TIGER 1.2.0-beta – Toolbox for Integrating Genome-scale metabolism, Expression, and Regulation

TIGER 1.2.0-beta

:: DESCRIPTION

TIGER is a software platform for building and analyzing genome-scale models of metabolism. TIGER provides methods for combining gene-protein-reaction associations, transcriptional regulation, and other biological constraints into a single mixed-integer linear programming (MILP) framework.

::DEVELOPER

the Computational Systems Biology Laboratory, Department of Biomedical Engineering, University of Virginia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab
:: DOWNLOAD

 TIGER

:: MORE INFORMATION

Citation

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks.
Jensen PA, Lutz KA, Papin JA.
BMC Syst Biol. 2011 Sep 23;5:147. doi: 10.1186/1752-0509-5-147.

PGEToolbox 3.0 – Matlab Toolbox for Population Genetics and Evolution

PGEToolbox 3.0

:: DESCRIPTION

PGEToolbox is a Matlab-based software package for analysis of polymorphism and divergence data for population genetics and evolution. It estimates several basic statistics of DNA sequence variation and carries out statistical tests of selective neutrality under the infinite alleles model, such as Tajima’s D test, Fu & Li’s tests and Fay & Wu’s H test. The significance of tests is determined from the distribution of the statistics obtained by coalescent simulation. The toolbox performs McDonald-Kreitman test (and several extensions). PGEToolbox also contains functions for handling SNP (Single Nucleotide Polymorphism) genotype data. PGEToolbox is open-sourced, can be easily extended or tailored for specific tasks, and scaled up for large data sets.

::DEVELOPER

Cai Laborary

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  PGEToolbox

:: MORE INFORMATION

Citation:

Cai JJ (2008)
PGEToolbox: A Matlab toolbox for population genetics and evolution
Journal of Heredity Jul-Aug;99(4):438-40. doi:10.1093/jhered/esm127

FAST 1.7 – FAST Analysis of Sequences Toolbox

FAST 1.7

:: DESCRIPTION

FAST ,built on BioPerl, provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data.

::DEVELOPER

Travis Lawrence

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl
  • BioPerl

:: DOWNLOAD

 FAST

:: MORE INFORMATION

Citation

FAST: FAST Analysis of Sequences Toolbox.
Lawrence TJ, Kauffman KT, Amrine KC, Carper DL, Lee RS, Becich PJ, Canales CJ, Ardell DH.
Front Genet. 2015 May 19;6:172. doi: 10.3389/fgene.2015.00172. eCollection 2015.

MolQuest 2.4.5 – Bioinformatics Toolbox for Analysis of Biomedical Data

MolQuest 2.4.5

:: DESCRIPTION

MolQuest is the most comprehensive, easy-to-use desktop application for sequence analysis and molecular biology data management.Each package provides an user-friendly interface for primer design, internet database searches, gene prediction, promoter identification, regulatory elements mapping, patterns discovery protein analysis, multiple sequences alignment, phylogenetic reconstruction, and a wide variety of other functions.

::DEVELOPER

Softberry, Inc

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MolQuest

:: MORE INFORMATION

ParTIES – PARamecium Toolbox for Interspersed DNA Elimination Studies

ParTIES

:: DESCRIPTION

ParTIES was designed for Paramecium species, that (i) identifies eliminated sequences, (ii) measures their presence in a sequencing sample and (iii) detects rare elimination polymorphisms.

::DEVELOPER

ParTIES team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 ParTIES

:: MORE INFORMATION

Citation

ParTIES : a toolbox for Paramecium interspersed DNA elimination studies.
Denby Wilkes C, Arnaiz O, Sperling L.
Bioinformatics. 2015 Nov 20. pii: btv691.

compdiagTools 1.8.8 – A Toolbox for Microarray Analysis

compdiagTools 1.8.8

:: DESCRIPTION

compdiagTools is an R package containing tools for analysis and illustration of microarray experiments.

::DEVELOPER

Institute of Functional Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • R

:: DOWNLOAD

 compdiagTools

:: MORE INFORMATION

Citation

A toolbox for performing and illustrating microarray data analyses – user’s guide to the R package compdiagTools
Scheid S, Jäger J and Lottaz C
CompDiag Technical Report Nr. 2005/01 Mar. 2005

DOTcvpSB 2010_E4 – Matlab Toolbox for Dynamic Optimization in Systems Biology

DOTcvpSB 2010_E4

:: DESCRIPTION

DOTcvpSB is a software toolbox which uses the CVP approach for handling continuous and mixed integer DO problems. DOTcvpSB has been successfully applied to several problems in systems biology and bioprocess engineering. The toolbox is written in MATLAB and provides an easy to use environment while maintaining a quite good performance. DOTcvpSB is designed for the Windows operating systems. The toolbox also contains a function for importing SBML models.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

 DOTcvpSB

:: MORE INFORMATION

Citation:

T. Hirmajer, E. Balsa-Canto and J. R. Banga:
DOTcvpSB, a software toolbox for dynamic optimization in systems biology.
BMC Bioinformatics 2009, 10:199

SBEToolbox 1.3.2 – MATLAB Systems Biology & Evolution Toolbox

SBEToolbox 1.3.2

:: DESCRIPTION

SBEToolbox (Systems Biology and Evolution Toolbox) is being developed in MATLAB as a menu-driven GUI software to determine various statistics of the biological network. Some of its features include (but not limited to) algorithms to create random networks (small-world, ring lattice etc..), deduce clusters in the network (MCL, mCode, clusterOne), compute various network topology measures etc…

::DEVELOPER

Cai Laborary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SBEToolbox

:: MORE INFORMATION

Citation

Evol Bioinform Online. 2013 Sep 1;9:355-62. doi: 10.4137/EBO.S12012. eCollection 2013.
SBEToolbox: A Matlab Toolbox for Biological Network Analysis.
Konganti K1, Wang G, Yang E, Cai JJ.

PATBox – P-Type ATPase Toolbox

PATBox

:: DESCRIPTION

The PATBox is a resource for researchers in the field of P-Type ATPases which aims to aid researchers by giving them access to easy-to-use, efficient and up-to-date computational tools for the prediction of the subtype of P-Type ATPase sequences.

::DEVELOPER

Bioinformatics Research Centre (BiRC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2015 Sep 30;10(9):e0139571. doi: 10.1371/journal.pone.0139571. eCollection 2015.
PATBox: A Toolbox for Classification and Analysis of P-Type ATPases.
Søndergaard D, Pedersen CN.

irootlab 20150223 – MATLAB toolbox for Vibrational Spectroscopy

irootlab 20150223

:: DESCRIPTION

IRootLab is an open-source project dedicated to providing a MATLAB framework for vibrational spectroscopy. The goal of the project is to provide a comprehensive and user-friendly environment for analysis, whilst facilitating development and validation of algorithms for computational biology using vibrational spectroscopy.

::DEVELOPER

Lancaster Centre for Biophotonics Information

:: SCREENSHOTS

irootlab

:: REQUIREMENTS

  • Linux /  MacOsX / Window
  • matlab

:: DOWNLOAD

 irootlab

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Apr 15;29(8):1095-7. doi: 10.1093/bioinformatics/btt084. Epub 2013 Feb 19.
IRootLab: a free and open-source MATLAB toolbox for vibrational biospectroscopy data analysis.
Trevisan J, Angelov PP, Scott AD, Carmichael PL, Martin FL.