Difference between revisions of "BASE"
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| author = Johan Vallon-Christersson, Nicklas Nordborg, Martin Svensson, and Jari Häkkinen | | author = Johan Vallon-Christersson, Nicklas Nordborg, Martin Svensson, and Jari Häkkinen | ||
| developer = The Lund BASE team | | developer = The Lund BASE team | ||
| released = {{Start date| | | released = {{Start date|2002|05|18}} (1.0)<ref name="BASENewsOld">{{cite web |url=http://base.thep.lu.se/news_old.phtml |archiveurl=https://web.archive.org/web/20050412201703/http://base.thep.lu.se/news_old.phtml |title=BioArray Software Environment - Site news archive |publisher=Lund BASE team |date=21 October 2004 |archivedate=12 April 2005 |accessdate=22 May 2014}}</ref> | ||
| discontinued = | | discontinued = | ||
| frequently updated = yes<!-- Release version update? Don't edit this page, just click on the version number! --> | | frequently updated = yes<!-- Release version update? Don't edit this page, just click on the version number! --> | ||
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| website = [http://base.thep.lu.se/ base.thep.lu.se] | | website = [http://base.thep.lu.se/ base.thep.lu.se] | ||
}} | }} | ||
'''BASE''' 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."<ref name="BASEDoc">{{cite web |url=http://base.thep.lu.se/chrome/site/latest/html/overview.html |title=Part I. Overview |work=BASE 3.2.4 Documentation |publisher=Lund BASE team |date=14 March 2013 |accessdate=22 May 2014}}</ref> | '''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."<ref name="BASEDoc">{{cite web |url=http://base.thep.lu.se/chrome/site/latest/html/overview.html |title=Part I. Overview |work=BASE 3.2.4 Documentation |publisher=Lund BASE team |date=14 March 2013 |accessdate=22 May 2014}}</ref> | ||
==Product history== | ==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,"<ref name="BASE10Paper">{{cite journal |url=http://genomebiology.com/2002/3/8/software/0003 |journal=Genome Biology |title=BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data |author=Saal, Lao H.; Troein, Carl; Vallon-Christersson, Johan; Gruvberger, Sofia; Borg, Åke; Peterson, Carsten |volume=3 |page=software0003-software0003.6 |year=2002 |doi=10.1186/gb-2002-3-8-software0003}}</ref> 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,.<ref name="BASENewsOld" /> | |||
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<ref name="BASENewsOld" />, 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,"<ref name="BASE20Abst">{{cite web |url=http://www.microarrays.ca/MGED/Abstracts/Hakkinen.pdf |archiveurl=https://web.archive.org/web/20050313163040/http://www.microarrays.ca/MGED/Abstracts/Hakkinen.pdf |format=PDF |title=Update on a Microarray Database and Analysis System: BioArray Software Environment (BASE) |author=Häkkinen, J.; Nordborg, N.; Saal, L.; Troein, C.; Vallon-Christersson, J. |date=06 September 2004 |archivedate=13 March 2005 |accessdate=22 May 2014}}</ref> stated the group. They anticipated the software would be ready by that fall<ref name="BASE20Abst" />; however, it wasn't until August 31, 2006 that version 2.0 of the software was released.<ref name="BASE20">{{cite web |url=http://base.thep.lu.se/log/tags/2.0?rev=6370 |title=tags/2.0 @ 6370 |publisher=Lund BASE team |accessdate=22 May 2014}}</ref> | |||
==Features== | ==Features== | ||
Features of BASE include: | Features of BASE include<ref name="BASEFeats">{{cite web |url=http://base.thep.lu.se/chrome/site/latest/html/features.html |title=Chapter 2. BASE features |work=BASE 3.2.4 Documentation |publisher=Lund BASE team |date=14 March 2013 |accessdate=22 May 2014}}</ref>: | ||
* multi-user local data repository with a web-based interface | * multi-user local data repository with a web-based interface | ||
| Line 35: | Line 36: | ||
* annotations for clinical other types of information | * annotations for clinical other types of information | ||
* hierarchical overview of analysis | * hierarchical overview of analysis | ||
* data grouping, sharing, and privacy policies | |||
* integrated file system | |||
* integrated tools like MultiExperiment Viewer | * 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== | ==Hardware/software requirements== | ||
The following requirements exist for an installation of BASE version 3.2.4<ref name="BASEInst">{{cite web |url=http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html |title=20.2. Installation instructions |work=BASE 3.2.4 Documentation |publisher=Lund BASE team |date=14 March 2013 |accessdate=22 May 2014}}</ref>: | |||
* Java SE 6 | |||
* [[Apache Tomcat]] 6.0.20 or any later 6.x release | |||
* [[MySQL]] 5.1 or [[PostgreSQL]] 9.1 | |||
Note that requirements may be different for earlier or later versions. Consult [http://base.thep.lu.se/chrome/site/latest/html/index.html the documentation] for more installation information. | |||
==Videos, screenshots, and other media== | ==Videos, screenshots, and other media== | ||
* [http://base.thep.lu.se/wiki/DownloadPage Newer BASE downloads] | |||
* [http://base.thep.lu.se/wiki/DownloadOld Older BASE downloads] | |||
* [http://base.thep.lu.se/chrome/site/latest/html/index.html BASE documentation] | |||
* [http://base2.thep.lu.se/demo/ BASE demo server] (Login and Password = base2) | |||
==Entities using BASE== | ==Entities using BASE== | ||
| Line 53: | Line 67: | ||
==Further reading== | ==Further reading== | ||
* {{cite journal |url=http://www.biomedcentral.com/1471-2105/10/330 |journal=BMC Bioinformatics |title=BASE - 2nd generation software for microarray data management and analysis |author=Vallon-Christersson, Johan; Nordborg, Nicklas; Svensson, Martin; Häkkinen, Jari | | * {{cite journal |url=http://genomebiology.com/2002/3/8/software/0003 |journal=Genome Biology |title=BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data |author=Saal, Lao H.; Troein, Carl; Vallon-Christersson, Johan; Gruvberger, Sofia; Borg, Åke; Peterson, Carsten |volume=3 |page=software0003-software0003.6 |year=2002 |doi=10.1186/gb-2002-3-8-software0003}} | ||
* {{cite journal |url=http://www.biomedcentral.com/1471-2105/10/330 |journal=BMC Bioinformatics |title=BASE - 2nd generation software for microarray data management and analysis |author=Vallon-Christersson, Johan; Nordborg, Nicklas; Svensson, Martin; Häkkinen, Jari |volume=10 |page=330 |year=2009 |doi=10.1186/1471-2105-10-330}} | |||
==External links== | ==External links== | ||
Revision as of 21:20, 22 May 2014
 | |
| 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)[1] |
| Stable release |
3.19.9 (June 7, 2023) [±] |
| 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[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]
Features
Features of BASE include[6]:
- 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 3.2.4[7]:
- Java SE 6
- Apache Tomcat 6.0.20 or any later 6.x release
- MySQL 5.1 or PostgreSQL 9.1
Note that requirements may be different for earlier or later versions. Consult the documentation for more installation information.
Videos, screenshots, and other media
- Newer BASE downloads
- Older BASE downloads
- BASE documentation
- BASE demo server (Login and Password = base2)
Entities using BASE
Further reading
- 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.
- Vallon-Christersson, Johan; Nordborg, Nicklas; Svensson, Martin; Häkkinen, Jari (2009). "BASE - 2nd generation software for microarray data management and analysis". BMC Bioinformatics 10: 330. doi:10.1186/1471-2105-10-330. http://www.biomedcentral.com/1471-2105/10/330.
External links
References
- ↑ 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.
- ↑ "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.
- ↑ 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.
- ↑ 4.0 4.1 Häkkinen, J.; Nordborg, N.; Saal, L.; Troein, C.; Vallon-Christersson, J. (6 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.
- ↑ "tags/2.0 @ 6370". Lund BASE team. http://base.thep.lu.se/log/tags/2.0?rev=6370. Retrieved 22 May 2014.
- ↑ "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.
- ↑ "20.2. Installation instructions". BASE 3.2.4 Documentation. Lund BASE team. 14 March 2013. http://base.thep.lu.se/chrome/site/latest/html/admin/installation.main.html. Retrieved 22 May 2014.
