publication . Article . 2010

Next generation tools for genomic data generation, distribution, and visualization

Nix, David A; Di Sera, Tonya L; Dalley, Brian K; Milash, Brett A; Cundick, Robert M; Quinn, Kevin S; Courdy, Samir J;
Open Access
  • Published: 01 Sep 2010 Journal: BMC Bioinformatics, volume 11 (eissn: 1471-2105, Copyright policy)
  • Publisher: Springer Science and Business Media LLC
Abstract
<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 vett...
Subjects
free text keywords: Biochemistry, Molecular Biology, Computer Science Applications, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5, Software
Related Organizations
28 references, page 1 of 2

Nicol, JW, Helt, GA, Blanchard, SG, Raja, A, Loraine, AE. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics. 2009; 25 (20): 2730-1 [OpenAIRE] [PubMed] [DOI]

University of Utah's GNomEx Installation.

Whetzel, PL, Parkinson, H, Causton, HC, Fan, L, Fostel, J, Fragoso, G, Game, L, Heiskanen, M, Morrison, N, Rocca-Serra, P, Sansone, SA, Taylor, C, White, J, Stoeckert, CJ. The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics. 2006; 22 (7): 866-73 [OpenAIRE] [PubMed] [DOI]

Apache Lucene Search Engine.

Blankenberg, D, Von Kuster, G, Coraor, N, Ananda, G, Lazarus, R, Mangan, M, Nekrutenko, A, Taylor, J. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010: 1-21 [PubMed]

Reich, M, Liefeld, T, Gould, J, Lerner, J, Tamayo, P, Mesirov, JP. GenePattern 2.0. Nat Genet. 2006; 38 (5): 500-1 [OpenAIRE] [PubMed] [DOI]

USeq Next Generation Analysis Package.

Nix, DA, Courdy, SJ, Boucher, KM. Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics. 2008; 9: 523 [OpenAIRE] [PubMed] [DOI]

TiMAT2 Tiling Microarray Analyis Tools.

Gene Expression Omnibus and Short Read Archive.

ArrayExpress.

Kuhn, RM, Karolchik, D, Zweig, AS, Wang, T, Smith, KE, Rosenbloom, KR, Rhead, B, Raney, BJ, Pohl, A, Pheasant, M, Meyer, L, Hsu, F, Hinrichs, AS, Harte, RA, Giardine, B, Fujita, P, Diekhans, M, Dreszer, T, Clawson, H, Barber, GP, Haussler, D, Kent, WJ. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 2009 (37 Database): D755-61 [OpenAIRE] [PubMed] [DOI]

UCSC Genome Bioinformatics.

BioDas.

Hubbard, T, Birney, E. Open annotation offers a democratic solution to genome sequencing. Nature. 2000; 403 (6772): 825 [OpenAIRE] [PubMed] [DOI]

28 references, page 1 of 2
Abstract
<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 vett...
Subjects
free text keywords: Biochemistry, Molecular Biology, Computer Science Applications, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5, Software
Related Organizations
28 references, page 1 of 2

Nicol, JW, Helt, GA, Blanchard, SG, Raja, A, Loraine, AE. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics. 2009; 25 (20): 2730-1 [OpenAIRE] [PubMed] [DOI]

University of Utah's GNomEx Installation.

Whetzel, PL, Parkinson, H, Causton, HC, Fan, L, Fostel, J, Fragoso, G, Game, L, Heiskanen, M, Morrison, N, Rocca-Serra, P, Sansone, SA, Taylor, C, White, J, Stoeckert, CJ. The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics. 2006; 22 (7): 866-73 [OpenAIRE] [PubMed] [DOI]

Apache Lucene Search Engine.

Blankenberg, D, Von Kuster, G, Coraor, N, Ananda, G, Lazarus, R, Mangan, M, Nekrutenko, A, Taylor, J. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010: 1-21 [PubMed]

Reich, M, Liefeld, T, Gould, J, Lerner, J, Tamayo, P, Mesirov, JP. GenePattern 2.0. Nat Genet. 2006; 38 (5): 500-1 [OpenAIRE] [PubMed] [DOI]

USeq Next Generation Analysis Package.

Nix, DA, Courdy, SJ, Boucher, KM. Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics. 2008; 9: 523 [OpenAIRE] [PubMed] [DOI]

TiMAT2 Tiling Microarray Analyis Tools.

Gene Expression Omnibus and Short Read Archive.

ArrayExpress.

Kuhn, RM, Karolchik, D, Zweig, AS, Wang, T, Smith, KE, Rosenbloom, KR, Rhead, B, Raney, BJ, Pohl, A, Pheasant, M, Meyer, L, Hsu, F, Hinrichs, AS, Harte, RA, Giardine, B, Fujita, P, Diekhans, M, Dreszer, T, Clawson, H, Barber, GP, Haussler, D, Kent, WJ. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 2009 (37 Database): D755-61 [OpenAIRE] [PubMed] [DOI]

UCSC Genome Bioinformatics.

BioDas.

Hubbard, T, Birney, E. Open annotation offers a democratic solution to genome sequencing. Nature. 2000; 403 (6772): 825 [OpenAIRE] [PubMed] [DOI]

28 references, page 1 of 2
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