EditFrom NeuroLex
Resource:SMD
| Name: | Resource:SMD |
| Description: | Database to store, annotate, view, analyze and share microarray data. In addition to providing registered users 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, they 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. 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. SMD search options allow the user to Search By Experiments, Search By Datasets, or Search By Gene Names. Web services are provided using common standards, such as Simple Object Access Protocol (SOAP). This enables both local and remote researchers to connect to an installation of the database and retrieve data using pre-defined methods, without needing to resort to use of a web browser.[1] |
| Other Name(s): | Stanford Microarray Database |
| Parent Organization: | Stanford University School of Medicine; California; USA |
| Supporting Agency: | NHGRI, National Cancer Institute, Howard hughes medical institute, Stanford University School of Medicine; California; USA |
| Related to: | Resource:3DVC |
| Resource Type(s): | Database, Data repository, Data analysis service, Source code, Web service |
| Keywords: | Data set, microarray, gene |
| Grant: | R01 HG003469 |
| Abbreviation: | SMD |
| Resource: | Resource |
| URL: | http://smd.stanford.edu/ |
| PMID: | PMID 18953035, 17182626, 15608265, 12519956, 11125075 |
| Availability: | Public, The community can contribute to this resource., Open-source license |
| Address: | Department of Genetics, Stanford University School of Medicine, CA 94305, USA. |
| Id: | nlx_94141 |
| Link to OWL / RDF: | Download this content as OWL/RDF |
Categories related to Resource:SMD
Resource:Longhorn Array Database
Parts of Resource:SMD
Curation status: Curated
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References
- ↑ Hubble J et al. (2009) Implementation of GenePattern within the Stanford Microarray Database. Nucleic Acids Res 37: D898-901 PubMed
Notes
This page uses this default form:Resource
Old URL: http://genome-www.stanford.edu/microarray/
| Abbrev | SMD + |
| Address | Department of Genetics +, Stanford University School of Medicine +, CA 94305 +, and USA. + |
| Availability | Public +, The community can contribute to this resource. +, and Open-source license + |
| Comment | org-id: smd_stanford |
| CurationStatus | curated + |
| DefiningCitation | http://smd.stanford.edu/ + |
| Definition | Database to store, annotate, view, analyze … Database to store, annotate, view, analyze and share microarray data. In addition to providing registered users 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, they 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. 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. SMD search options allow the user to Search By Experiments, Search By Datasets, or Search By Gene Names. Web services are provided using common standards, such as Simple Object Access Protocol (SOAP). This enables both local and remote researchers to connect to an installation of the database and retrieve data using pre-defined methods, without needing to resort to use of a web browser. needing to resort to use of a web browser. |
| EditorialNote | *Note: According to the website on 5-6-13, the SMD is being moved to Princeton University and will be down until further notice. |
| ExampleImage |  + |
| Grant | Category:R01 HG003469 + |
| Has default formThis property is a special property in this wiki. | Resource + |
| Has role | Database +, Data repository +, Data analysis service +, Source code +, and Web service + |
| Id | nlx_94141 + |
| Is part of | Stanford University School of Medicine; California; USA + |
| Keywords | Data set +, Microarray +, and Gene + |
| Label | Resource:SMD + |
| ModifiedDate | 14 May 2013 + |
| PMID | 18953035, 17182626, 15608265, 12519956, 11125075 + |
| Page has default formThis property is a special property in this wiki. | Resource + |
| RelatedTo | Resource:3DVC + |
| SuperCategory | Resource + |
| Supporting Agency | NHGRI +, National Cancer Institute +, Howard hughes medical institute +, and Stanford University School of Medicine; California; USA + |
| Synonym | Stanford Microarray Database + |
