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.

RobiNA 1.2.4 – Open Source Microarray and RNA-Seq Processing

RobiNA 1.2.4

:: DESCRIPTION

RobiNA is an integrated solution that consolidates all steps of RNA-Seq-based differential gene-expression analysis in one user-friendly cross-platform application featuring a rich graphical user interface. RobiNA accepts raw FastQ files, SAM/BAM alignment files and counts tables as input. It supports quality checking, flexible filtering and statistical analysis of differential gene expression based on state-of-the art biostatistical methods developed in the R/Bioconductor projects. In-line help and a step-by-step manual guide users through the analysis.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Java

:: DOWNLOAD

RobiNA

:: MORE INFORMATION

Citation

Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. (2012)
RobiNA: A user-friendly, integrated software solution for RNA-Seq-based transcriptomics.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7.

BioBlender 1.0 – Software built on the Open-source 3D Modeling software Blender

BioBlender 1.0

:: DESCRIPTION

BioBlender is a open source viewer that includes features for morphing proteins and visualization of lipophilic and electrostatic potentials.

::DEVELOPER

the SciVis Group of the Institute of Clinical Physiology – CNR, Italy.

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux

:: DOWNLOAD

BioBlender

:: MORE INFORMATION

Citation

Andrei R.M. et al.
Intuitive representation of surface properties of biomolecules using BioBlender.
BMC Bioinformatics 2012, 13(Suppl 4):S16. Published: 28 March 2012

Aequatus – Open-source Homology Browser

Aequatus

:: DESCRIPTION

Aequatus is an open-source web-based tool to visualise homologous gene structures among differing species or subtypes of a common species.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser/ Linux

:: DOWNLOAD

Aequatus

:: MORE INFORMATION

Citation

Aequatus: an open-source homology browser.
Thanki AS, Soranzo N, Herrero J, Haerty W, Davey RP.
Gigascience. 2018 Nov 1;7(11). doi: 10.1093/gigascience/giy128.

OSCAR 6.1.1 – Open Source Cluster Application Resources

OSCAR 6.1.1

:: DESCRIPTION

OSCAR (Open Source Cluster Application Resources) is a snapshot of the best known practices for building, programming and using a cluster. The toolkit is geared towards a modest sized cluster (50+ nodes) and features a wizard-based GUI for cluster installation.

::DEVELOPER

The Open Cluster Group

:: SCREENSHOTS