Next generation tools for genomic data generation, distribution, and visualization
<p>Abstract</p> <p>Background</p> <p>With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing,...
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| Format: | Article |
| Language: | English |
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BMC
2010-09-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/11/455 |
| _version_ | 1818663224171560960 |
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| author | Nix David A Di Sera Tonya L Dalley Brian K Milash Brett A Cundick Robert M Quinn Kevin S Courdy Samir J |
| author_facet | Nix David A Di Sera Tonya L Dalley Brian K Milash Brett A Cundick Robert M Quinn Kevin S Courdy Samir J |
| author_sort | Nix David A |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing, analyzing, and sharing genomic data.</p> <p>Results</p> <p>Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx); an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub); and a standalone Java Swing application (GWrap) that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser.</p> <p>Conclusions</p> <p>These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See <url>http://sourceforge.net/projects/gnomex/</url>, <url>http://sourceforge.net/projects/genoviz/</url>, and <url>http://sourceforge.net/projects/useq</url>.</p> |
| first_indexed | 2024-12-17T05:13:27Z |
| format | Article |
| id | doaj.art-8319cf5588fd4739a512306c7dace498 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-17T05:13:27Z |
| publishDate | 2010-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-8319cf5588fd4739a512306c7dace4982022-12-21T22:02:11ZengBMCBMC Bioinformatics1471-21052010-09-0111145510.1186/1471-2105-11-455Next generation tools for genomic data generation, distribution, and visualizationNix David ADi Sera Tonya LDalley Brian KMilash Brett ACundick Robert MQuinn Kevin SCourdy Samir J<p>Abstract</p> <p>Background</p> <p>With the rapidly falling cost and availability of high throughput sequencing and microarray technologies, the bottleneck for effectively using genomic analysis in the laboratory and clinic is shifting to one of effectively managing, analyzing, and sharing genomic data.</p> <p>Results</p> <p>Here we present three open-source, platform independent, software tools for generating, analyzing, distributing, and visualizing genomic data. These include a next generation sequencing/microarray LIMS and analysis project center (GNomEx); an application for annotating and programmatically distributing genomic data using the community vetted DAS/2 data exchange protocol (GenoPub); and a standalone Java Swing application (GWrap) that makes cutting edge command line analysis tools available to those who prefer graphical user interfaces. Both GNomEx and GenoPub use the rich client Flex/Flash web browser interface to interact with Java classes and a relational database on a remote server. Both employ a public-private user-group security model enabling controlled distribution of patient and unpublished data alongside public resources. As such, they function as genomic data repositories that can be accessed manually or programmatically through DAS/2-enabled client applications such as the Integrated Genome Browser.</p> <p>Conclusions</p> <p>These tools have gained wide use in our core facilities, research laboratories and clinics and are freely available for non-profit use. See <url>http://sourceforge.net/projects/gnomex/</url>, <url>http://sourceforge.net/projects/genoviz/</url>, and <url>http://sourceforge.net/projects/useq</url>.</p>http://www.biomedcentral.com/1471-2105/11/455 |
| spellingShingle | Nix David A Di Sera Tonya L Dalley Brian K Milash Brett A Cundick Robert M Quinn Kevin S Courdy Samir J Next generation tools for genomic data generation, distribution, and visualization BMC Bioinformatics |
| title | Next generation tools for genomic data generation, distribution, and visualization |
| title_full | Next generation tools for genomic data generation, distribution, and visualization |
| title_fullStr | Next generation tools for genomic data generation, distribution, and visualization |
| title_full_unstemmed | Next generation tools for genomic data generation, distribution, and visualization |
| title_short | Next generation tools for genomic data generation, distribution, and visualization |
| title_sort | next generation tools for genomic data generation distribution and visualization |
| url | http://www.biomedcentral.com/1471-2105/11/455 |
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