BASE

BASE
Original author(s)	Johan Vallon-Christersson, Nicklas Nordborg, Martin Svensson, and Jari Häkkinen
Developer(s)	The Lund BASE team
Initial release	May 18, 2002 (1.0)
Stable release	3.19.9 (June 7, 2023; 10 months ago) [±]
Preview release	none [±]
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