UGENE 33.0 – Integrated Bioinformatics Tools

UGENE 33.0

:: DESCRIPTION

UGENE is a visual environment for biomolecular research, integrating ever-growing set of bioinformatics algorithms.

::DEVELOPER

UniPro

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

 UGENE 

:: MORE INFORMATION

Citation

Unipro UGENE: a unified bioinformatics toolkit.
Okonechnikov K, Golosova O, Fursov M; UGENE team.
Bioinformatics. 2012 Apr 15;28(8):1166-7. doi: 10.1093/bioinformatics/bts091. Epub 2012 Feb 24.

GENtle2 0.7.0 – Web-Based DNA Editor for Synthetic Biology

GENtle2 0.7.0

:: DESCRIPTION

GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more.

::DEVELOPER

Synbiota Inc.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

  GENtle

:: MORE INFORMATION

Biopieces 2.0 – Bioinformatic Framework of Tools

Biopieces 2.0

:: DESCRIPTION

The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services.

::DEVELOPER

Martin Asser Hansen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Biopieces

:: MORE INFORMATION

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

NCBI C++ Toolkit 22.0 – Collection of C++ Modules for Bioinformatics

NCBI C++ Toolkit 22.0

:: DESCRIPTION

NCBI C++ Toolkit is a collection of C++ modules developed by the NCBI for writing bioinformatics software and applications. NCBI C++ Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI.

::DEVELOPER

NCBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

NCBI C++ Toolkit

:: MORE INFORMATION

Citation

The NCBI C++ Toolkit Book [Internet].
Vakatov D, editor.

BioMet Toolbox 2.0 – Genome-wide analysis of Metabolism and Omics data

BioMet Toolbox 2.0

:: DESCRIPTION

The BioMet ToolBox is a web-based resource for exploiting the capabilites of metabolic networks described in genome scale models using flux analysis and random sampling, powered by RAVEN, gene set analysis and basic microarray analysis using PIANO, thereby providing an integrated analysis to identify coregulated subnetwork structures within the metabolic network and also for identifying statistically significant gene sets enabling biological interpretation.

:: DEVELOPER

Systems & Synthetic Biology – SYSBIO, Chalmers University of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.
Garcia-Albornoz M, Thankaswamy-Kosalai S, Nilsson A, V?remo L, Nookaew I, Nielsen J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W175-81. doi: 10.1093/nar/gku371.

BioInfoServ 6.0 – Bioinformatic Platform

BioInfoServ 6.0

:: DESCRIPTION

The ideal Operation System, BioInfoServOS, which is a specially customised system for scientists handling and analysing biological data, but also for easy use of daily official business handing, has been distributed.

::DEVELOPER

BioInfoServ team

:: SCREENSHOTS

BioInfoServOS

:: REQUIREMENTS

  • DVD ROM

:: DOWNLOAD

  BioInfoServ

:: MORE INFORMATION

Staden 2.0.0b11 – DNA Sequence Assembly , Editing and Analysis

Staden 2.0.0b11

:: DESCRIPTION

Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) .

::DEVELOPER

Staden Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

Staden

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jul 15;26(14):1699-703. doi: 10.1093/bioinformatics/btq268. Epub 2010 May 30.
Gap5–editing the billion fragment sequence assembly.
Bonfield JK1, Whitwham A.

Rodger Staden, David P. Judge and James K. Bonfield.
Analysing Sequences Using the Staden Package and EMBOSS.
Introduction to Bioinformatics. A Theoretical and Practical Approach. Eds. Stephen A. Krawetz and David D. Womble. Human Press Inc., Totawa, NJ 07512 (2003)

Galaxy 18.09 – Evolutionary and Data Processing Module Development

Galaxy 18.09

:: DESCRIPTION

Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.

::DEVELOPER

Galaxy Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux
  • Python

:: DOWNLOAD

 Galaxy

:: MORE INFORMATION

Citation

Genome Res. 2009 Nov;19(11):2144-53. Epub 2009 Oct 9.
Windshield splatter analysis with the Galaxy metagenomic pipeline.
Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A; Galaxy Team.

BioLite 1.0.0 – Bioinformatics Framework with automated Tracking of Diagnostics and Provenance

BioLite 1.0.0

:: DESCRIPTION

BioLite is a bioinformatics framework written in Python/C++ that automates the collection and reporting of diagnostics, tracks provenance, and provides lightweight tools for building out customized analysis pipelines.

::DEVELOPER

The Dunn Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python/C++

:: DOWNLOAD

 BioLite

:: MORE INFORMATION

Citation

Howison M, Sinnott-Armstrong NA, Dunn CW. 2012.
BioLite, a lightweight bioinformatics framework with automated tracking of diagnostics and provenance.
In Proceedings of the 4th USENIX Workshop on the Theory and Practice of Provenance (TaPP ’12), 14-15 June 2012, Boston, MA, USA.