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SLIMarray: lightweight software for microarray facility management.

Marzolf B, Troisch P - Source Code Biol Med (2006)

Bottom Line: Although these different needs could be handled separately, an integrated management system provides benefits in organization, automation and reduction in errors.SLIMarray Lite, a version of the software that is especially easy to install and run, is also available.SLIMarray addresses the previously unmet need for free and open source software for managing the logistics of a microarray core facility.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington, USA. bmarzolf@systemsbiology.org

ABSTRACT

Background: Microarray core facilities are commonplace in biological research organizations, and need systems for accurately tracking various logistical aspects of their operation. Although these different needs could be handled separately, an integrated management system provides benefits in organization, automation and reduction in errors.

Results: We present SLIMarray (System for Lab Information Management of Microarrays), an open source, modular database web application capable of managing microarray inventories, sample processing and usage charges. The software allows modular configuration and is well suited for further development, providing users the flexibility to adapt it to their needs. SLIMarray Lite, a version of the software that is especially easy to install and run, is also available.

Conclusion: SLIMarray addresses the previously unmet need for free and open source software for managing the logistics of a microarray core facility.

No MeSH data available.


Hybridization entry interface. Screenshot showing a web browser view of the interface used to enter information about hybridizations. Other interfaces in SLIMarray are similar in appearance.
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Figure 2: Hybridization entry interface. Screenshot showing a web browser view of the interface used to enter information about hybridizations. Other interfaces in SLIMarray are similar in appearance.

Mentions: The hybridization entry interface (Figure 2) allows facility staff to create records of hybridizations performed, and automatically records accompanying changes to inventories and charges. The hybridization entry interface presents a list of submitted samples. The user selects all or a subset of these, and chooses options that determine how they will be charged. Once the user has compiled a list of samples to hybridize, they are able to reorder the list as desired. Upon creation of the hybridization records, the software produces inventory transactions that record the number of arrays used in the inventories of the appropriate lab groups. Charge records are created and filed under the appropriate lab group's set of charges for the most recent charge period. In addition, if Affymetrix samples are being recorded, files can be output for immediate and automated sample record generation in Affymetrix GeneChip Operating System (GCOS) software [9].


SLIMarray: lightweight software for microarray facility management.

Marzolf B, Troisch P - Source Code Biol Med (2006)

Hybridization entry interface. Screenshot showing a web browser view of the interface used to enter information about hybridizations. Other interfaces in SLIMarray are similar in appearance.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1636632&req=5

Figure 2: Hybridization entry interface. Screenshot showing a web browser view of the interface used to enter information about hybridizations. Other interfaces in SLIMarray are similar in appearance.
Mentions: The hybridization entry interface (Figure 2) allows facility staff to create records of hybridizations performed, and automatically records accompanying changes to inventories and charges. The hybridization entry interface presents a list of submitted samples. The user selects all or a subset of these, and chooses options that determine how they will be charged. Once the user has compiled a list of samples to hybridize, they are able to reorder the list as desired. Upon creation of the hybridization records, the software produces inventory transactions that record the number of arrays used in the inventories of the appropriate lab groups. Charge records are created and filed under the appropriate lab group's set of charges for the most recent charge period. In addition, if Affymetrix samples are being recorded, files can be output for immediate and automated sample record generation in Affymetrix GeneChip Operating System (GCOS) software [9].

Bottom Line: Although these different needs could be handled separately, an integrated management system provides benefits in organization, automation and reduction in errors.SLIMarray Lite, a version of the software that is especially easy to install and run, is also available.SLIMarray addresses the previously unmet need for free and open source software for managing the logistics of a microarray core facility.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington, USA. bmarzolf@systemsbiology.org

ABSTRACT

Background: Microarray core facilities are commonplace in biological research organizations, and need systems for accurately tracking various logistical aspects of their operation. Although these different needs could be handled separately, an integrated management system provides benefits in organization, automation and reduction in errors.

Results: We present SLIMarray (System for Lab Information Management of Microarrays), an open source, modular database web application capable of managing microarray inventories, sample processing and usage charges. The software allows modular configuration and is well suited for further development, providing users the flexibility to adapt it to their needs. SLIMarray Lite, a version of the software that is especially easy to install and run, is also available.

Conclusion: SLIMarray addresses the previously unmet need for free and open source software for managing the logistics of a microarray core facility.

No MeSH data available.