%0 Journal Article %1 Hubble2009Implementation %A Hubble, Jeremy %A Demeter, Janos %A Jin, Heng %A Mao, Maria %A Nitzberg, Michael %A Reddy, T. B. %A Wymore, Farrell %A Zachariah, Zachariah K. %A Sherlock, Gavin %A Ball, Catherine A. %D 2009 %J Nucleic acids research %K database microarray %N Database issue %P D898--D901 %R 10.1093/nar/gkn786 %T Implementation of GenePattern within the Stanford Microarray Database. %U http://dx.doi.org/10.1093/nar/gkn786 %V 37 %X Hundreds of researchers across the world use the Stanford Microarray Database (SMD; http://smd.stanford.edu/) to store, annotate, view, analyze and share microarray data. In addition to providing registered users at Stanford access to their own data, SMD also provides access to public data, and tools with which to analyze those data, to any public user anywhere in the world. Previously, the addition of new microarray data analysis tools to SMD has been limited by available engineering resources, and in addition, the existing suite of tools did not provide a simple way to design, execute and share analysis pipelines, or to document such pipelines for the purposes of publication. To address this, we have incorporated the GenePattern software package directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. In this article, we describe our implementation of the GenePattern microarray analysis software package into the SMD code base. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability.

@article{Hubble2009Implementation, abstract = {Hundreds of researchers across the world use the Stanford Microarray Database ({SMD}; http://smd.stanford.edu/) to store, annotate, view, analyze and share microarray data. In addition to providing registered users at Stanford access to their own data, {SMD} also provides access to public data, and tools with which to analyze those data, to any public user anywhere in the world. Previously, the addition of new microarray data analysis tools to {SMD} has been limited by available engineering resources, and in addition, the existing suite of tools did not provide a simple way to design, execute and share analysis pipelines, or to document such pipelines for the purposes of publication. To address this, we have incorporated the {GenePattern} software package directly into {SMD}, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through {SMD}. In this article, we describe our implementation of the {GenePattern} microarray analysis software package into the {SMD} code base. This extension is available with the {SMD} source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of {SMD} with an enriched data analysis capability.}, added-at = {2018-12-02T16:09:07.000+0100}, author = {Hubble, Jeremy and Demeter, Janos and Jin, Heng and Mao, Maria and Nitzberg, Michael and Reddy, T. B. and Wymore, Farrell and Zachariah, Zachariah K. and Sherlock, Gavin and Ball, Catherine A.}, biburl = {https://www.bibsonomy.org/bibtex/2946f26bd13478095a9f4cc79bdb5de9b/karthikraman}, citeulike-article-id = {3502209}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkn786}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/content/37/suppl\_1/D898.abstract}, citeulike-linkout-2 = {http://nar.oxfordjournals.org/content/37/suppl\_1/D898.full.pdf}, citeulike-linkout-3 = {http://nar.oxfordjournals.org/cgi/content/abstract/37/suppl\_1/D898}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/18953035}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=18953035}, day = 1, doi = {10.1093/nar/gkn786}, interhash = {16c92edf4b4654cca51bf275aa93cf94}, intrahash = {946f26bd13478095a9f4cc79bdb5de9b}, issn = {1362-4962}, journal = {Nucleic acids research}, keywords = {database microarray}, month = jan, number = {Database issue}, pages = {D898--D901}, pmid = {18953035}, posted-at = {2015-01-15 12:25:16}, priority = {2}, timestamp = {2018-12-02T16:09:07.000+0100}, title = {Implementation of {GenePattern} within the Stanford Microarray Database.}, url = {http://dx.doi.org/10.1093/nar/gkn786}, volume = 37, year = 2009 }