BaMFA – Bayesian Metabolic Flux Analysis

BaMFA

:: DESCRIPTION

BaMFA is a matlab package of Bayesian metabolic flux analysis that models the reactions of the whole genome-scale cellular system in probabilistic terms, and can infer the full flux vector distribution of genome-scale metabolic systems based on exchange and intracellular (e.g. 13C) flux measurements, steady-state assumptions, and objective function assumptions.

::DEVELOPER

Computational systems biology group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

BaMFA

:: MORE INFORMATION

Citation

Bioinformatics, 35 (14), i548-i557 2019 Jul 15
Bayesian Metabolic Flux Analysis Reveals Intracellular Flux Couplings
Markus Heinonen et al.

MultiTF-PPI – Competitive Transcription Factor Binding Prediction

MultiTF-PPI

:: DESCRIPTION

MultiTF-PPI is a probabilistic protein-protein interaction guided method for competitive transcription factor binding prediction.

::DEVELOPER

Computational systems biology group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Matlab

:: DOWNLOAD

MultiTF-PPI

:: MORE INFORMATION

Sorad 20130721 – Infer and Analyze Dynamic Signaling Pathways

Sorad 20130721

:: DESCRIPTION

Sorad is a systems biology approach to predict and modulate dynamic signaling pathway response from phosphoproteome time-course measurements

::DEVELOPER

Computational systems biology group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

 Sorad

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 15;29(10):1283-91. doi: 10.1093/bioinformatics/btt130. Epub 2013 Mar 16.
Sorad: a systems biology approach to predict and modulate dynamic signaling pathway response from phosphoproteome time-course measurements.
Äijö T, Granberg K, Lähdesmäki H.

LIGAP 20130505 – Identify Condition/Lineage Specific Time-course Profiles

LIGAP 20130505

:: DESCRIPTION

LIGAP allows integrative analysis and visualization of multiple lineages over whole time-course profiles.

::DEVELOPER

Computational systems biology group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

 LIGAP

:: MORE INFORMATION

Citation

BMC Genomics. 2012 Oct 30;13:572. doi: 10.1186/1471-2164-13-572.
An integrative computational systems biology approach identifies differentially regulated dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation.
Aijö T, Edelman SM, Lönnberg T, Larjo A, Kallionpää H, Tuomela S, Engström E, Lahesmaa R, Lähdesmäki H.

CHRONOS 1.14.0 – microRNA-mediated sub-pathway Enrichment Analysis

CHRONOS 1.14.0

:: DESCRIPTION

CHRONOS (time-vaRying enriCHment integrOmics Subpathway aNalysis tOol) is an R package by integrating time-series mRNA/microRNA expression data with KEGG pathway maps and microRNA-target interactions.

::DEVELOPER

the Biosignal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 CHRONOS

:: MORE INFORMATION

Citation

CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis.
Vrahatis AG, Dimitrakopoulou K, Balomenos P, Tsakalidis AK, Bezerianos A.
Bioinformatics. 2015 Nov 14. pii: btv673

IMPaLA 9 – Integrated Molecular Pathway Level Analysis

IMPaLA 9

:: DESCRIPTION

IMPaLA is a web tool for the joint pathway analysis of transcriptomics or proteomics and metabolomics data.

::DEVELOPER

IMPaLA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Oct 15;27(20):2917-8. doi: 10.1093/bioinformatics/btr499. Epub 2011 Sep 4.
Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA.
Kamburov A1, Cavill R, Ebbels TM, Herwig R, Keun HC.

NASFinder – Identify Tissue-specific, Omics-determined Sub-networks

NASFinder

:: DESCRIPTION

The NASFinder (Network Activity Score Finder) is a web service for topological and functional analysis of sub-networks connecting an omics-determined module.

::DEVELOPER

The Microsoft Research – University of Trento Centre for Computational and Systems Biology

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • JRE

:: DOWNLOAD

NASFinder

:: MORE INFORMATION

Citation

Sci Rep, 6, 28851 2016 Jul 7
Systems View of Adipogenesis via Novel Omics-Driven and Tissue-Specific Activity Scoring of Network Functional Modules
Isar Nassiri et. al.

HSimulator 1.0 – Multithread Hybrid stochastic/deterministic simulation of Biochemical Reaction Networks

HSimulator 1.0

:: DESCRIPTION

HSimulator is an optimized, multithread Java simulator compatible with Java 6.0 or higher versions. The simulator works both in terminal and in a graphical environment thanks to an ad hoc GUI.

::DEVELOPER

The Microsoft Research – University of Trento Centre for Computational and Systems Biology

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • JRE

:: DOWNLOAD

HSimulator

:: MORE INFORMATION

Citation

L. Marchetti, R. Lombardo, C. Priami.
HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks, Complexity, Volume 2017, Article ID 1232868, DOI: 10.1155/2017/1232868, 2017.

BetaWB – Study Dynamics of Biological Systems

BetaWB

:: DESCRIPTION

BetaWB (Beta Workbench) builds molecular and scalable models as well as manages complexity and the combinatorial explosions of models

::DEVELOPER

The Microsoft Research – University of Trento Centre for Computational and Systems Biology

:: SCREENSHOTS

BetaWB

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BetaWB

:: MORE INFORMATION

Citation

The Beta Workbench: a computational tool to study the dynamics of biological systems.
Dematté L, Priami C, Romanel A.
Brief Bioinform. 2008 Sep;9(5):437-49. doi: 10.1093/bib/bbn023. Epub 2008 May 7.

Graph 1.0 – Constructs, Visualizes and Modifies Graphs

Graph 1.0

:: DESCRIPTION

Graph constructs, visualizes and modifies graphs as well as calculates measures and layouts

::DEVELOPER

The Microsoft Research – University of Trento Centre for Computational and Systems Biology

:: SCREENSHOTS

Graph

:: REQUIREMENTS

  • Windows
  • .NET Framework

:: DOWNLOAD

 Graph

:: MORE INFORMATION

Citation

Roberto Valentini, Ferenc Jordan.
COSBILab Graph: the network analysis module of COSBILab Environmental Modelling and Software, 25:886-888, 2010