MetaReg – Graphical Interface for Modeling and Evaluation of Biological Systems

MetaReg.

:: DESCRIPTION

MetaReg is a Java application aimed to provide the biologist with an intuitive graphical interface for both definition and analysis of system models. The application makes it possible to navigate the model network and compare its predicted and observed behavior.

::DEVELOPER

Prof. Ron Shamir’s Computational Genomics Group at Tel Aviv University.

:: SCREENSHOTS

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 MetaReg

:: MORE INFORMATION

Citation

I. Gat-Viks and R. Shamir.
MetaReg application: a graphical interface for modeling and evaluation of biological systems.
Genome Biology (2008) Vol. 9 No. R1

Spartan 3.0.2 – Understanding Uncertainty in Simulations of Biological Systems

Spartan 3.0.2

:: DESCRIPTION

Successful integration of computer simulation with wet-lab research requires the relationship between simulation and the real-world system to be established. Spartan (Simulation Parameter Analysis RToolkit ApplicatioN) is a package of statistical techniques specifically designed to help researchers understand this relationship and provide novel biological insight.

::DEVELOPER

Kieran Alden

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R

:: DOWNLOAD

Spartan

 :: MORE INFORMATION

Citation:

PLoS Comput Biol. 2013;9(2):e1002916. doi: 10.1371/journal.pcbi.1002916. Epub 2013 Feb 28.
Spartan: a comprehensive tool for understanding uncertainty in simulations of biological systems.
Alden K1, Read M, Timmis J, Andrews PS, Veiga-Fernandes H, Coles M.

mlegp 3.1.4 – Statistical Analysis for Computer Models of Biological Systems

mlegp 3.1.4

:: DESCRIPTION

 mlegp (Maximum Likelihood Estimates of Gaussian Processes) is an R package to analyze computer models of complex systems.

::DEVELOPER

Bioinformatics Laboratory at Eastern Connecticut State University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows / MacOsX
  • R Package

:: DOWNLOAD

 mlegp

:: MORE INFORMATION

Citation

Dancik GM, Dorman KS (2007)
mlegp: statistical analysis for computer models of biological systems using R.
Bioinformatics (2008) 24 (17): 1966-1967.

BOSS – Predicting Biological System Objectives de novo from internal State Measurements

BOSS

:: DESCRIPTION

BOSS (Biological Objective Solution Search) is a novel method for the inference of an objective function of a biological system from its underlying network stoichiometry as well as experimentally-measured state variables.

::DEVELOPER

the Computational Systems Biology Laboratory, Department of Biomedical Engineering, University of Virginia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • GAMS

:: DOWNLOAD

 BOSS

:: MORE INFORMATION

Citation:

Gianchandani, E.P., M.A. Oberhardt, A.P. Burgard, C.D. Maranas, and J.A. Papin. 2008.
Predicting biological system objectives de novo from internal state measurements.
BMC Bioinformatics, 9:43

Waldo – Modeling and Simulating Biological Systems

Waldo

:: DESCRIPTION

Waldo is a reaction-based tool for easily modeling and simulating biological systems

::DEVELOPER

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

:: SCREENSHOTS

Waldo

:: REQUIREMENTS

  • Windows
  • .Net Framework

:: DOWNLOAD

 Waldo

:: MORE INFORMATION

KInfer – Calibration of Dynamic Models of Biological Systems

KInfer

:: DESCRIPTION

KInfer generates a generalized mass action model from the chemical equations of reactions and an estimation of the structural parameters of these reactions

::DEVELOPER

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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • JRE

:: DOWNLOAD

 KInfer

:: MORE INFORMATION

Citation

Eur Biophys J. 2010 May;39(6):1019-39. doi: 10.1007/s00249-009-0520-3. Epub 2009 Aug 11.
Calibration of dynamic models of biological systems with KInfer.
Lecca P1, Palmisano A, Ihekwaba A, Priami C.

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.

MetaPlab 1.3 / MP-GeneticSynth – Virtual laboratory for Biological Systems

MetaPlab 1.3 / MP-GeneticSynth

:: DESCRIPTION

MetaPlab is a virtual laboratory which aims at assisting modellers both to understand the internal mechanisms of biological systems and to forecast, in silico, their response to external stimuli, environmental condition alterations or structural changes. MetaPlab framework is based on a core module which enables to design and manage biological models, and an extensible set of plugins by which MP models can be generated, optimized, simulated and analysed.

MP-GeneticSynth is a Java tool for discovering the logic and regulation mechanisms responsible for observed biological dynamics in terms of finite difference recurrent equations.

::DEVELOPER

MetaPlab team

:: SCREENSHOTS

MetaPlab

::REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 MetaPlab

:: MORE INFORMATION

Citation

MP-GeneticSynth: Inferring Biological Network Regulations from Time Series.
Castellini A, Paltrinieri D, Manca V.
Bioinformatics. 2014 Oct 24. pii: btu694

Castellini A, Manca V. (2008)
MetaPlab: A Computational Framework for Metabolic P Systems.
Pre-proceedings of Workshop on membrane computing, 9th International Workshop, WMC 2008, Edinburgh, Scotland, 2008.

Tav4SB 0.2.2 – Web service operations for analysis of the Kinetic models of Biological Systems

Tav4SB 0.2.2

:: DESCRIPTION

The Tav4SB (Taverna services for Systems Biology) project is a simple grid environment providing a set of Web service (WS) operations, together with bundling them workflows, prepared for the Taverna Workbench. Target application area is the System Biology field, in particular, analysis of kinetic models of biological systems.

::DEVELOPER

CompBio@MIMUW

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java
  • Taverna

:: DOWNLOAD

 Tav4SB

:: MORE INFORMATION

Citation

BMC Syst Biol. 2012 Apr 5;6:25. doi: 10.1186/1752-0509-6-25.
Tav4SB: integrating tools for analysis of kinetic models of biological systems.
Rybiński M, Lula M, Banasik P, Lasota S, Gambin A.