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.

SeqAn 2.2.0 – Open Source C++ Library of Sequences Analysis

SeqAn 2.2.0

:: DESCRIPTION

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance.

::DEVELOPER

SeqAn Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 SeqAn

:: MORE INFORMATION

Citation

SeqAn an efficient, generic C++ library for sequence analysis.
Döring A, Weese D, Rausch T, Reinert K.
BMC Bioinformatics. 2008 Jan 9;9:11.

Bioconductor 3.2 – Open Source Software for Bioinformatics

Bioconductor 3.2

:: DESCRIPTION

Bioconductor is an open source, open development software project to provide tools for the analysis and comprehension of high-throughput genomic data. It is based primarily on the R programming language.

::DEVELOPER

Bioconductor Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Bioconductor

:: MORE INFORMATION

Publications

YouScope 1.2 Beta – Open-source Microscope Control software

YouScope 1.2 Beta

:: DESCRIPTION

YouScope is a free, open-source microscope control software compatible with most present-day automized microscopes. YouScope allows to easily automatize complex microscopy protocols using an user-friendly graphical interface

::DEVELOPER

CSB – Computational Systems Biology Group

:: SCREENSHOTS

YouScope

::REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 YouScope

:: MORE INFORMATION

Citation

Curr Protoc Mol Biol. 2012 Apr;Chapter 14:Unit 14.21.1-23. doi: 10.1002/0471142727.mb1421s98.
Use of YouScope to implement systematic microscopy protocols.
Lang M, Rudolf F, Stelling J.

IOCBio 1.2.2 – Open-source Software from the Laboratory of Systems Biology

IOCBio 1.2.2

:: DESCRIPTION

The IOCBio project provides open-source software that is developed in Laboratory of Systems Biology at Institute of Cybernetics. The project is created to publish the software, this includes distributing the source codes, continuing software development, supporting users as well as attracting users to contribute to the software.

::DEVELOPER

Laboratory of Systems Biology at Institute of Cybernetics.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

IOCBio

:: MORE INFORMATION

Citation

J Microsc. 2011 Aug;243(2):124-40. doi: 10.1111/j.1365-2818.2011.03486.x. Epub 2011 Feb 15.
Application of regularized Richardson-Lucy algorithm for deconvolution of confocal microscopy images.
Laasmaa M, Vendelin M, Peterson P.

InterMine 1.5.3 – Open Source Biological Data Warehouse System

InterMine 1.5.3

:: DESCRIPTION

InterMine is an open source data warehouse built specifically for the integration and analysis of complex biological data.InterMine enables the creation of biological databases accessed by sophisticated web query tools.

::DEVELOPER

the Micklem lab at the University of Cambridge

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web Server
  • Java
  • PostgreSQL
  • TomCat
  • Perl

:: DOWNLOAD

 InterMine

:: MORE INFORMATION

Citation

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.
Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, Stepan R, Sullivan J, Wakeling M, Watkins X, Micklem G.
Bioinformatics. 2012 Dec 1;28(23):3163-5. doi: 10.1093/bioinformatics/bts577.

aroma.affymetrix 2.13.2 – Open-source R framework for your Microarray Analysis

aroma.affymetrix 2.13.2

:: DESCRIPTION

Aroma.affymetrix is an R package for analyzing large Affymetrix data sets.  It allows you to analyze 100-1,000s of arrays of various chip types, e.g. expression arrays, SNP chips, exon arrays and so on.

::DEVELOPER

Henrik Bengtsson et al. 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • R package

:: DOWNLOAD

 aroma.affymetrix

:: MORE INFORMATION

Citation

ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays.
Ortiz-Estevez M, Bengtsson H, Rubio A.
Bioinformatics. 2010 Aug 1;26(15):1827-33. doi: 10.1093/bioinformatics/btq300

Estimation and assessment of raw copy numbers at the single locus level.
Bengtsson H, Irizarry R, Carvalho B, Speed TP.
Bioinformatics. 2008 Mar 15;24(6):759-67. doi: 10.1093/bioinformatics/btn016.

BioUML 0.9.8 – Open Source Java Framework for Systems Biology

BioUML 0.9.8

:: DESCRIPTION

BioUML is open source integrated Java platform for building virtual cell and virtual physiological human. It spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts (R, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data.

::DEVELOPER

BioUML Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

 BioUML

:: MORE INFORMATION

Citation

Adv Exp Med Biol. 2012;736:235-45. doi: 10.1007/978-1-4419-7210-1_13.
A modular model of the apoptosis machinery.
Kutumova EO1, Kiselev IN, Sharipov RN, Lavrik IN, Kolpakov FA.

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, Golm, Germany.

:: 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

BioBlender

:: 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