Cytoscape 3.7.2 – Platform for Complex-Network Analysis & Visualization

Cytoscape 3.7.2

:: DESCRIPTION

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.

::DEVELOPER

Cytoscape Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Cytoscape

:: MORE INFORMATION

Citation:

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Genome Research 2003 Nov; 13(11):2498-504

Viroverse – Platform for Storage, Analysis of Experimental data for Laboratory Workflows

Viroverse

:: DESCRIPTION

Viroverse is a platform for the collection, storage, retrieval, and analysis of experimental data for laboratory workflows.

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser/ Linux ,VirtualBox

:: DOWNLOAD

Viroverse

:: MORE INFORMATION

expVIP 20180914 – RNA-seq Data Analysis and Visualization Platform

expVIP 20180914

:: DESCRIPTION

ExpVIP (expression visualization and integration platfor) is a tool that enables the integration of different RNA-Seq studies by analysing the data uniformly across experiments and provides a web interface to query the data.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

expVIP

:: MORE INFORMATION

Citation

expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform.
Borrill P, Ramirez-Gonzalez R, Uauy C.
Plant Physiol. 2016 Apr;170(4):2172-86. doi: 10.1104/pp.15.01667.

Probemapper 2.1.0 – Connect to QBRC’s ProbeMapper platform

Probemapper 2.1.0

:: DESCRIPTION

The ProbeMapper project aims to correlate microarray probes with Entrez IDs according to various sources including Vendor’s annotations, Bioconductor’s Annotate package, and a manual BLAST alignment of the probe sequences.

::DEVELOPER

The Quantitative Biomedical Research Center (QBRC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R package

:: DOWNLOAD

 Probemapper

:: MORE INFORMATION

Citation

Brief Bioinform. 2012 Sep;13(5):547-54. doi: 10.1093/bib/bbr076. Epub 2011 Dec 23.
Probe mapping across multiple microarray platforms.
Allen JD, Wang S, Chen M, Girard L, Minna JD, Xie Y, Xiao G.

geWorkbench 2.6.0.3 – Open-source Platform for Integrated Genomics

geWorkbench 2.6.0.3

:: DESCRIPTION

geWorkbench (genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available plug-ins supporting the visualization and analysis of gene expression and sequence data.

::DEVELOPER

Center for Computational Biology & Bioinformatics, Columbia University

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

 geWorkbench

:: MORE INFORMATION

Citation:

Floratos A, Smith K, Ji Z, Watkinson J, Califano A. (2010).
geWorkbench: an open source platform for integrative genomics.
Bioinformatics 26(14):1779-80. Epub 2010 May 28.

Seqcrawler 0.6.2 – Biological Data Indexing and Browsing Platform

Seqcrawler 0.6.2

:: DESCRIPTION

Seqcrawler provides a complete open source search and store solution for labs or platforms needing to manage large amount of data/meta-data with a flexible and customizable web interface.

::DEVELOPER

Seqcrawler team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 Seqcrawler

:: MORE INFORMATION

Citation

Seqcrawler: biological data indexing and browsing platform.
Sallou O, Bretaudeau A, Roult A.
BMC Bioinformatics. 2012 Jul 24;13:175. doi: 10.1186/1471-2105-13-175.

GenePattern 3.9.7 – Genomic Analysis Platform

GenePattern 3.9.7

:: DESCRIPTION

GenePattern is a powerful genomic analysis platform that provides access to more than 125 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

GenePattern provides access to a broad array of computational methods used to analyze genomic data. Its extendable architecture makes it easy for computational biologists to add analysis and visualization modules, which ensures that GenePattern users have access to new computational methods on a regular basis.

::DEVELOPER

The GenePattern team at the Broad Institute of MIT and Harvard.

:: SCREENSHOTS

:: REQUIREMENTS

  • Java VM
  • MacOSX/Windows/Linux
  • Other Java-enabled Platforms

:: DOWNLOAD

GenePattern

:: MORE INFORMATION

Citation

ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens.
Shao DD, Tsherniak A, Gopal S, Weir BA, Tamayo P, Stransky N, Schumacher SE, Zack TI, Beroukhim R, Garraway LA, Margolin AA, Root DE, Hahn WC, Mesirov JP.
Genome Res. 2013 Apr;23(4):665-78. doi: 10.1101/gr.143586.112.

Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP
GenePattern 2.0
Nature Genetics 38 no. 5 (2006): pp500-501

Virtual Pharmacist – A Platform for Pharmacogenomics

Virtual Pharmacist

:: DESCRIPTION

Virtual Pharmacist (VP) is a web tool that interprets personal genome for the impact of genetic variation on drug response. It can take variants data (VCF format), microarray SNP genotyping data and high-throughput sequencing data as input, and report to the users how the variants in their personal genomes impact their drug response, including drug efficacy, dosage and toxicity.

::DEVELOPER

Virtual Pharmacist team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Virtual Pharmacist: A Platform for Pharmacogenomics.
Cheng R, Leung RK, Chen Y, Pan Y, Tong Y, Li Z, Ning L, Ling XB, He J.
PLoS One. 2015 Oct 23;10(10):e0141105. doi: 10.1371/journal.pone.0141105

OpenSPIM 20150427 – Open-access Light-sheet Microscopy Platform

OpenSPIM 20150427

:: DESCRIPTION

OpenSPIM is an Open Access platform for applying and enhancing Selective Plane Illumination Microscopy (SPIM).

::DEVELOPER

OpenSPIM team

:: SCREENSHOTS

OpenSPIM

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 OpenSPIM

:: MORE INFORMATION

Citation

Nat Methods. 2013 Jul;10(7):598-9. doi: 10.1038/nmeth.2507. Epub 2013 Jun 9.
OpenSPIM: an open-access light-sheet microscopy platform.
Pitrone PG, Schindelin J, Stuyvenberg L, Preibisch S, Weber M, Eliceiri KW, Huisken J, Tomancak P.

Chemozart 1.0 – Web-based 3D Molecular Structure Editor and Visualizer Platform

Chemozart 1.0

:: DESCRIPTION

Chemozart is a web-based 3d molecule editor and visualization platfrom.

::DEVELOPER

Mohamad Mohebifar

:: SCREENSHOTS

Chemozart

:: REQUIREMENTS

  • Web browser
  • JS

:: DOWNLOAD

 Chemozart

:: MORE INFORMATION

Citation

Chemozart: a web-based 3D molecular structure editor and visualizer platform.
Mohebifar M, Sajadi F.
J Cheminform. 2015 Nov 19;7:56. eCollection 2015.