in import in batch our existing > experiments. I have been checking the base mailin

Re: [base] RawData import, error when reporterID=null

Pablo Lemos Ochandio wrote: > Hi, > > I have moved on in importing raw data sets and I came across the following > problems. Since we are using costum cDNA arrays when have some array desings > whith feature positions where no DNA has been spotted. This means that the > feature gets the va

Re: [base] RawData import, error when reporterID=null

Pablo Lemos Ochandio wrote: > Hi /Nicklas!! > > Well let me i explain my problem. > > I have a lot of grp files. I try to upload to BASE2. These files have a cDNAs > data, reference types and empty slots. GenePix extract information all of them > (Mean, Median, SD, ratios etc.). For empty slots,

Re: [base] regular expression and wildcards

Reha Yildirimman wrote: > Hello, > > I am trying to configure a raw data importer plugin and want to use > wildcards for reading raw data files. The dataheader inside those files > always contains some changing elements and I would like to use base2 > directly on the raw data without preprocess

Re: [base] how to link labeled extracts to intensity columns or channels

Petr Divina wrote: > Hello, > > how can I link (= associate) a particular labeled extract that was > used in a multi-color hybridization to a particular intensity column > in the raw bioassays (or particular channel in the experiment) ? It is not possible. /Nicklas > > I have an 8-channel raw

Re: [base] initdb.sh execution problem

Chris Wiita wrote: > I'm installing BASE2 RC2 on a FC5 system and every installation step was > going perfectly until I attempted to run initdb.sh . The following > error gets spat out: It seems like the Sun's JDK hasn't been installed correctly. The error message comes from a GNU Java runtime,

Re: [base] Migrate script fails, no error messages

Chris Wiita wrote: > I fixed the init.db problem I was having (simply using the wrong Java!), > but now I'm stumped with my migration. Base2 is running perfectly, as > is my 1.2 install. I can access the mysql databases correctly with the > information in migrate.properties, the root password

Re: [base] Migrate script fails, no error messages

Chris Wiita wrote: > Alright, that makes sense. The first time I ran the script the error > was different, and in repeating the script, I never noticed it was way > off in the first place! I turned logging, dropped both BASE2 DBs and > recreated them, and ran initdb.sh. It was successful. Co

Re: [base] Nimblegen

Keith Ching wrote: > Hi, > > I am looking into using BASE2 to store ChIP-chip data from the NimbleGen > platform. > Each whole genome scan has 14 million probes, divided up into 38 arrays > of 370k probes each. > > What is the feasibility of storing this information in BASE2? Say we > had 100

Re: [base] BASE 1.2.10 to 1.2.17

Steve Taylor wrote: > Hi Kjell, > >> It might look like you've updated to the latest CVS instead of the >> official latest release 1.2.17 ? >> >> The error message is related to the code related to MAGE-ML export to be >> released as part of 1.2.18. The error message should be harmless, but >>

[base] BASE 2.0 has been released

Hello all, I am happy to announce that BASE 2.0 is now available for download: http://base.thep.lu.se/wiki/DownloadPage Installation instructions and other documentation are available at the BASE 2 home page: http://base.thep.lu.se/ /Nicklas

Re: [base] Migrate script fails, no error messages

meone else on the list can help? Send a reply to me off the list. Thank you very much. /Nicklas > > --Chris W > > Nicklas Nordborg wrote: >> Chris Wiita wrote: >> >>> Alright, that makes sense. The first time I ran the script the error >>>

Re: [base] MySQL error : "could not resolve property: null..."

Reha Yildirimman wrote: > Hello everybody, > > I am using Base 2.0 and try to fill the system with data, doing the route > biosources, samples, extracts, labeled extracts. > > When I try to access the "labeled extracts" list I get the following error > message. > *** > could not resolve propert

Re: [base] Nimblegen

ps of > 10k or 100k? then we're talking about millions of rows instead of billions. > > i've heard that oracle can handle billions of rows of data, but i can't > imagine that its very fast > even if indexed properly.. > > -keith > > Nicklas Nordborg wro

Re: [base] BASE2 + Solaris crashes & recommended JVM

Emil Lundberg wrote: > Hi all, > > We are trying to go from BASE 2 RC1 to 2.0, and neither updating nor > initializing a new database seems to be working properly. Question is; > is it just us, or a BASE/Java/MySQL versions mismatch? If the latter, > are there any officially recommended/supp

Re: [base] BASE2 + Solaris crashes & recommended JVM

I am not able to reproduce the error. Unfortunately there is a glitch in the error handling which causes a second error to hide the original one. If you turn on debugging there might be some more information displayed. You turn on debugging by editing the /www/WEB-INF/classes/log4j.properti

Re: [base] BASE2 + Solaris crashes & recommended JVM

Emil Lundberg wrote: >> I am not able to reproduce the error. Unfortunately there is a glitch >> in >> the error handling which causes a second error to hide the original >> one. >>If you turn on debugging there might be some more information >> displayed. You turn on debugging by editing the

Re: [base] text data tyep inside extended-properties

Reha Yildirimman wrote: > Hi all, > > I would like to modify a property inside the extended-properties.xml file, > changing it from string[255] to text - I need more than 255 characters for > one property. > While running the updatedb.sh script I get an error stating that the only > possible ty

Re: [base] Reporter annotation

Robin LIECHTI wrote: > Dear Base2 users and developers, > > Is there a more or less easy way to add columns to reporter > annotations in Base 2 ? > You can do this in the extended-properties.xml file. It should be located in the www/WEB-INF/classes folder. If you already have installed the d

Re: [base] reporter name synonyms in BASE2

Bob MacCallum wrote: > We'll be installing and test-driving BASE 2.x in the coming weeks, so > apologies if this question is too trivial. > > It is possible that a reporter could have different names on different arrays > (e.g. oligos designed by different labs using the same software and gene > d

[base] Base 2.0.1 released

Hello all, BASE 2.0.1 is now available for download at: http://base.thep.lu.se/wiki/DownloadPage Most fixes are related to the migration program and the Base 1 plugin executor. /Nicklas - Take Surveys. Earn Cash. Influence

Re: [base] BASE2 API: interacting with multiple BASE2 installs

Micha Bayer wrote: > Hi, > > I am working on a web service that talks to a BASE2 install to get data > out (for an analysis pipeline) and then store data back into it. > > We are supporting three separate institutions which eventually will all > have separate BASE2 installs, but I would like the

Re: [base] change owner

Robin LIECHTI wrote: > Dear Base2 Users, > > I am a curator (and administrator) of a Base2 installation and I have to > load experiment data from several users. So I log in as the > administrator, I create the samples, extracts... and load the data. Is > there a way of changing the owner of the

[base] Any interest in running BASE on Oracle?

Hello all, I am just wondering if anybody is interested in running BASE 2 on an Oracle database? The reason that I ask is that I think it is possible to fix the things that is causing the current implementation not to work on Oracle. But we are not spending time on this if there is no interest

Re: [base] demo server updates and presets Q's

Lepp, Dion wrote: > Hi all, > > > > I was wondering how often the base2 demo server is updated ie. are the > changes shown in the Trac timeline reflected in the server immediately? No, the server has the latest released version. The reason is that there is a risk that updates won't work be

Re: [base] BASE2: Hibernate caching problem

Micha Bayer wrote: > Hi, > > We have just installed the latest version of BASE2 (2.0.2 binaries) and > are running some of our own client code against it. BASE is running > under Tomcat 5.5.20 and with a MySQL 5.0.22 backend. > > When our code calls Application.start(), the following exception is

Re: [base] external ontologies in BASE 2.x

Bob MacCallum wrote: > Hi, > > I may not be able to test drive BASE 2 in enough detail before a meeting in 10 > days time, so I have a quick question. > > Can you annotate samples and other objects in BASE 2 according to external > ontologies (e.g. MGED and the databases/ontologies referenced fro

Re: [base] BASE2: extended properties -- hyperlinks

Micha Bayer wrote: > Hi, > > I would like to add additional properties to the extended-properties.xml > config file, and would like to include URLs with them. > > In the following example entry, > > name="omim" >title="OMIM" >description="" >column="omim" >type="string" >

Re: [base] BASE2: extended properties -- hyperlinks

Micha Bayer wrote: > Hi Nicklas, > > Thanks for the prompt response. In this particular case, the URL of the > cgi script I want to call happens to contain the word "value" itself: > > regexp=".++" >url="http://germinate.scri.ac.uk/cgi-bin/atnopdb/get-all- > data?type=more&value={value}"

Re: [base] updating to Base 2.1 with postgresql

Emmanuel Courcelle wrote: > Hello > > I have setup for a few days a new Base2 installation, running with > postgresQL. > I know that the update process wan "not safe" with psql, due a bug in > hibernate. However, the updating process ran without problem from 2.0.2 > to 2.0.3 This updgrade didn

[base] Workaround for upgrading a Postgres database

Hello Postgres users, We have now published some information about a workaround to make it possible to upgrade a BASE installation running on a Postgres database. The instructions and files are available at: http://base.thep.lu.se/wiki/UpgradePostgres /Nicklas

Re: [base] Workaround for upgrading a Postgres database

Emmanuel Courcelle wrote: > Nicklas Nordborg a écrit : >> Hello Postgres users, >> >> We have now published some information about a workaround to make it >> possible to upgrade a BASE installation running on a Postgres database. >> >> > Hi Nicklas &

Re: [base] 2 questions about Plugin configuration

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 > -configur

Re: [base] 2 questions about Plugin configuration

Emmanuel Courcelle wrote: > Hi Nicklas > > Here are the first 44 lines of the file > I tried to dos2unix-ify, it did not change anything for Base. > > Thanks for your help ! I have now tested with your file and it works perfectly. Perhaps it is a browser-related problem. I have tested with Int

Re: [base] logging in BASE2

Micha Bayer wrote: > Hi, > > I am running BASE2.1 under Tomcat 5.5 and I am getting my catalina.out > log swamped by BASE log statements. Is there any way I can turn this > off? It doesn't sound normal. What kind of log messages do you get? > I have tried to change the log levels in the log4j.p

[base] create slide wizard numbering

> Under Array Slides / Create multiple > the Start at field is limited to 3 digits. > > is it possible to increase this to 4 digits as we continuously number > our slides > and it's in the thousands already. ( ie. i'd like to make slides 1100-1150 ) Oops, it shouldn't be. Only the number of

Re: [base] logging in BASE2

Micha Bayer wrote: > Hi Nicklas, > > the output I am getting is mostly info level messages from both the BASE > core and hibernate (no errors or warnings, and BASE generally seems > happy otherwise). When I load the BASE front page into the browser, the > log starts up with this: > > INFO: Server

Re: [base] Plugin configuration (nearly fixed !)

Emmanuel Courcelle wrote: > Nicklas Nordborg a écrit : >> Emmanuel Courcelle wrote: >> >>> Hi Nicklas >>> >>> Here are the first 44 lines of the file >>> I tried to dos2unix-ify, it did not change anything for Base. >>> >>> T

Re: [base] Plugin configuration (nearly fixed !)

Emmanuel Courcelle wrote: >> The only significant change you have made is Rgn R? to Rgn R. Does it >> still work if you change this to "Rgn R\E.\Q"? >> >> > Great: I took the autogenerated regex, replaced Rgn ? by Rgn R\E.\Q > without changing anything else and it worked. > > However, I chang

Re: [base] Plugin configuration (still some pb)

Emmanuel Courcelle wrote: > >> file we have been testing on the "Rgn R²" column should be column number >> 32 and the mapping to use \32\. >> > hum... rather 33, I think (it was 33 in Base 1.2). > Does the column numbers start at 0 or at 1 ? As I wrote in the previous mail: The columns a

Re: [base] BASE 2 API: creating subdirectories in users' home directories

Micha Bayer wrote: > Directory subDir = Directory.getNew(dc,dataDir); > String fileName = uploadedFile.getFilename(); > String fileNameNoExt = fileName.substring(0, fileName.indexOf(".")); > subDir.setName(fileNameNoExt); > subDir.checkPermission(Permission.CREATE); Remove t

Re: [base] how to import reporters ?

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. >

Re: [base] file storage system question

Keith Ching wrote: > it seems you can make a String annotation type and attach it to raw > bioassay and fill it with > > > src="/base2/images/download.gif"> > > which will produce a link to the specified raw file. Wow, that's a bug, HTML tags should be escaped. Besides, it won't work anyway,

Re: [base] file storage system question

Keith Ching wrote: > True, the session id is good only once.. but in subsequent logins, BASE2 > will ask to reauthenticate and after success you can still download the > file. > > still, of course.. i would rather have the download link be auto > generated upon > import of the datafile. > > is

Re: [base] logging in BASE2

Micha Bayer wrote: > Mystery solved. This is nothing to do with BASE -- it's Tomcat's fault. > It looks like the Tomcat people have changed tack and they are now > including a log4j.xml config file by default with Tomcat (it used to be > a log4j.properties file, which is what I was initially lookin

Re: [base] question on biosources and messages in base2

Audrey Bihouee wrote: > Hi everybody, > > I just upgrade from base1.2 to base2, and I have a few questions : > > - What are exactly Biosources ? Does it match with the sample origin in > base 1 ? But, I can't see any ontology (tree structure) as in base 1. > Have anybody details on it ? It re

Re: [base] error deleting jobs inside trashcan

Reha Yildirimman wrote: > Hello, > > I have a few import jobs that froze and never finished the imports. > After I started a jobs that finished the task I am left with those > unfinished jobs still listed > inside the "execute" section of "Jobs" which I can't delete after moved > to the trashca

Re: [base] JEP extra value calculator

Emmanuel Courcelle wrote: > Hello > > I am testing the analysis capabilities of Base 2.1, and I do not > understand the plugin called "JEP extra value calculator": > what is its aim, and how does it work ? It can calculate new values for each spot using the intensities and other already existin

Re: [base] refreshing in BASE 2

Bob MacCallum wrote: > Hi all, > > The popup job progress page refreshes every 10 seconds and works fine, but the > actual "View"->"Jobs" page does not seem to do any refreshing. That's fine, > because I can reload the page myself. However doing this takes me to the > login page (*) unless I do

Re: [base] Offline files

Giovanni Coppola wrote: > Hi everybody, > I have two questions: > 1) is there a way to download images or raw data files in batches? No. > 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

Re: [base] Imagene data import

Anup Parikh wrote: > We have been using base 1.2 for a year now. The batch importer we had > created for base 1 is useless for base2. Therefore we are moving to > using the UI to import each chip. We are using the ImaGene quantitation > software and which seems to be supported in base2. But I ca

Re: [base] Offline files

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

Re: [base] Offline files

Emmanuel Courcelle wrote: > What does mean to "move offline" ? > Is it the same as: Delete THEN Empty trash ? > No it is not. A file exists in two places. As an entry in the database and as a file on the disk. The "Move offline" feature is used when you want to delete the file on disk but keep

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 u

Re: [base] Offline files

Micha Bayer wrote: > 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

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/[email protected]/msg00228.html) > where he says that it is best to not u

Re: [base] JEP extra value calculator again...

Emmanuel Courcelle wrote: > Hi all. > Sorry to bother you again with this point, but I still does not > understand everything... > > I tried to define a new type, called "float colored": it is a float, > colored with min value as 0, max as 0, mid as 5 > I want to add 2 values to my data: > -2 *

Re: [base] Offline files

Micha Bayer wrote: > > So am I right in thinking that if I change this to the following... > > > public class ZipFileImporter extends AbstractPlugin implements > InteractivePlugin, AutoDetectingImporter > { > private static final Set guiContexts = > Collections.singleton(n

Re: [base] Location of original source files

Keith Ching wrote: > Hi, > > I am trying to write a plugin that will download the original source > files used to > populate the RawBioAssay objects. When you import data into a RawBioAssay, > is the name of the original source file saved somewhere in the database? > > I am at the point where i

Re: [base] Réplicates in base 2

Emmanuel Courcelle wrote: > Hello > > We are trying to create an experiment composed with: > > -4 slides > -3 times each reporter on each slide > > So, we have up to 12 replicates for each reporter (sometimes less > because some flagged spots were filtered out). > How to make a final bioassay s

Re: [base] Location of original source files

filename is kept in the database. There is however no information that links a rawbioassay to the file that was used for importing the data. It has nothing to do with the file names. /Nicklas > > Am I off track? > > Cheers > > Charles > > On Dec 8, 2006, at 9:00 AM,

Re: [base] Conversion from string to int after plate import

david vilanova wrote: > Hi, > I'm importing the following plate information through the plate > "384_wells import plate". > > 384_number 384_column 384_row 384_position oligo_id > plate_1 1 A A1 SEQ12345 > plate_1 2 A A2 SEQ12346 > plate_1 3 A A3 SEQ12347 > > The importing works fine but the row

Re: [base] Conversion from string to int after plate import - bug while exporting

david vilanova wrote: > Thanks Nicklas for you quick answer regarding the conversion from string > to int. > > I have decided to import the data using the string to int conversion. > However I'm trying to export the plate wells back again to a file using > the default exporter and get a bug. I

Re: [base] Réplicates in base 2

Emmanuel Courcelle wrote: > Nicklas Nordborg a écrit : >> Emmanuel Courcelle wrote: >> >>> Hello >>> >>> We are trying to create an experiment composed with: >>> >>> -4 slides >>> -3 times each reporter on each slide >

Re: [base] how to get a db connection after call dc.commit()

Keith Ching wrote: > Hi, > > I am trying to write a plugin to automatically make objects from sample > -> rawbioassay. > however, after you call dc.commit() it closes the connection. what is > the normal way to > re-establish a connection? dc.reconnect() does not seem to work. > getting a ne

Re: [base] downloading files

Keith Ching wrote: > I have a List of File objects. what is the best way to zip them all > together and download it? I assume that you want to this with a plugin. I think the best way is to create a new File (net.sf.basedb.core.File) object and then use java.util.zip.ZipOutputStream for writin

Re: [base] downloading files

Keith Ching wrote: > Hi, > > I am getting a peculiar stack trace upon trying to define the plugin. > do you think it could be caused by using Base2.2 classes in a Base2.1.1 > codebase? i tried to include the revised classes in the plugin JAR.. but > i suppose this probably doesn't work.. > > i h

Re: [base] walk thru

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. > The test procedure that we use before a ne

Re: [base] GPR import plugin error

david vilanova wrote: > Hello, > I'm trying to import a GPR file and had some problems. I have submitted > the bug to the base ticketing system. The problem comes from assigning > incorrect wavelengths to the dyes CY5 and CY3 (view opened ticket #467). > In the bug descriptions I also submit the

Re: [base] pb with spot images

Emmanuel Courcelle wrote: > Hello > > I click on View Raw BioAssays / Spot Images, the spot images are created. > But when I click rawdata, I click any spot, this opens a popup with the > data corresponding to this spot, and at the left of the popup there is a > Spot image field with a black squ

Re: [base] Add new plates

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 plat

Re: [base] Spot images

david vilanova wrote: > Hello, > Following the advise given to emanuel for the generation of the spots, I > went through the example but could'nt manage to create the spots. > Do i have to submit three time the tiff file to create the spots in the > editor (it's asking for jpeg files°. Anyway the

Re: [base] Windows

[EMAIL PROTECTED] wrote: > Hello, > > I have use the package Easyphp1.7 (PHP4, PHPMyAdmin) on windows to developp a > database, and I would like to know if it is possible to install BASE with it > or > How to install BASE on Windows? BASE 1 is using PHP and in some parts C/C++. It is not possibl

Re: [base] Spot images follow-up

david vilanova wrote: > Hello, > I have tried with: > PixelSize="10" > ImageOrigin="4440,1000" > I have double checked the image within genepix and the coordinates > (expressed in µm) are correct (gpr file matches with the tiff file). 1µm > correspond to 10pixels in genepix. I think it is the ot

Re: [base] Fwd: Permissions question

david vilanova wrote: > Hello, > I'm having problem to setup permissions. > > How can i give permissions to all users to create a new raw bioassay > from a scan. Actually I can only do it with account root. I did try to > allow the group of users to write access,use,read to raw bioassays in > t

Re: [base] SPOT IMAGES Problem found

david vilanova wrote: > Hi folks, > I finally managed to identify the problem. As i said in my previous > email i tried a tif image with only a signe channel: > > [EMAIL PROTECTED] SPOTS]$ ls * > -rw-r--r-- 1 david bioinfo 9,1M Jan 23 12:19 532.tif > -rw-r--r-- 1 david bioinfo 9,3M Jan 23 12:20 6

Re: [base] can you run a plugin outside of the web interface?

Keith Ching wrote: > Hi, > > i have written a plugin that takes a spreadsheet and creates samples -> > rawbioassay > and links the data file to the rawbioassay. > > is there a way i can also run the plugin without going through the web > interface.. ie. > initiate running it from another progra

Re: [base] null reporter

Emmanuel Courcelle wrote: > Hello > > Some users have a gene whose ID is null :-\ > this means "nothing here, just a control". It could also be "blank" > > The problem is that the Importer plugin sends me a message for this "gene": > "Invalid use of null. The 'externalId' value cannot be set

Re: [base] Create reporters columns

Ana Conesa wrote: >> Hi, > > > I am creating my reporters db in BASE and I have reporters annotations > different from the ones given in the current BASE configuration which I > would like to include. I would like to know if it is possible (an then > how) to create new columns for reporters.

Re: [base] rawba need data for expt

Keith Ching wrote: > Hi, > > just wondering why RawBioAssays must have spot data before being added > to an Experiment. > will it blow somewhere else down the line? or is it just for semantics? > The main reason is that it is only allowed to have one type of raw data in a single experiment, bu

Re: [base] Stopping Base after MySQL crash

Marie Mooney wrote: > Hi. I don't know much about BASE 1.2 but I think that you must have the MySQL running for stopBase.php to work. And you must also have MySQL running to be able to upgrade from 1.2.14 to 1.2.17. So you have to find a way to start the MySQL server again. /Nicklas > > I am

Re: [base] Problem importing into ReporterLists

Reha Yildirimman wrote: > Hello, > > I am trying to import Reporter into a new reporter list inside a > fresh,new base2 installation, getting the following error: > > Caused by: java.sql.SQLException: Unknown column 'reporterda0_.' in > 'field list' Can you please submit the entire stacktr

Re: [base] Problem importing into ReporterLists

ment.java:76) > at > org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:186) > at org.hibernate.loader.Loader.getResultSet(Loader.java:1668) > at org.hibernate.loader.Loader.doQuery(Loader.java:662) > at > org.hibernate.loader.Load

Re: [base] Imagene data format

Emmanuel Courcelle wrote: > Hello > > I am trying to configuration the Raw data importer plugin for use with > Imagene files. > I do not know how to map theproperties Block, MetaGridX, MetaGridY > > 1/ There is no "Block" column in the file, but I think this is replaced > by the MetaGrid data.

Re: [base] File format for plate mapping

Audrey Bihouee wrote: > Hi, > > Where can I find any information about the file format required to > import a new plate mapping ? > Thanks for help. Check the javadoc for the import plugin: http://base.thep.lu.se/chrome/site/doc/api/net/sf/basedb/plugins/PlateMappingImporter.html You can also t

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