JSim 2.21 – Simulation System for Building and Analyzing Quantitative Numeric Models

JSim 2.15

:: DESCRIPTION

JSim is a Java-based simulation system for building and analyzing quantitative numeric models. JSim’s primary focus has been in physiology and bio-medicine, however its computation engine is quite general and applicable to a wide range of scientific domains.

::DEVELOPER

the NSR Physiome Project!

:: SCREENSHOTS

:: REQUIREMENTS

Windows/ Linux / Mac OsX
JAVA

:: DOWNLOAD

JSim

:: MORE INFORMATION

Citation

JSim, an open-source modeling system for data analysis.
Butterworth E, Jardine BE, Raymond GM, Neal ML, Bassingthwaighte JB.
F1000Res. 2013 Dec 30;2:288. doi: 10.12688/f1000research.2-288.v1.

metano 1.3.0 – Analyzing the Capabilities of Metabolic Networks

metano 1.3.0

:: DESCRIPTION

metano is an open-source software toolbox for analyzing the capabilities of metabolic networks and for assisting in metabolic reconstruction.

::DEVELOPER

metano team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows / MacOsX
Python

:: DOWNLOAD

metano

:: MORE INFORMATION

Citation

Riemer SA, Rex R, Schomburg D.
A metabolite-centric view on flux distributions in genome-scale metabolic models.
BMC Syst Biol, 7:33 (2013).

MetaOmGraph 1.8.1 – Plotting and Analyzing large sets of Biological data

MetaOmGraph 1.8.1

:: DESCRIPTION

MetaOmGraph is a tool for plotting and analyzing large sets of data while using as little memory as possible. It was designed with biological experiment data in mind.

::DEVELOPER

Wurtele Lab

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

MetaOmGraph

:: MORE INFORMATION

Citation:

Chem Biodivers. 2012 May;9(5):868-87. doi: 10.1002/cbdv.201100355.
Massive human co-expression network and its medical applications.
Feng Y, Hurst J, Almeida-De-Macedo M, Chen X, Li L, Ransom N, Wurtele ES.

Comb-p 0.50.2 – Combining, Analyzing, Grouping and Correcting Spatially Correlated P-values

Comb-p 0.50.2

:: DESCRIPTION

comb-p is a command-line tool and a python library that manipulates BED files of possibly irregularly spaced P-values and (1) calculates auto-correlation, (2) combines adjacent P-values, (3) performs false discovery adjustment, (4) finds regions of enrichment (i.e. series of adjacent low P-values) and (5) assigns significance to those regions.

::DEVELOPER

Katerina Kechris , Brent Pedersen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux
Python

:: DOWNLOAD

Comb-p

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2986-8. doi: 10.1093/bioinformatics/bts545. Epub 2012 Sep 5.
Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values.
Pedersen BS1, Schwartz DA, Yang IV, Kechris KJ.

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.

MetATT – Metabolomics tool for Analyzing Two-factor and Time-series data

MetATT

:: DESCRIPTION

MetATT is a easy-to-use, web-based tool designed for time-series and two-factor metabolomics data analysis. MetATT offers a number of complementary approaches including 3D interactive principal component analysis, two-way heatmap visualization, two-way ANOVA, ANOVA-simultaneous component analysis and multivariate empirical Bayes time-series analysis.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Java
R package
Apache Tomcat 6.0 or Glassfish v2/v3.

:: DOWNLOAD

MetATT

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Sep 1;27(17):2455-6. doi: 10.1093/bioinformatics/btr392. Epub 2011 Jun 27.
MetATT: a web-based metabolomics tool for analyzing time-series and two-factor datasets.
Xia J, Sinelnikov IV, Wishart DS.

nucloc 1.06 – Analyzing Gene Positions in the Yeast Nucleus

nucloc 1.06

:: DESCRIPTION

nucloc is a set of computational tools designed to analyze gene positioning in yeast nuclei by automated processing of fluorescence microscopy images.

::DEVELOPER

Computational Imaging & Modeling Group, Institut Pasteur

:: SCREENSHOTS

:: REQUIREMENTS

Linux/Windows/MacOsX
Matlab

:: DOWNLOAD

nucloc

:: MORE INFORMATION

Citation:

Nat Methods. 2008 Dec;5(12):1031-7. doi: 10.1038/nmeth.1266. Epub 2008 Nov 2.
High-resolution statistical mapping reveals gene territories in live yeast.
Berger AB, Cabal GG, Fabre E, Duong T, Buc H, Nehrbass U, Olivo-Marin JC, Gadal O, Zimmer C.

RDNAanalyzer – Secondary Structure Pprediction and Analyzing DNA

RDNAanalyzer

:: DESCRIPTION

RDNAanalyzer is a computer based tool designed for analysis of nucleotide sequences in DNA and RNA.

::DEVELOPER

Muhammad Afzal @ CEMB

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

RDNAanalyzer

:: MORE INFORMATION

Citation

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.
Afzal M, Shahid AA, Shehzadi A, Nadeem S, Husnain T.
Bioinformation. 2012;8(14):687-90. doi: 10.6026/97320630008687. Epub 2012 Jul 21

MassSorter 3.1 – Administrating and Analyzing data from Mass Spectrometry experiments on Proteins

MassSorter 3.1

:: DESCRIPTION

MassSorter is a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences

::DEVELOPER

Harald Barsnes

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Java

:: DOWNLOAD

MassSorter

:: MORE INFORMATION

Citation

MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences
Harald Barsnes, Svein-Ole Mikalsen and Ingvar Eidhammer
BMC Bioinformatics 2006, 7:42