CONTOUR v2 – Cancer (Onco) geNes from disrupTed mOdUles and their Relationships

CONTOUR v2

:: DESCRIPTION

CONTOUR is a systematic tracking of dysregulated modules identifies novel genes in cancer

::DEVELOPER

CONTOUR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C/C++ Compiler

:: DOWNLOAD

 CONTOUR

:: MORE INFORMATION

Citation

Srihari S & Ragan MA (2013)
Systematic tracking of dysregulated modules identifies novel genes in cancer,
Bioinformatics 29(12):1553–1561. doi: 10.1093/bioinformatics/btt191

PathBuilder 1.0 – open source Software for Annotating and Developing Pathway Resources

PathBuilder 1.0

:: DESCRIPTION

PathBuilder is an open source software to annotate biological information pertaining to signaling pathways and, with minimal additional effort, to create web-based pathway resources. PathBuilder enables annotation of molecular events including protein-protein interactions, enzyme-substrate relationships and protein translocation events via manual or automatic methods.

::DEVELOPER

The Pandey Lab

:: SCREENSHOTS

PathBuilder

:: REQUIREMENTS

  • Linux / MacOsX /Windows
  • Zope
  • MySQL
  • Python

:: DOWNLOAD

   PathBuilder

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Nov 1;25(21):2860-2. doi: 10.1093/bioinformatics/btp453.
PathBuilder–open source software for annotating and developing pathway resources.
Kandasamy K, Keerthikumar S, Raju R, Keshava Prasad TS, Ramachandra YL, Mohan S, Pandey A.

LibSBMLSim 1.4.0 – The library for Simulating SBML models

LibSBMLSim 1.4.0

:: DESCRIPTION

LibSBMLSim is a library for simulating an SBML model which contains Ordinary Differential Equations (ODEs). LibSBMLSim provides simple command-line tool and several APIs to load an SBML model, perform numerical integration (simulate) and export its results. Both explicit and implicit methods are supported on libSBMLSim.

::DEVELOPER

Funahashi Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 LibSBMLSim

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1474-6. doi: 10.1093/bioinformatics/btt157.
LibSBMLSim: A reference implementation of fully functional SBML simulator.
Takizawa H, Nakamura K, Tabira A, Chikahara Y, Matsui T, Hiroi N, Funahashi A.

SBEToolbox 1.3.3 – MATLAB Systems Biology & Evolution Toolbox

SBEToolbox 1.3.3

:: 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.

CNApy 1.0.6 – Integrated Environment for Metabolic Network analysis

CNApy 1.0.6

:: DESCRIPTION

CNApy is an open source cross-platform desktop application written in Python, which offers a state-of-the-art graphical front-end for the intuitive analysis of metabolic networks with COBRA methods.

::DEVELOPER

CNApy Organization

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

CNApy

:: MORE INFORMATION

Citation:

Thiele S, von Kamp A, Bekiaris PS, Schneider P, Klamt S.
CNApy: a CellNetAnalyzer GUI in Python for Analyzing and Designing Metabolic Networks.
Bioinformatics. 2021 Dec 8:btab828. doi: 10.1093/bioinformatics/btab828. Epub ahead of print. PMID: 34878104.

OCSANA – Optimal Combinations of Interventions from Network Analysis

OCSANA

:: DESCRIPTION

OCSANA is a new software designed to identify and prioritize optimal and minimal combinations of interventions to disrupt the paths between source nodes and target nodes

::DEVELOPER

U900 Institut Curie – INSERM/Mines ParisTech “Bioinformatics and Computational Systems Biology of Cancer

:: SCREENSHOTS

OCSANA

:: REQUIREMENTS

:: DOWNLOAD

 OCSANA

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 15;29(12):1571-3. doi: 10.1093/bioinformatics/btt195. Epub 2013 Apr 26.
OCSANA: optimal combinations of interventions from network analysis.
Vera-Licona P, Bonnet E, Barillot E, Zinovyev A.

DISTILLER 2.0 – Data Integration System To Identify Links in Expression Regulation

DISTILLER 2.0

:: DESCRIPTION

DISTILLER (Data Integration System To Identify Links in Expression Regulation) is a data integration framework that searches for transcriptional modules by combining expression data with information on the direct interaction between a regulator and its corresponding target genes. The framework builds upon advanced itemset mining approaches that have been designed to have good scalability, efficient memory use, and a small number of user parameters. It includes a condition selection or bicluster strategy in which co-expression of genes is required in only a significant subset of the complete condition set. By including this condition selection we can apply the algorithm to large expression compendia where interesting genes are not necessarily co-expressed in all measured conditions. Our approach also makes it straightforward to include any number of data sources related to transcriptional interactions such as additional microarrays, ChIP-chip or motif data.

::DEVELOPER

Kathleen Marchal 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
:: DOWNLOAD

 DISTILLER

:: MORE INFORMATION

Citation

Lemmens K, De Bie T, Dhollander T, De Keersmaecker SC, Thijs IM, Schoofs G, De Weerdt A, De Moor B, Vanderleyden J, Collado-Vides J, Engelen K, Marchal K.
DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli“.
Genome Biology , 10:R27 doi:10.1186/gb-2009-10-3-r27 (2009).

SynTReN 1.2 – Generator of Synthetic Gene Expression data for Design and Analysis of Structure Learning algorithms

SynTReN 1.2

:: DESCRIPTION

Syntren  (Synthetic Transcriptional Regulatory Networks) is a network generator that creates synthetic transcriptional regulatory networks and produces simulated gene expression data that approximates experimental data. Network topologies are generated by selecting subnetworks from previously described regulatory networks. Interaction kinetics are modeled by equations based on Michaelis-Menten and Hill kinetics. Our results show that the statistical properties of these topologies more closely approximate those of genuine biological networks than do those of different types of random graph models. Several user-definable parameters adjust the complexity of the resulting data set with respect to the structure learning algorithms.

::DEVELOPER

Kathleen Marchal 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
:: DOWNLOAD

  Syntren

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Jan 26;7:43.
SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms.
Van den Bulcke T, Van Leemput K, Naudts B, van Remortel P, Ma H, Verschoren A, De Moor B, Marchal K.

go2ppi 1.06 – Prediction of Protein-protein Interactions

go2ppi 1.06

:: DESCRIPTION

go2ppi is a predictor for protein-protein interactions (PPI) based on Gene Ontology (GO) annotations.

::DEVELOPER

go2ppi team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

  go2ppi

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jan 1;28(1):69-75. doi: 10.1093/bioinformatics/btr610.
Gene Ontology-driven inference of protein-protein interactions using inducers.
Maetschke SR, Simonsen M, Davis MJ, Ragan MA.