Tag: Toolkit

TST 1.4.3 – Tissue Simulation Toolkit

TST 1.4.3

:: DESCRIPTION

TST is a two-dimensional library for the Cellular Potts Model (Graner and Glazier 1992; Phys. Rev. Lett. 69, 2013), which is increasingly used by computational biologists to study tissue patterning and developmental mechanisms.

::DEVELOPER

The Biomodeling and Biosystems Analysis Group

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  •  Linux
  • C++ Compiler

:: DOWNLOAD

 TST

:: MORE INFORMATION

Citation

R M H Merks, & J A Glazier. (2005).
A cell-centered approach to developmental biology.
Physica A, 352(1), 113–130. doi:10.1016/j.physa.2004.12.028.

DynaMIT 1.1.5 – Dynamic Motif Integration Toolkit

DynaMIT 1.1.5

:: DESCRIPTION

DynaMIT is a flexible platform for sequence and structure motifs integration, providing the means to execute multiple motif search tools, integrate their output and display the obtained results in a plethora of different ways.

::DEVELOPER

Laboratory of Translational Genomics , CIBIO

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 DynaMIT

:: MORE INFORMATION

Citation

DynaMIT: the dynamic motif integration toolkit.
Dassi E, Quattrone A.
Nucleic Acids Res. 2015 Aug 7. pii: gkv807

DistMap 1.0 – A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster

DistMap 1.0

:: DESCRIPTION

DistMap is a user-friendly pipeline designed to map short reads in a MapReduce framework on a local Hadoop cluster.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java
  • Perl
  • Mapper executable
  •  MergeSamFiles.jar and SortSam.jar from PICARD (http://picard.sourceforge.net).
  • A working Hadoop cluster.

:: DOWNLOAD

 DistMap

:: MORE INFORMATION

Citation:

Pandey RV, Schlötterer C. (2013)
DistMap: a toolkit for distributed short read mapping on a Hadoop cluster.
PLoS One. 8(8):e72614.

BAMTOOLS 2.5.1 – C++ API and Toolkit for Analyzing and Managing BAM files

BAMTOOLS 2.5.1

:: DESCRIPTION

BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files.

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 BAMTOOLS

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 15;27(12):1691-2. Epub 2011 Apr 14.
BamTools: a C++ API and toolkit for analyzing and managing BAM files.
Barnett DW, Garrison EK, Quinlan AR, , Strömberg MP, Marth GT.

ITEP 1.1 – Integrated Toolkit for Exploration of Pan-genomes

ITEP 1.1

:: DESCRIPTION

ITEP is a suite of scripts and Python libraries for the comparison of microbial genomes. It includes tools for de novo protein family prediction by clustering, ortholog detection, analysis of functional domains, identification of core and variable genes and gene regions, sequence alignments and tree generation, cluster curation, and the integration of cross-genome analysis and metabolic networks for study of metabolic network evolution.

::DEVELOPER

The Hood-Price Lab for Systems Biomedicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Python

:: DOWNLOAD

 ITEP

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jan 3;15:8. doi: 10.1186/1471-2164-15-8.
ITEP: an integrated toolkit for exploration of microbial pan-genomes.
Benedict MN, Henriksen JR, Metcalf WW, Whitaker RJ, Price ND1.

AnyExpress 1.0 – an integrated Toolkit for Cross-platform Gene Expression data

AnyExpress 1.0

:: DESCRIPTION

AnyExpress is a software package that combines cross-platform gene expression data using a fast interval-matching algorithm.

::DEVELOPER

AnyExpress team

:: SCREENSHOTS

AnyExpress

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

  AnyExpress

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Mar 17;12:75. doi: 10.1186/1471-2105-12-75.
AnyExpress: integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm.
Kim J1, Patel K, Jung H, Kuo WP, Ohno-Machado L.

MMTK 2.7.9 – The Molecular Modelling Toolkit

MMTK 2.7.9

:: DESCRIPTION

MMTK (The Molecular Modelling Toolkit) is an Open Source program library for molecular simulation applications. In addition to providing ready-to-use implementations of standard algorithms, MMTK serves as a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular simulations.

::DEVELOPER

Konrad Hinsen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Python

:: DOWNLOAD

 MMTK

:: MORE INFORMATION

Citation:

K Hinsen (2000)
The Molecular Modeling Toolkit: A New Approach to Molecular Simulations
J. Comp. Chem. 21:79-85.

ProSAT – PROtein reSidue Annotation Toolkit

ProSAT

:: DESCRIPTION

ProSAT toolkit is a set of programs that allow building SVM based models for annotating amino acid residues in protein sequences using user supplied features (like PSI-BLAST profiles, or PSIPred profiles). In particular, the toolkit builds features using a window around the residue, and is equipped with a specialized kernel function (normalized second order exponential kernel function nsoe ) along with the standard svm kernel function.

:: DEVELOPER

Professsor Huzefa Rangwala (rangwala@cs.gmu.edu) and  Professsor George Karypis

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

 ProSAT

:: MORE INFORMATION

Citation

“A kernel framework for protein residue annotation“.
Huzefa Rangwala, Christopher Kauffman and George Karypis.
Lecture Notes in Computer Science Volume 5476, 2009, pp 439-451

Mocapy++ 1.07 – Dynamic Bayesian Network toolkit

Mocapy++ 1.07

:: DESCRIPTION

Mocapy++ is a Dynamic Bayesian Network toolkit, implemented in C++. It supports discrete, multinomial, Gaussian, Kent, Von Mises and Poisson nodes. Inference and learning is done by Gibbs sampling/Stochastic-EM.

::DEVELOPER

The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Mocapy++

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 Mar 12;11:126. doi: 10.1186/1471-2105-11-126.
Mocapy++–a toolkit for inference and learning in dynamic Bayesian networks.
Paluszewski M, Hamelryck T.

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