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From: Nicklas N. <nic...@me...> - 2023-06-07 07:24:50
|
Hello all, We have released BASE 3.19.9 today. This is a bugfix release that mainly fixes a few annotation-related issues. For more information, see: http://base.thep.lu.se/query?milestone=BASE+3.19.9&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
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From: Nicklas N. <nic...@me...> - 2023-04-21 12:01:58
|
Hello all, We have released BASE 3.19.8 today. This is a bugfix release that among other things fixes the problems with BASE and Java 18 and higher. For more information, see: http://base.thep.lu.se/query?milestone=BASE+3.19.8&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
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From: Nicklas N. <nic...@me...> - 2021-12-15 07:56:50
|
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&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
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From: Nicklas N. <nic...@me...> - 2021-08-13 06:40:42
|
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: http://base.thep.lu.se/query?milestone=BASE+3.19&group=type&groupdesc=1 Upgrading follows the usual procedure: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Nicklas N. <nic...@me...> - 2021-06-14 08:24:39
|
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&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Nicklas N. <nic...@me...> - 2021-05-04 12:41:00
|
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&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
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From: Nicklas N. <nic...@me...> - 2021-02-24 10:47:39
|
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&group=type&groupdesc=1 Upgrading follows the usual procedure: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Nicklas N. <nic...@me...> - 2021-01-19 15:14:13
|
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&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
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From: Nicklas N. <nic...@me...> - 2020-10-22 06:46:33
|
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: http://base.thep.lu.se/query?milestone=BASE+3.17&group=type&groupdesc=1 Upgrading follows the usual procedure: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
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From: Nicklas N. <nic...@me...> - 2020-05-19 12:36:05
|
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&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Nicklas N. <nic...@me...> - 2020-03-03 08:15:01
|
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 and exporting data from
parent items in some table listings
For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.16&group=type&groupdesc=1
Upgrading follows the usual procedure:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html
As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage
/Nicklas
|
|
From: Nicklas N. <nic...@me...> - 2019-09-16 06:53:35
|
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&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Nicklas N. <nic...@me...> - 2019-08-14 07:18:47
|
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&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Pugliese, P. <phi...@fa...> - 2019-06-28 11:31:37
|
Hi Jari, thank you for your quick response, that helps me :) I'll implement your notes. Best, Philipp -------------------- Am 2019-06-25 11:57, schrieb Jari Häkkinen: > Hi Philipp, > > Thank you for your interest in BASE. > > Some of the information you listed is outdated. Here are updates > you can use. > > > 1) Brief description of BASE: > > BASE is a comprehensive free web-based database LIMS solution for > tracking of information and data generated in sequencing and > microarray experiments from sample to analysis. BASE is released under > the GNU General Public License version 3. > > > 2) The reference list could be updated to include > > - Häkkinen et al. 2016, https://doi.org/10.1101/038976 > - Vallon-Christersson et al. 2009, PMID: 19822003 > > If only one reference can be retained then you should use > Vallon-Christersson et al. > > > 3) Under miscellaneous you might add that source code is available at > http://base.thep.lu.se? It is open, browsable, searchable, has issue > tracking, and more. Actually predates GitHub ;-) > > > 4) Regarding compliance to standards. We are not actively pursuing > (MIAME) standards compliance, and the public repository upload > functionality is semi-automatic at best. > > > Cheers, > > Jari > > > On 2019-06-16 14:54, Pugliese, Philipp wrote: >> Dear support team, >> >> briefly to me: my name is Philipp Pugliese and I researched for the >> Friedrich-Alexander-Universität Erlangen-Nürnberg about functions that >> BASE seems to fulfill. >> >> For a congress publication I created a matrix in which BASE is >> mentioned. Could you please give me some feedback as to whether the >> information I found in the literature is correct or up to date? >> >> The information is: >> >> Brief description of BASE: Is an information and analysis tool for >> microarrays that tracks all materials from biosource to raw data to >> analyses. The elements can be annotated and used as factors in the >> downstream analysis >> >> >> General >> Abbreviation: BioArray Software Environment >> FAIR reference: unknown >> Note: - >> >> Community >> Institution: Lund University >> Reference: Saal et al. 2002 >> PMID: 12186655 >> Software availability: open source >> License: GNU >> User mailing list or support: Yes >> URL: http://base.thep.lu.se >> >> System requirements >> Operating system: Platform independent >> DB managing System: MySQL,PostgreSQL >> Main programming language: Java >> Client-side interface: web browser >> >> Support >> Installation procedures: Yes >> Configuration documentation: Yes >> User documentation: Yes >> Regular maintenance: Yes >> >> Miscellaneous >> GitHub availability: - >> Demo server availability: Yes >> >> Requirements for data management in system biology >> Compliance to standards: MIAME >> Metadata model: MIAME-related >> Automation of data collection: batch import >> Upload to public repositories: ArrayExpress, GEO, CIBEX >> Extensibility: Java plugins / extentions >> Integration with other DMS: via java servlets >> >> >> >> Please give me feedback by 30th June 2019 so that your feedback can be >> considered until publication. >> >> Thanks in advance and best regards, >> Philipp Pugliese >> mailto:phi...@fa... >> >> P.S.: hope you are the right contact person. If not, could you provide >> me the right contact person? >> >> >> _______________________________________________ >> basedb-devel mailing list >> bas...@li... >> https://lists.sourceforge.net/lists/listinfo/basedb-devel |
|
From: Jari H. <jar...@me...> - 2019-06-25 10:12:26
|
Hi Philipp, Thank you for your interest in BASE. Some of the information you listed is outdated. Here are updates you can use. 1) Brief description of BASE: BASE is a comprehensive free web-based database LIMS solution for tracking of information and data generated in sequencing and microarray experiments from sample to analysis. BASE is released under the GNU General Public License version 3. 2) The reference list could be updated to include - Häkkinen et al. 2016, https://doi.org/10.1101/038976 - Vallon-Christersson et al. 2009, PMID: 19822003 If only one reference can be retained then you should use Vallon-Christersson et al. 3) Under miscellaneous you might add that source code is available at http://base.thep.lu.se? It is open, browsable, searchable, has issue tracking, and more. Actually predates GitHub ;-) 4) Regarding compliance to standards. We are not actively pursuing (MIAME) standards compliance, and the public repository upload functionality is semi-automatic at best. Cheers, Jari On 2019-06-16 14:54, Pugliese, Philipp wrote: > Dear support team, > > briefly to me: my name is Philipp Pugliese and I researched for the > Friedrich-Alexander-Universität Erlangen-Nürnberg about functions that > BASE seems to fulfill. > > For a congress publication I created a matrix in which BASE is > mentioned. Could you please give me some feedback as to whether the > information I found in the literature is correct or up to date? > > The information is: > > Brief description of BASE: Is an information and analysis tool for > microarrays that tracks all materials from biosource to raw data to > analyses. The elements can be annotated and used as factors in the > downstream analysis > > > General > Abbreviation: BioArray Software Environment > FAIR reference: unknown > Note: - > > Community > Institution: Lund University > Reference: Saal et al. 2002 > PMID: 12186655 > Software availability: open source > License: GNU > User mailing list or support: Yes > URL: http://base.thep.lu.se > > System requirements > Operating system: Platform independent > DB managing System: MySQL,PostgreSQL > Main programming language: Java > Client-side interface: web browser > > Support > Installation procedures: Yes > Configuration documentation: Yes > User documentation: Yes > Regular maintenance: Yes > > Miscellaneous > GitHub availability: - > Demo server availability: Yes > > Requirements for data management in system biology > Compliance to standards: MIAME > Metadata model: MIAME-related > Automation of data collection: batch import > Upload to public repositories: ArrayExpress, GEO, CIBEX > Extensibility: Java plugins / extentions > Integration with other DMS: via java servlets > > > > Please give me feedback by 30th June 2019 so that your feedback can be > considered until publication. > > Thanks in advance and best regards, > Philipp Pugliese > mailto:phi...@fa... > > P.S.: hope you are the right contact person. If not, could you provide > me the right contact person? > > > _______________________________________________ > basedb-devel mailing list > bas...@li... > https://lists.sourceforge.net/lists/listinfo/basedb-devel -- "For a successful technology, reality must take precedence over public relations, for nature cannot be fooled." - Richard P. Feynman, Rogers Commission Report 1986 |
|
From: Pugliese, P. <phi...@fa...> - 2019-06-16 12:54:27
|
Dear support team,
briefly to me: my name is Philipp Pugliese and I researched for the
Friedrich-Alexander-Universität Erlangen-Nürnberg about functions that
BASE seems to fulfill.
For a congress publication I created a matrix in which BASE is
mentioned. Could you please give me some feedback as to whether the
information I found in the literature is correct or up to date?
The information is:
Brief description of BASE: Is an information and analysis tool for
microarrays that tracks all materials from biosource to raw data to
analyses. The elements can be annotated and used as factors in the
downstream analysis
General
Abbreviation: BioArray Software Environment
FAIR reference: unknown
Note: -
Community
Institution: Lund University
Reference: Saal et al. 2002
PMID: 12186655
Software availability: open source
License: GNU
User mailing list or support: Yes
URL: http://base.thep.lu.se
System requirements
Operating system: Platform independent
DB managing System: MySQL,PostgreSQL
Main programming language: Java
Client-side interface: web browser
Support
Installation procedures: Yes
Configuration documentation: Yes
User documentation: Yes
Regular maintenance: Yes
Miscellaneous
GitHub availability: -
Demo server availability: Yes
Requirements for data management in system biology
Compliance to standards: MIAME
Metadata model: MIAME-related
Automation of data collection: batch import
Upload to public repositories: ArrayExpress, GEO, CIBEX
Extensibility: Java plugins / extentions
Integration with other DMS: via java servlets
Please give me feedback by 30th June 2019 so that your feedback can be
considered until publication.
Thanks in advance and best regards,
Philipp Pugliese
mailto:phi...@fa...
P.S.: hope you are the right contact person. If not, could you provide
me the right contact person?
|
|
From: Nicklas N. <nic...@me...> - 2019-04-11 07:56:02
|
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 For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.15&group=type&groupdesc=1 Upgrading follows the usual procedure: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Nicklas N. <nic...@me...> - 2019-02-06 12:23:13
|
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&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
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From: Nicklas N. <nic...@me...> - 2019-01-08 08:38:15
|
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: http://base.thep.lu.se/query?milestone=BASE+3.14&group=type&groupdesc=1 http://base.thep.lu.se/query?milestone=BASE+3.13.1&group=type&groupdesc=1 Upgrading follows the usual procedure: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Nicklas N. <nic...@me...> - 2018-08-23 10:17:03
|
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&group=type&groupdesc=1 Upgrading follows the usual procedure: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Nicklas N. <nic...@me...> - 2018-06-04 06:53:25
|
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&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Nicklas N. <nic...@me...> - 2018-04-16 07:07:23
|
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&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
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From: Nicklas N. <nic...@me...> - 2018-04-03 07:42:00
|
Hello all, We have released BASE 3.12.1 today. This is a bugfix release that fixes a critical bug in the annotation importer plug-in. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.12.1&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
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From: Nicklas N. <nic...@me...> - 2018-03-14 13:38:08
|
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&group=type&groupdesc=1 Upgrading follows the usual procedure: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.upgrade.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Nicklas N. <nic...@me...> - 2017-11-23 10:24:46
|
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&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
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