Tag: toolbox

ACES – Machine Learning Toolbox for Clustering analysis and Visualization

ACES

:: DESCRIPTION

ACES is a machine learning toolbox for clustering analysis and visualization of both biological data and other types data. Given the biological data or their distance/probability matrix, ACES can automatically extract the features of each identity and cluster them by various widely used clustering algorithms.

::DEVELOPER

Grabherr Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

ACES

:: MORE INFORMATION

Citation

Gao J, Sundström G, Moghadam BT, Zamani N, Grabherr MG.
ACES: a machine learning toolbox for clustering analysis and visualization.
BMC Genomics. 2018 Dec 27;19(1):964. doi: 10.1186/s12864-018-5300-y. PMID: 30587115; PMCID: PMC6307290.

irootlab 0.17.8.22 – MATLAB toolbox for Vibrational Spectroscopy

irootlab 0.17.8.22

:: 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

irootlab team

:: 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.

compdiagTools 1.5.3 – A Toolbox for Microarray Analysis

compdiagTools 1.5.3

:: 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

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

RAVEN 2.5.1 – Reconstruction, Analysis, and Visualization of Metabolic Networks Toolbox

RAVEN 2.5.1

:: DESCRIPTION

The RAVEN Toolbox is a complete environment for reconstruction, analysis, simulation, and visualization of GEMs and runs within MATLAB.

:: DEVELOPER

Systems & Synthetic Biology – SYSBIO, Chalmers University of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Matlab
  • Excel

:: DOWNLOAD

 RAVEN

:: MORE INFORMATION

Citation

Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, Kerkhoven EJ.
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor.
PLoS Comput Biol. 2018 Oct 18;14(10):e1006541. doi: 10.1371/journal.pcbi.1006541. PMID: 30335785; PMCID: PMC6207324.

PLoS Comput Biol. 2013;9(3):e1002980. doi: 10.1371/journal.pcbi.1002980. Epub 2013 Mar 21.
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.
Agren R1, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J.

PlantMAT v1.0 – Plant Metabolite Annotation Toolbox

PlantMAT v1.0

:: DESCRIPTION

PlantMAT is a computational tool combining library search and combinatorial enumeration to facilitate the structural identification of plant specialized metabolites, e.g., saponins and flavonoid glycosides.

::DEVELOPER

Sumner Research Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Excel

:: DOWNLOAD

PlantMAT

:: MORE INFORMATION

Citation

Qiu F, Fine DD, Wherritt DJ, Lei Z, Sumner LW.
PlantMAT: A Metabolomics Tool for Predicting the Specialized Metabolic Potential of a System and for Large-Scale Metabolite Identifications.
Anal Chem. 2016 Dec 6;88(23):11373-11383. doi: 10.1021/acs.analchem.6b00906. Epub 2016 Nov 23. PMID: 27934098.

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.

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

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.

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.