Implementation

BASE
BASE os logo.png
Original author(s) Johan Vallon-Christersson, Nicklas Nordborg, Martin Svensson, and Jari Häkkinen
Developer(s) The Lund BASE team
Initial release May 18, 2002 (2002-05-18) (1.0)[1]
Stable release

 (June 24, 2020; 6 months ago (2020-06-24))

[]
Preview release []
Written in Java
Operating system Cross-platform
Type Laboratory informatics software
License(s) GNU General Public License v3.0
Website base.thep.lu.se

BASE (BioArray Software Environment) is a free open-source laboratory informatics application "designed for laboratories looking for a single point of storage for all information related to their experimentation and for storing, managing, and analysing genomics/transcriptomics data."[2]

Product history

Unable to find a unified informatics system "capable of organizing all the information surrounding microarray experimentation and which also integrate[s] this information with tools for the analysis of quantified microarray hybridization data,"[3] researchers at Lund University and its associated hospital set out to develop the BioArray Software Environment (BASE) sometime in 2001. After several beta releases in early 2002, the group released version 1.0 of the PHP-based open-source software to the public on May 18, 2002,.[1]

During the 7th International Meeting of the Microarray Gene Expression Data Society on September 8–10, 2004, the development team discussed among other things the transition to BASE 2.0 from 1.2[1], including a change from PHP to Java. "The switch to Java will make the source code structure more transparent and facilitate in-depth understanding of the software by advanced users and developers, thereby increasing accessibility to an even broader community,"[4] stated the group. They anticipated the software would be ready by that fall[4]; however, it wasn't until August 31, 2006 that version 2.0 of the software was released.[5]

Version 3.0.0 of the software was released on November 2, 2011.[6]

Releases

These are the known release dates of stable BASE releases[7][8][9][10][11][6]:

Version Release date
3.7.1 07 March 2016
3.7.0 11 January 2016
3.6.3 25 November 2015
3.6.2 12 November 2015
3.6.1 19 October 2015
3.6.0 08 October 2015
3.5.3 17 September 2015
3.5.3 05 May 2015
3.5.1 29 April 2015
3.5.0 21 April 2015
3.4.2 18 March 2015
3.4.1 10 February 2015
3.4.0 14 January 2015
3.3.4 04 December 2014
3.3.3 17 November 2014
Version Release date
3.3.2 22 October 2014
3.3.1 26 September 2014
3.3.0 18 August 2014
3.2.4 06 December 2013
3.2.3 09 September 2013
3.2.2 10 April 2013
3.2.1 13 December 2012
3.2.0 13 September 2012
3.1.2 31 July 2012
3.1.1 29 March 2012
3.1.0 19 March 2012
3.0.4 05 March 2012
3.0.3 22 February 2012
3.0.2 25 January 2012
3.0.1 10 November 2011
3.0.0 02 November 2011
2.17.2 17 June 2011
2.17.1 08 May 2011
2.17.0 23 February 2011
2.16.2 18 February 2011
Version Release date
2.16.1 22 November 2010
2.16.0 03 November 2010
2.15.0 20 April 2010
2.14.2 22 February 2010
2.14.1 05 November 2009
2.14.0 22 October 2009
2.13.1 15 October 2009
2.13.0 31 August 2009
2.12.1 15 June 2009
2.12.0 27 May 2009
2.11.1 27 May 2009
2.11.0 30 March 2009
2.10.1 24 March 2009
2.10.0 24 February 2009
2.9.3 19 February 2009
2.9.2 08 January 2009
2.9.1 18 December 2008
2.9.0 26 November 2008
2.8.4 27 October 2008
2.8.3 15 October 2008
Version Release date
2.8.2 18 September 2008
2.8.1 10 September 2008
2.8.0 08 September 2008
2.7.2 02 July 2008
2.7.1 18 June 2008
2.7.0 13 May 2008
2.6.3 09 May 2008
2.6.2 17 April 2008
2.6.1 25 March 2008
2.6.0 22 January 2008
2.5.1 18 January 2008
2.5.0 07 December 2007
2.4.6 11 November 2007
2.4.5 31 October 2007
2.4.4 17 October 2007
2.4.3 26 September 2007
2.4.2 24 September 2007
2.4.1 13 September 2007
2.4.0 20 August 2007
2.3.2 30 June 2007
Version Release date
2.3.1 14 June 2007
2.3.0 31 May 2007
2.2.3 23 April 2007
2.2.2 12 March 2007
2.2.1 08 February 2007
2.2.0 07 February 2007
2.1.2 14 January 2007
2.1.1 01 December 2006
2.1.0 31 October 2006
2.0.3 26 October 2006
2.0.2 18 October 2006
2.0.1 02 October 2006
2.0.0 31 August 2006
1.2.17 06 November 2005
1.2.16 05 February 2005
1.2.15 08 November 2004
1.2.14 10 September 2004
1.2.13 17 August 2004
1.2.12b 08 June 2004
1.2.11 28 May 2004
Version Release date
1.2.10 27 October 2003
1.2.9 07 October 2003
1.2.8 19 August 2003
1.2.7 20 June 2003
1.2.6b 23 May 2003
1.2.6 23 May 2003
1.2.5 29 April 2003
1.2.4 28 April 2003
1.2.3 08 April 2003
1.2.2 07 April 2003
1.2.1 21 March 2003
1.2.0 14 March 2003
1.0.7a 09 November 2002
1.0.6 09 August 2002
1.0.5 30 July 2002
1.0.4 22 July 2002
1.0.3 16 July 2002
1.0.2 13 July 2002
1.0.1 21 May 2002
1.0.0 18 May 2002

Features

Features of BASE include[12]:

  • multi-user local data repository with a web-based interface
  • laboratory information management system (LIMS) for both biomaterials and array production
  • annotations for clinical other types of information
  • hierarchical overview of analysis
  • data grouping, sharing, and privacy policies
  • integrated file system
  • integrated tools like MultiExperiment Viewer
  • plugin and extension infrastructure
  • batch upload and download of data
  • support for many array platforms and raw data formats
  • extended support for sequencing applications such as RNAseq

Hardware/software requirements

The following requirements exist for an installation of BASE version 3.6 to 3.7.1[13]:

Note that requirements may be different for earlier or later versions. Consult the documentation for the latest installation information.

Videos, screenshots, and other media

Entities using BASE

Further reading

External links

References

  1. 1.0 1.1 1.2 "BioArray Software Environment - Site news archive". Lund BASE team. 21 October 2004. Archived from the original on 12 April 2005. https://web.archive.org/web/20050412201703/http://base.thep.lu.se/news_old.phtml. Retrieved 22 May 2014. 
  2. "Part I. Overview". BASE 3.2.4 Documentation. Lund BASE team. 14 March 2013. http://base.thep.lu.se/chrome/site/latest/html/overview.html. Retrieved 22 May 2014. 
  3. Saal, Lao H.; Troein, Carl; Vallon-Christersson, Johan; Gruvberger, Sofia; Borg, Åke; Peterson, Carsten (2002). "BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data". Genome Biology 3: software0003-software0003.6. doi:10.1186/gb-2002-3-8-software0003. http://genomebiology.com/2002/3/8/software/0003. 
  4. 4.0 4.1 Häkkinen, J.; Nordborg, N.; Saal, L.; Troein, C.; Vallon-Christersson, J. (06 September 2004). "Update on a Microarray Database and Analysis System: BioArray Software Environment (BASE)" (PDF). Archived from the original on 13 March 2005. https://web.archive.org/web/20050313163040/http://www.microarrays.ca/MGED/Abstracts/Hakkinen.pdf. Retrieved 22 May 2014. 
  5. "tags/2.0 @ 6370". Lund BASE team. http://base.thep.lu.se/log/tags/2.0?rev=6370. Retrieved 22 May 2014. 
  6. 6.0 6.1 "Download BASE". Lund BASE team. 06 December 2013. http://base.thep.lu.se/wiki/DownloadPage. Retrieved 22 May 2014. 
  7. "BASE Download: Registered User". Lund BASE team. 08 November 2004. Archived from the original on 18 December 2004. https://web.archive.org/web/20041218032958/http://base.thep.lu.se/download/dl.phtml. Retrieved 22 May 2014. 
  8. Troein, Carl (05 February 2005). "-base- BASE 1.2.16 released". SourceForge. http://sourceforge.net/p/basedb/mailman/message/8845150/. Retrieved 22 May 2014. 
  9. Troein, Carl (06 November 2005). "-base-announce- BASE 1.2.17 released". SourceForge. http://sourceforge.net/p/basedb/mailman/message/116989/. Retrieved 22 May 2014. 
  10. "Download BASE". Lund BASE team. 18 January 2008. Archived from the original on 10 February 2008. https://web.archive.org/web/20080210092535/http://base.thep.lu.se/wiki/DownloadPage. Retrieved 22 May 2014. 
  11. "Older BASE 2.x versions". Lund BASE team. 02 November 2011. http://base.thep.lu.se/wiki/DownloadOld. Retrieved 22 May 2014. 
  12. "Chapter 2. BASE features". BASE 3.2.4 Documentation. Lund BASE team. 14 March 2013. http://base.thep.lu.se/chrome/site/latest/html/features.html. Retrieved 22 May 2014. 
  13. "21.2. Installation instructions". BASE 3.7.1 Documentation. Lund BASE team. 08 October 2015. http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html. Retrieved 14 March 2016. 

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