[base] BASE 3.19.1 has been released

2021-12-14 Thread Nicklas Nordborg via basedb-users
Hello all, We have released BASE 3.19.1 today. This is a bugfix release that contains fixes for some minor problems and a few enhancements. For more information, see: http://base.thep.lu.se/query?milestone=BASE+3.19.1=type Installation/upgrade instructions:

[base] BASE 3.19 has been released

2021-08-13 Thread Nicklas Nordborg
Hello all, We have released BASE 3.19 today. This is a new major release with some new features and improvements as well as some bugfixes. File uploading now support drag-and-drop from the local computer to upload multiple files in one go. For a complete list of changes, see:

[base] BASE 3.18.2 has been released

2021-06-14 Thread Nicklas Nordborg
Hello all, We have released BASE 3.18.2 today. This is a bugfix release that contains enhancements and fixes for some minor problems. For more information, see: http://base.thep.lu.se/query?milestone=BASE+3.18.2=type Installation/upgrade instructions:

[base] BASE 3.18.1 has been released

2021-05-04 Thread Nicklas Nordborg
Hello all, We have released BASE 3.18.1 today. This is a bugfix release that contains enhancements and fixes for some minor problems. For more information, see: http://base.thep.lu.se/query?milestone=BASE+3.18.1=type Installation/upgrade instructions:

[base] BASE 3.18 has been released

2021-02-24 Thread Nicklas Nordborg
Hello all, We have released BASE 3.18 today. This is a new major release which several new features and improvements. Most of them are related to improvements in Item list functionality and filtering. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.18=type=1

[base] BASE 3.17.1 has been released

2021-01-19 Thread Nicklas Nordborg
Hello all, We have released BASE 3.17.1 today. This is a bugfix release that contains enhancements and fixes for some minor problems. For more information, see: http://base.thep.lu.se/query?milestone=BASE+3.17.1=type Installation/upgrade instructions:

[base] BASE 3.17 has been released

2020-10-22 Thread Nicklas Nordborg
Hello all, We have released BASE 3.17 today. This is a new major release which several new features and improvements. Some examples: * Support for listing and filtering on child items in table lists * Annotations on files For a complete list of changes, see:

[base] BASE 3.16.1 has been released

2020-05-19 Thread Nicklas Nordborg
Hello all, We have released BASE 3.16.1 today. This is a bugfix release that contains enhancements and fixes for some minor problems. For more information, see: http://base.thep.lu.se/query?milestone=BASE+3.16.1=type Installation/upgrade instructions:

[base] BASE 3.16 has been released

2020-03-03 Thread Nicklas Nordborg
Hello all, We have released BASE 3.16 today. This is a new major release with a main focus on support for newer versions of Java, Tomcat and PosgreSQL. * Java 11 or higher and Tomcat 9 or higher is now required * PostgreSQL 11 or higher is recommended * Support for displaying, filtering

[base] BASE 3.15.2 has been released

2019-09-16 Thread Nicklas Nordborg
Hello all, We have released BASE 3.15.2 today. This is a bugfix release that fixes for some minor problems. For more information, see: http://base.thep.lu.se/query?milestone=BASE+3.15.2=type Installation/upgrade instructions:

[base] BASE 3.15.1 has been released

2019-08-14 Thread Nicklas Nordborg
Hello all, We have released BASE 3.15.1 today. This is a bugfix release that contains enhancements and fixes for some minor problems. For more information, see: http://base.thep.lu.se/query?milestone=BASE+3.15.1=type Installation/upgrade instructions:

[base] BASE 3.15 has been released

2019-04-11 Thread Nicklas Nordborg
Hello all, We have released BASE 3.15 today. This is a new major release which several new features and improvements. Some examples: * Excel file support in batch importers and exporters * Support for Java 11, Tomcat 9 and PostgreSQL 11 * Better handling of text files with unknown encoding

[base] BASE 3.14.1 has been released

2019-02-06 Thread Nicklas Nordborg
Hello all, We have released BASE 3.14.1 today. This is a bugfix release that fixes an issue that prevents a user from changing the password and a few other things. For more information, see: http://base.thep.lu.se/query?milestone=BASE+3.14.1=type Installation/upgrade instructions:

[base] BASE 3.14 and BASE 3.13.1 has been released

2019-01-08 Thread Nicklas Nordborg
Hello all, We have released BASE 3.14 and BASE 3.13.1 today. This 3.14 release which mostly consists of preparations for supporting Java 11 (and newer) and improvements to the login system. The 3.13.1 release is a bugfix release with some minor fixes. For a complete list of changes, see:

[base] BASE 3.13 has been released

2018-08-23 Thread Nicklas Nordborg
Hello all, We have released BASE 3.13 today. This is a new major release which mostly consists of improvements targeted for plug-in and extension developers. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.13=type=1 Upgrading follows the usual procedure:

[base] BASE 3.12.3 has been released

2018-06-04 Thread Nicklas Nordborg
Hello all, We have released BASE 3.12.3 today. This is a bugfix release that fixes some minor issues. For more information, see: http://base.thep.lu.se/query?milestone=BASE+3.12.3=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As

[base] BASE 3.12.2 has been released

2018-04-16 Thread Nicklas Nordborg
Hello all, We have released BASE 3.12.2 today. This is a bugfix release that fixes a critical bug in the annotation importer plug-in. For more information, see: http://base.thep.lu.se/query?milestone=BASE+3.12.2=type Installation/upgrade instructions:

[base] BASE 3.12 has been released

2018-03-14 Thread Nicklas Nordborg
Hello all, We have released BASE 3.12 today. This is a new major release which consists of several unrelated improvements and bug fixes. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.12=type=1 Upgrading follows the usual procedure:

Re: [base] xdoclet in ant build

2017-12-10 Thread Nicklas Nordborg
No, we have not really considered moving away from using xdoclet for creating the mapping files to Hibernate. I am aware that this is not the most modern approach, but it has served us well so far. It might be possible to move to JPA, but I am pretty sure that this will not be an easy task.

[base] BASE 3.11.2 has been relased

2017-11-23 Thread Nicklas Nordborg
Hello all, We have released BASE 3.11.2 today. This is a bugfix release that fixes some minor bugs. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.11.2=type Installation/upgrade instructions:

[base] BASE 3.11.1 has been released

2017-06-07 Thread Nicklas Nordborg
Hello all, We have released BASE 3.11.1 today. This is a bugfix release that fixes some old and new bugs. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.11.1=type Installation/upgrade instructions:

Re: [base] Question about BASE

2017-05-16 Thread Nicklas Nordborg
On 2017-05-15 23:32, Tyree Lush wrote: > Good evening, > > I was wondering if someone could confirm whether the BASE software can > be installed on a virtual server with full functionality. If it does and > there are specs that are mandatory, could that be provided? BASE should work just fine on

[base] BASE 3.11 has been released

2017-05-10 Thread Nicklas Nordborg
Hello all, We have released BASE 3.11 today. This is a new major release which mostly consists of improvements related to project-specific annotations that was introduced in the previous BASE relase. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.11=type=1

[base] BASE 3.10.1 has been released

2017-04-28 Thread Nicklas Nordborg
Hello all, We have released BASE 3.10.1 today. This is a bugfix release that fixes a few minor issues. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.10.1=type Installation/upgrade instructions:

[base] BASE 3.10 has been released

2017-01-31 Thread Nicklas Nordborg
Hello all, We have released BASE 3.10 today. This is a new major release which among other things include some interesting new features for projects and annotations. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.10=type=1 Upgrading follows the usual

[base] BASE 3.9.2 has been released

2016-11-23 Thread Nicklas Nordborg
Hello all, We have released BASE 3.9.2 today. It is mainly a fix for an upgrade problem that may cause an upgrade from BASE 3.7 to BASE 3.8 to fail. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.9.2=type Installation/upgrade instructions:

[base] BASE 3.9.1 has been released

2016-08-23 Thread Nicklas Nordborg
Hello all, We have released BASE 3.9.1 today. This is a bugfix release that fixes a few minor issues. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.9.1=type Installation/upgrade instructions:

[base] BASE 3.9 has been released

2016-06-09 Thread Nicklas Nordborg
Hello all, We have released BASE 3.9 today. This is a new major release which among other things include performance enhancements when using PostgreSQL and better support for files larger than 2GB. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.9=type=1

[base] BASE 3.8 has been released

2016-04-27 Thread Nicklas Nordborg
Hello all, We have released BASE 3.8 today. This is a new major release which among other things include a major performance improvement in the Annotation batch importer plug-in and several other enhancements related to annotations. For a complete list of changes, see:

[base] BASE 3.7.2 has been released

2016-04-22 Thread Nicklas Nordborg
Hello all, We have released BASE 3.7.2 today. This is a critical bugfix release that fixes an issue that may cause unauthorized users to access files on the BASE web server. BASE versions between 2.11 and 3.7.1 are affected and we recommend all users to upgrade to this BASE release. If

[base] BASE 3.7.1 has been released

2016-03-07 Thread Nicklas Nordborg
Hello all, We have released BASE 3.7.1 today. This is a bugfix release that fixes a few minor issues. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.7.1=type Installation/upgrade instructions:

[base] BASE 3.7 has been released

2016-01-11 Thread Nicklas Nordborg
Hello all, We have released BASE 3.7 today. This is a new major release which among other things introduces a 'Kit' item for keeping track of chemicals and other things used in the lab. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.7=type=1 Upgrading

[base] BASE 3.6.3 has been released

2015-11-25 Thread Nicklas Nordborg
Hello all, We have released BASE 3.6.3 today. This is a bugfix release that includes a fix for a critical permission issue related to projects and some other minor fixes and improvements. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.6.3=type

[base] BASE 3.6.1 has been released

2015-10-19 Thread Nicklas Nordborg
Hello all, We have released BASE 3.6.1 today. This is a bugfix release that fixes a critical issue with some JSP files that could not be compiled. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.6.1=type Installation/upgrade instructions:

[base] BASE 3.6 has been released

2015-10-08 Thread Nicklas Nordborg
Hello all, We have released BASE 3.6 today. This is a new major release that has been focused on giving more control over experimental factor values to the owner of the experiment. * Experimental factors are now stored as part of the experiment instead of as part of the raw bioassays.

[base] BASE 3.5.3 has been released

2015-09-18 Thread Nicklas Nordborg
Hello all, We have released BASE 3.5.3 today. This is a bugfix release that fixes a few minor issues. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.5.3=type Installation/upgrade instructions:

[base] BASE 3.5.2 has been released

2015-05-05 Thread Nicklas Nordborg
Hello all, We have released BASE 3.5.2 today. This is a bugfix release that fixes a critical issue related to item lists that was introduced in the BASE 3.5.1 release. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.5.2group=type Installation/upgrade

[base] BASE 3.5.1 has been released

2015-04-29 Thread Nicklas Nordborg
Hello all, We have released BASE 3.5.1 today. This is a bugfix release that fixes a critical issue related to item lists and some other minor issues. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.5.1group=type Installation/upgrade instructions:

[base] BASE 3.5-beta-1 has been released

2015-03-31 Thread Nicklas Nordborg
Hello all, We have released BASE 3.5-beta-1 today. This is a new major release that is focusing on new features for filtering and annotations. Among other things: * It is possible to filter with OR logic in tables * Batch inhering annotations * Filtering on inherited annotation in tables

[base] BASE 3.4.2 has been released

2015-03-18 Thread Nicklas Nordborg
Hello all, We have released BASE 3.4.2 today. This is a bugfix release that fixes a few minor problems. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.4.2group=type Installation/upgrade instructions:

[base] BASE 3.4.1 has been released

2015-02-10 Thread Nicklas Nordborg
Hello all, We have released BASE 3.4.1 today. This is a bugfix release that fixes a few minor problems. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.4.1group=type Installation/upgrade instructions:

[base] BASE 3.4 has been released

2015-01-14 Thread Nicklas Nordborg
Hello all, After fixing a few issues with the beta version, BASE 3.4.0 has now been released. One new feature is the possibility to install skins. Check out the example skins at http://baseplugins.thep.lu.se/wiki/net.sf.basedb.skincollection For a complete list of changes, see:

[base] BASE 3.3.3 has been released

2014-11-16 Thread Nicklas Nordborg
Hello all, We have released BASE 3.3.2 today. This is a bugfix release that includes fixes for several issues as well as some enhancements. Most importantly it fixes a bug that caused the remaining quantity for biomaterial items to become incorrect in some cases (ticket #1873). The bug was

[base] BASE 3.3.2 has been released

2014-10-22 Thread Nicklas Nordborg
Hello all, We have released BASE 3.3.2 today. This is a bugfix release that includes fixes for several issues as well as some enhancements. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.3.2group=type Installation/upgrade instructions:

[base] BASE 3.3.1 hase been released

2014-09-26 Thread Nicklas Nordborg
Hello all, We have released BASE 3.3.1 today. This is a bugfix release that fixes a few minor problems. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.3.1group=type Installation/upgrade instructions:

Re: [base] BASE Schema

2014-09-04 Thread Nicklas Nordborg
On 2014-09-03 19:45, Rachad El-Badrawi wrote: Hi All, We are considering BASE as the molecular diagnostics backend system for a project, and I was trying to figure out some of the backend workings of the schema. I would appreciate some feedback on the following: 1) Is there a document that

[base] BASE 3.3 has been released

2014-08-18 Thread Nicklas Nordborg
Hello all, We have released BASE 3.3! It is a new major release that includes several new features and enhancements. It may require some changes to the BASE server and/or and upgrade of the browser used to access BASE: * We now require Java 7 and Tomcat 7 on the server. If you are

[base] BASE 3.3-beta-2 has been released

2014-06-26 Thread Nicklas Nordborg
Message Subject: [basedb-devel] BASE 3.3-beta-1 has been released Date: Wed, 4 Jun 2014 09:52:30 +0200 From: Nicklas Nordborg nicklas.nordb...@med.lu.se Reply-To: BASE dev basedb-de...@lists.sourceforge.net To: BASE ML basedb-users@lists.sourceforge.net, BASE dev basedb-de

Re: [base] Files with FTP locations only

2014-06-26 Thread Nicklas Nordborg
So, I am currently working on an extension that add support for accessing external files via FTP, FTPS and SFTP (see http://baseplugins.thep.lu.se/wiki/net.sf.basedb.xfiles). I might be able to release a first version later this week if you want to try it. I have now Xfiles

Re: [base] Files with FTP locations only

2014-06-24 Thread Nicklas Nordborg
On 2014-06-24 11:55, Bob MacCallum wrote: Hi Nicklas et al, Getting up to speed with BASE3 and NGS - so far all seems good - even upgrading our own API code has gone smoother than I expected. Thanks! Great to hear that it is going well. A possible feature request for general discussion:

[base] BASE 3.3-beta-1 has been released

2014-06-04 Thread Nicklas Nordborg
Hello all, We have released BASE 3.3-beta-1 today! It is a new major release that includes several new features and enhancements. * We now require Java 7 and Tomcat 7 on the server. If you are still using older versions, they should be upgraded before upgrading BASE. * The

Re: [base] array design GTF import - not 9 columns

2014-05-26 Thread Nicklas Nordborg
Thanks for testing this. It feels like it was a long time ago this was implemented and we have not really started to use it yet. Anyway, you are correct that the problem is something deeper than the usual importer. To make GTF files parsable by the regular importers, there is a pre-parsing

Re: [base] reseting root password

2014-02-16 Thread Nicklas Nordborg
On 2014-02-17 02:39, Ross Chapman wrote: Hi all I have inherited the management of a BASE 2 solution for managing microarray data. I do not have access to the Root password, but I do have administrator rights. Am I able to reset the root password, will this have any impact on how BASE

Re: [base] Base 3.2 installation on Mac OS 10.6 server

2013-09-11 Thread Nicklas Nordborg
wrote: Le 10 sept. 2013 à 20:26, Nicklas Nordborg nicklas.nordb...@med.lu.se mailto:nicklas.nordb...@med.lu.se a écrit : On 2013-09-10 16:35, Laurent Troxler wrote: Thank you Nicolas for your answer. It helped me to find out that I had missed the base.config file password setting. I thus could

Re: [base] Base 3.2 installation on Mac OS 10.6 server

2013-09-10 Thread Nicklas Nordborg
On 2013-09-09 16:04, Laurent Troxler wrote: Hello all, Ì am new at Base and trying to install it on a Mac OS 10.6 server. Looking in the mailing list archives did not bring me any helping information, Mac OS does not appear often. Therefore I submit you my problem. After downloading and

[base] BASE 3.2.3 has been released

2013-09-09 Thread Nicklas Nordborg
Hello all, We have released BASE 3.2.3 today. This is a bugfix release that fixes a few minor problems. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.2.3group=type Installation/upgrade instructions:

[base] BASE 3.2.2 has been released

2013-04-10 Thread Nicklas Nordborg
Hello all, We have released BASE 3.2.2 today. This is a bugfix release that fixes a few minor problems. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.2.2group=type Installation/upgrade instructions:

[base] BASE 3.2.1 has been released

2012-12-13 Thread Nicklas Nordborg
Hello all, We have released BASE 3.2.1 today. This is a bugfix release that fixes a few minor problems. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.2.1group=type Installation/upgrade instructions:

Re: [base] Error on Biomaterials LIMS

2012-11-22 Thread Nicklas Nordborg
On 2012-11-22 19:40, Paulo Nuin wrote: Hi We have a couple of instances of BASE installed in our systems. We are getting a problem whenever we are accessing entities created in the Biomaterial LIMS, either samples or biosources: This is a Tomcat configuration problem and is described in the

Re: [base] Schema

2012-11-12 Thread Nicklas Nordborg
On 2012-11-13 03:32, Paulo Nuin wrote: Hi Is there any available image/diagram of the current schema? Not really. The closest thing is the diagrams that can be found in each of the subsections at http://base.thep.lu.se/chrome/site/latest/html/developer/api/data_api.html The diagrams give an

Re: [base] DataQuery.order(...) 2.x API question

2012-10-09 Thread Nicklas Nordborg
On 2012-10-09 13:11, Bob MacCallum wrote: Hi all, I'm trying to get a Reporter query from the BASE2.x API which is basically ORDER BY RAND(123) - to get reproducible random order (I can explain *why* in another email if anyone cares to know). I tried this

Re: [base] DataQuery.order(...) 2.x API question

2012-10-09 Thread Nicklas Nordborg
On 2012-10-09 17:24, Bob MacCallum wrote: Just for closure, I am now in business. [mysqld] tmp_table_size = 5G Background for whoever cares: I'm running something reporter-wise in parallel (4 threads) and wanted roughly equal workload per chunk of reporters (some reporters have more

Re: [base] Setting up a new root bioassay set

2012-10-02 Thread Nicklas Nordborg
On 2012-10-02 00:27, McClelland, Erin wrote: Hi Tried to post this earlier but it didn't seem to work - apologies if this is a duplicate message. We have run into a problem setting up a new root bioassay set - we continually get an error message similar to the following: Duplicate entry

Re: [base] Can BASE (v2.12.1) import files directly from the server it's running on?

2012-09-20 Thread Nicklas Nordborg
On 2012-09-20 01:26, Hugh Brown wrote: Hi everyone -- my department is running BASE version 2.12.1. We have some users outside our department, and their network connection is rather slow. At the moment, they're importing files rather circuitously: uploading them to our server for

[base] BASE 3.2 has been released

2012-09-13 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 3.2. It is a new major release that includes several new features and enhancements. * Several new extension possibilities in table listings, the item overview and other places. * A new parent/child structure for derived

Re: [base] Change BASE's HTML title

2012-08-20 Thread Nicklas Nordborg
On 2012-08-20 17:09, Paulo Nuin wrote: Hi I have a quick question on configuring BASE's HTML page title. In the server we have installed now it appears BASE 3.1.1 @ unknown I found the jsp pages in the www directory but it is not clear to me where this title is coming from. I was able to

Re: [base] Change BASE's HTML title

2012-08-20 Thread Nicklas Nordborg
On 2012-08-20 18:56, Paulo Nuin wrote: Hi The computer has a name under /etc/HOSTNAME running SuSE, and network is fine. Check Tomcat's log file if there are any error messages. The name is set to 'unknown' if the name can't be retrieved from the system. /Nicklas

[base] BASE 3.1.2 has been released

2012-07-31 Thread Nicklas Nordborg
Hello all, We have released BASE 3.1.2 today. This is a bugfix release that fixes a few minor problems. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.1.2group=type Installation/upgrade instructions:

Re: [base] MeV: export bioassay set to TDMS file error

2012-06-14 Thread Nicklas Nordborg
On 2012-06-07 08:52, Nicklas Nordborg wrote: On 2012-06-05 22:52, Steven Charles Fan wrote: Running base v3.1.1 with mev-launcher-1.9 binary (current base version and MeV version 4.7.3) on Centos6. Tried to export a bioassay set of two bioassays to a TDMS file for analysis in MeV and got

Re: [base] MeV: export bioassay set to TDMS file error

2012-06-07 Thread Nicklas Nordborg
On 2012-06-05 22:52, Steven Charles Fan wrote: Running base v3.1.1 with mev-launcher-1.9 binary (current base version and MeV version 4.7.3) on Centos6. Tried to export a bioassay set of two bioassays to a TDMS file for analysis in MeV and got a unnamed error with the following stack trace:

[base] BASE 3.1.1 has been released

2012-03-29 Thread Nicklas Nordborg
Hello all, We have released BASE 3.1.1 today. This is a bugfix release that fixes a possibly critical issue with access permission to annotation values and a few other minor issues. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.1.1group=type

[base] BASE 3.1 has been released

2012-03-19 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 3.1. It is a new major release that among other things include: * A new and improved user interface * Possibility to clone reporter information to a local copy per experiment * A migration script for moving a BASE installation

[base] BASE 3.0.4 has been released

2012-03-05 Thread Nicklas Nordborg
Hello all, We have released BASE 3.0.4 today. This is a bugfix release that fixes a few minor bugs. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.0.4group=type Installation/upgrade instructions:

[base] BASE 3.0.3 has been released

2012-02-22 Thread Nicklas Nordborg
Hello all, We have released BASE 3.0.3 today. This is a bugfix release that fixes an annoying Internet Explorer issue with popup windows. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.0.3group=type Installation/upgrade instructions:

[base] BASE 3.0.2 has been released

2012-01-25 Thread Nicklas Nordborg
Hello all, We have released BASE 3.0.2 today. This is a bugfix release that fixes a few minor bugs. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.0.2group=type Installation/upgrade instructions:

Re: [base] Dealing wiht duplicate spots

2011-11-22 Thread Nicklas Nordborg
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

Re: [base] Dealing wiht duplicate spots

2011-11-21 Thread Nicklas Nordborg
On 2011-11-21 17:08, Nantel Andre wrote: Greetings, We are currently trying to integrate BASE into our lab and writing the necessary plug-ins to import normalized data from ImaGene. Let's just say that the lack of documentation has been challenging. Right now we are trying to figure out how

Re: [base] Dealing wiht duplicate spots

2011-11-21 Thread Nicklas Nordborg
On 2011-11-21 19:23, Nantel Andre wrote: That issue goes beyond the ImaGene format. When doing contact printing of microarrays it is still fairly common to spot the same probe 2 or more times as shown in the example here (http://www.digitalapoptosis.com/2005/10/12/dna-microarray/). It is

Re: [base] Dealing wiht duplicate spots

2011-11-21 Thread Nicklas Nordborg
On 2011-11-21 20:31, Nantel Andre wrote: On 2011-11-21, at 2:13 PM, Nicklas Nordborg wrote: The demo data set is a GenePix data set and for each spot the file contains the coordinates, reporter id and a lot of measured intensities and other values. So if your data is similar to this, then I

[base] BASE 3.0 has been released

2011-11-02 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 3.0. It is a new major release that contains a lost of new functionality, including (but not limited to): * Support for RNAseq experiments * A subtype feature for classifying generic items * Easier installation of plug-ins and extensions

Re: [base] Project defaults in batch-import and experiment validator

2011-10-26 Thread Nicklas Nordborg
On 2011-10-25 19:36, Pawel Sztromwasser wrote: That I didn't know. So when no column mapping is provided for a property, the project default is used (since the property is regarded as not initialized, and not null). I also like the expression solution in column mappings. It has an advantage

Re: [base] Project defaults in batch-import and experiment validator

2011-10-26 Thread Nicklas Nordborg
On 2011-10-25 19:36, Pawel Sztromwasser wrote: I like one-click fix-it buttons (one is available for inheriting annotations if I am not mistaken), and they would definitely speed up work with BASE removing some of the repetitive interactions. If it is possible to include them in the roadmap

Re: [base] MO terms (annotations) for experiments

2011-10-26 Thread Nicklas Nordborg
On 2011-10-25 13:34, Bob MacCallum wrote: +1 for annotatable experiments http://base.thep.lu.se/ticket/1644 /Nicklas -- The demand for IT networking professionals continues to grow, and the demand for specialized

Re: [base] Project defaults in batch-import and experiment validator

2011-10-25 Thread Nicklas Nordborg
On 2011-10-25 09:45, Pawel Sztromwasser wrote: Hello, I was wondering if the project defaults are used in batch importing, i.e. when a property is not specified in tab-delimited file but set as default in an active project? I did a quick test and it didn't work, so I thought I could suggest

[base] BASE 3.0-beta has been released

2011-10-12 Thread Nicklas Nordborg
Hello all, Today we are happy to announce the release of BASE 3.0-beta. If all goes well the final 3.0 release is expected within the near future. This release should contain all new functionality that is needed for supporting sequencing experiments with expression like data, but there may still

Re: [base] Anyone using BASE with PostgreSQL?

2011-09-30 Thread Nicklas Nordborg
On 2011-09-30 12:09, Pawel Sztromwasser wrote: Hi Nicklas, Our backup procedure is from before-WAL-times so it does not use WAL. Currently we make daily dumps which are stored if different from the previous one (based on md5). Not much help for the things that you asked for, sorry. Ok.

[base] Anyone using BASE with PostgreSQL?

2011-09-29 Thread Nicklas Nordborg
Hello, We are thinking about migrating our BASE production server from MySQL to PostgreSQL. The major reason is that PostgreSQL seems to have a lot more interesting solutions for backup. We are particularly interested in the WAL archiving solution. Possible combined with a warm standby server

Re: [base] Anyone using BASE with PostgreSQL?

2011-09-29 Thread Nicklas Nordborg
On 2011-09-29 12:29, Pawel Sztromwasser wrote: Hi Nicklas, We are using PostgreSQL as BASE's back-end and are very happy with it. I am not familiar with the details of the installation and backup setup, since it is a department-wide installation administered by our techs. I could ask about

Re: [base] base 3 RNAseq overview

2011-09-27 Thread Nicklas Nordborg
On 2011-09-26 22:19, Bob MacCallum wrote: Hi Nicklas et al, I've been scanning the 3.0 alfa documentation and have seen how biomaterials are handled with respect next gen (with the new library type). However, I can't see how raw data and analysis works. Do the concepts of reporters and

[base] BASE 3.0-alfa has been released

2011-09-15 Thread Nicklas Nordborg
Hello all, Today we are happy to announce the relase of BASE 3.0-alfa. If all goes well the final 3.0 release is expected in a couple of months. This release contains major changes which are mainly targeted at supporting sequencing experiments with expression like data. Do not use this

Re: [base] uploading files

2011-09-09 Thread Nicklas Nordborg
On 2011-09-09 09:48, Line Agledal wrote: Tried to upload files to my project in BASE, but I only get an empty window when using the upload tab. Is this a bug or am I doing something wrong? It's hard to tell, since you don't include any information about your environment. It would be useful

Re: [base] uploading files

2011-09-09 Thread Nicklas Nordborg
On 2011-09-09 11:24, Line Agledal wrote: Thanks. My storage quota is now increased and that fixed it. Ok, it seems like the error message about the quota doesn't show up for some reason. Don't know why that happens. Will try to fix this in the next BASE release:

Re: [base] Tab2Mage Importer configuration

2011-08-01 Thread Nicklas Nordborg
It seems like the Tab2MageImporter claims that it supports configurations when in reality it doesn't. The plug-in should be started from the experiment page and all parameters should be supplied as part of the job definition. /Nicklas On 2011-07-15 04:50, Irina 264 wrote: Dear team, Could

Re: [base] Save to BASE function in the MeV gui

2011-06-27 Thread Nicklas Nordborg
On 2011-06-24 05:50, Irina 264 wrote: Dear team, The idea to analyse data in MeV is great. I successfully transferred data to MeV, analyzed it and used ‘save to BASE’ function to create new child bioassays set. However, new created bioassays are the copy of the original one. I don’t have

[base] BASE 2.17.2 has been released

2011-06-17 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.17.2. This is a bugfix release that fixes a few minor bugs. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.17.2group=type Installation/upgrade instructions:

Re: [base] Tab2Mage exporter plugin

2011-06-13 Thread Nicklas Nordborg
On 2011-06-13 08:51, Irina 264 wrote: I upgrade BASE, but have anothe error message: Error: [EXPORT FAILED: Experiment - Experiment[id=27; name=Agilent IFNalpha time course] do not have a rawbiosay specified]. Add raw bioassays to your experiment. /Nicklas

Re: [base] Tab2Mage exporter plugin

2011-06-13 Thread Nicklas Nordborg
On 2011-06-13 09:17, Irina 264 wrote: Thanks, thay already there! Have you checked that the owner of the raw bioassays is the same as the owner of the experiment or that everything is shared to the same project which must also be the active project? /Nicklas

Re: [base] Tab2Mage exporter plugin

2011-06-10 Thread Nicklas Nordborg
This was fixed in BASE 2.16.1 (http://base.thep.lu.se/ticket/1553). I suggest that you upgrade. On the other hand... the Tab2Mage plug-in may require that you specify labeled extracts, extracts, samples and biosources or it may not work. /Nicklas On 2011-06-10 08:17, Irina 264 wrote: Dear

Re: [base] Tab2MageExporter

2011-05-25 Thread Nicklas Nordborg
On 2011-05-26 07:24, Irina 264 wrote: Dear team, I install Tab2MageExporter plugin into /base/plugins directory and addition copy Tab2MageExporter.jar and ebi-plugins-utils.jar into /base/www/WEB-INF/lib directory Never install the same jar file in two locations. It can result in random

Re: [base] Error: GC overhead limit exceeded

2011-05-23 Thread Nicklas Nordborg
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.

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