BioAnalyzer 2100 – Analysis of BioAnalyzer data

BioAnalyzer 2100

:: DESCRIPTION

The Agilent 2100 BioAnalyzer is a nanofluidics device that preforms size fractionation and quantification of small samples of DNA, RNA, or Protein. In addition, the BioAnalyzer is able to preform flow cytometry on small numbers of cells.

::DEVELOPER

the MIT BioMicro Center

:: SCREENSHOTS

BioAnalyzer

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BioAnalyzer

:: MORE INFORMATION

InteractoMIX – Exploit Interactomes in Biological and Clinical Research

InteractoMIX

:: DESCRIPTION

InteractoMIX is a suite of computational tools designed to exploit interactomics information at different levels ranging from genome-wide interactomes to their atomic 3D structural details.

::DEVELOPER

 Bioinformatics Lab :: IBERS :: Aberystwyth University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Biochem Soc Trans, 44 (3), 917-24 2016 Jun 15
InteractoMIX: A Suite of Computational Tools to Exploit Interactomes in Biological and Clinical Research
Daniel Poglayen et al.

Bioconda – Software Distribution for the Life Sciences

Bioconda

:: DESCRIPTION

Bioconda is a channel for the conda package manager specializing in bioinformatics software.

::DEVELOPER

Bioconda Team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

Bioconda

:: MORE INFORMATION

Citation

Nat Methods, 15 (7), 475-476 Jul 2018
Bioconda: Sustainable and Comprehensive Software Distribution for the Life Sciences
Bioconda Team

BIU 2.3.7 – Bioinformatic Utility Library

BIU 2.3.7

:: DESCRIPTION

BIU (Bioinformatic Utility Library) is a C++ programming library provides a classes and functions often used in the bioinformatics context. It collects data structures and class hierarchies for biomolecule modelling and general usefull functionalities as program parameter parsing, string conversions, etc.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BIU

:: MORE INFORMATION

GenePattern 3.9.11 – Genomic Analysis Platform

GenePattern 3.9.11

:: 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

:: 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

SEQ v0.9.4 – Language for Bioinformatics

SEQ v0.9.4

:: DESCRIPTION

SEQ is a programming language for computational genomics and bioinformatics. With a Python-compatible syntax and a host of domain-specific features and optimizations, Seq makes writing high-performance genomics software as easy as writing Python code, and achieves performance comparable to (and in many cases better than) C/C++.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

SEQ

:: MORE INFORMATION

Citation:

Ariya Shajii et al.
Seq: a high-performance language for bioinformatics
Proceedings of the ACM on Programming LanguagesOctober 2019 Article No.: 125 https://doi.org/10.1145/3360551

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

canEvolve – Integrative Cancer Genomics analysis of Expression, Copy Number, miRNAs and Network

canEvolve

:: DESCRIPTION

canEvolve query functionalities are designed to fulfill most frequent analysis needs of cancer researchers with a view to generate novel hypotheses. canEvolve stores gene, microRNA (miRNA) and protein expression profiles, copy number alterations for multiple cancer types, and protein-protein interaction information. canEvolve allows querying of results of primary analysis, integrative analysis and network analysis of oncogenomics data. The querying for primary analysis includes differential gene and miRNA expression as well as changes in gene copy number measured with SNP microarrays. At present canEvolve provides different types of information extracted from 90 cancer genomics studies comprising of more than 10,000 patients. The presence of multiple data types, novel integrative analysis for identifying regulators of oncogenesis, network analysis and ability to query gene lists/pathways are distinctive features of canEvolve. canEvolve will facilitate integrative and meta-analysis of oncogenomics datasets.

::DEVELOPER

CanEvolve Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

canEvolve: a web portal for integrative oncogenomics.
Samur MK, Yan Z, Wang X, Cao Q, Munshi NC, Li C, Shah PK.
PLoS One. 2013;8(2):e56228. doi: 10.1371/journal.pone.0056228.

KNOWENG – Knowledge Engine for Genomics

KNOWENG

:: DESCRIPTION

KnowEnG enables knowledge-guided machine learning and graph mining analysis on genomic datasets using scalable cloud computation and exploration of results with interactive visualizations.

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

KnowEnG: a knowledge engine for genomics.
Sinha S, Song J, Weinshilboum R, Jongeneel V, Han J.
J Am Med Inform Assoc. 2015 Nov;22(6):1115-9. doi: 10.1093/jamia/ocv090.

BioPig 2.0 – Hadoop-based analytic toolkit for large-scale Sequence data

BioPig 2.0

:: DESCRIPTION

BioPig is a framework for genomic data analysis using Apache Pig and Hadoop.

::DEVELOPER

Zhong Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • Apache’s Hadoop MapReduce system
  • Pig data flow language

:: DOWNLOAD

 BioPig

:: MORE INFORMATION

Citation

BioPig: a Hadoop-based analytic toolkit for large-scale sequence data.
Nordberg H, Bhatia K, Wang K, Wang Z.
Bioinformatics. 2013 Dec 1;29(23):3014-9. doi: 10.1093/bioinformatics/btt528.