mDraw 1.0 – Network Visualization Tool

UCSF structureViz is a Cytoscape plugin that links visualization of biological networks in Cytoscape with visualization and analysis of molecular structures in UCSF Chimera.

::DEVELOPER

the Resource for Biocomputing, Visualization, and Informatics (RBVI) at UCSF

:: SCREENSHOTS

:: REQUIREMENTS

Linux / MacOsX / Window
UCSF Chimera
Cytoscape

:: DOWNLOAD

structureViz

:: MORE INFORMATION

Citation:

Bioinformatics. 2007 Sep 1;23(17):2345-7. Epub 2007 Jul 10.
structureViz: linking Cytoscape and UCSF Chimera.
Morris JH1, Huang CC, Babbitt PC, Ferrin TE.

Cytoprophet 1.0 – A Cytoscape plug-in for Protein and Domain Interaction Networks Inference

Cytoprophet 1.0

:: DESCRIPTION

Cytoprophet is a project developed by the Laboratory for Computational Life Sciences at the Computer Science Department of the University of Notre Dame. It is a tool to help researchers to infer new potential protein (PPI) and domain (DDI) interactions. It is implemented as a Cytoscape plugin, where users input a set of proteins and retrieve a network of plausible protein and domain interactions with a score. Three algorithms are used for the estimation of PPI/DDI: Maximum Specificity Set Cover (MSSC) Approach, Maximum Likelihood Estimation (MLE) and the Sum-Product Algorithm (SPA) for protein networks.

::DEVELOPER

Cytoprophet team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java
Cytoscape

:: DOWNLOAD

Cytoprophet

:: MORE INFORMATION

Citation

Chengbang Huang , Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, and Jesús A. Izaguirre
Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol 4 pp. 78-87. Jan-March 2007

HEC 2.0.1 – Haploid Simulation of Bacterial Communities

HEC 2.0.1

:: DESCRIPTION

HEC (Haploid Evolutionary Constructor) is the tool for simulation of bacterial (more exactly prokaryotic) communities. It is based on the original modeling approach investigated in the Laboratory of molecular-genetic systems at the Institute of Cytology and Genetics (Novosibirsk, Russia).

::DEVELOPER

HEC Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux

:: DOWNLOAD

HEC

:: MORE INFORMATION

Citation:

Simulation of coevolution in community by using the “Evolutionary Constructor” program.
Lashin SA, Suslov VV, Kolchanov NA, Matushkin YG.
In Silico Biol. 2007;7(3):261-75.

KEGGParser 20140324 – Parsing and Editing KEGG Pathway Maps in Matlab

KEGGParser 20140324

:: DESCRIPTION

KEGGParser is a MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment.

::DEVELOPER

Arsen Arakelyan

:: SCREENSHOTS

::REQUIREMENTS

Linux/ Windows/MacOsX
MatLab

:: DOWNLOAD

KEGGParser

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):518-9. doi: 10.1093/bioinformatics/bts730. Epub 2013 Jan 3.
KEGGParser: parsing and editing KEGG pathway maps in Matlab.
Arakelyan A, Nersisyan L.

DatasetAssess – Estimate Error Rates in High-throughput Protein Interaction datasets

DatasetAssess

:: DESCRIPTION

DatasetAssess is a tool to estimate error rates in high-throughput protein interaction datasets and other functional genomic data.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

DatasetAssess

:: MORE INFORMATION

Citation:

Gilchrist, M.A., Salter, L.A., Wagner, A. (2004)
A statistical framework for combining and interpreting proteomic datasets.
Bioinformatics 20, 689-700

Glocal 1.1 – Robustness Analysis and Model Discrimination for Circadian Oscillators

Glocal 1.1

:: DESCRIPTION

Glocal was developed for a fast and optimized computation of the robustness of biological circuits such as those responsible for circadian cycles.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
Matlab

:: DOWNLOAD

Glocal

:: MORE INFORMATION

Citation:

Hafner, M., Koeppl, H., Hasler, M., Wagner, A.,(2009)
“Glocal” robustness analysis and model discrimination for circadian oscillators.
PloS Computational Biology 5(10): e1000534

HYPERSPACE – Exploring Parameter Spaces in Systems Biology

HYPERSPACE

:: DESCRIPTION

HYPERSPACE is a matlab package to sample high-dimensional parameter spaces in dynamical systems models of regulatory circuits in cell and developmental biology.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
Matlab

:: DOWNLOAD

HYPERSPACE

:: MORE INFORMATION

Citation:

Zamora-Sillero, E., Hafner, M., Ibig, A., Stelling, J., Wagner, A.
Efficient characterization of high-dimensional parameter spaces for systems biology.
BMC Systems Biology 2011, 5:142 doi:10.1186/1752-0509-5-142

FASIMU 2.3.4 – Flux-balance Analysis based SIMUlations

FASIMU 2.3.4

:: DESCRIPTION

FASIMU (Flux-balance Analysis based SIMUlations)is a command line oriented software implementing the most frequently applied FBA(Flux-balance Analysis) algorithms. Moreover, it offers the first freely available implementation of (i) weighted flux minimization, (ii) fitness maximization for partially inhibited enzymes, and (iii) the concentration-based thermodynamic feasibility constraint. It allows heterogenous computation series suited for network pruning, leak analysis, FVA, and systematic probing of metabolic objectives for network curation controlled by an intuitive description file. The metabolic network can be supplied in SBML, CellNetAnalyzer, and plain text format. FASIMU uses the optimization capabilities of free (lp solve and GLPK) and commercial solvers (CPLEX, LINDO). The results can be visualized in Cytoscape or BiNA using newly developed plugins.

::DEVELOPER

Andreas Hoppe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
CPLEX and BiNA
Java

:: DOWNLOAD

FASIMU

:: MORE INFORMATION

Citation

FASIMU: flexible software for flux-balance computation series in large metabolic networks
Andreas Hoppe , Sabrina Hoffmann , Andreas Gerasch , Christoph Gille and Hermann-Georg Holzhütter
BMC Bioinformatics 2011, 12:28