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

SBRT 2.0.0 – The Systems Biology Research Tool

SBRT 2.0.0

:: DESCRIPTION

SBRT (Systems Biology Research Tool) is a software to facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SBRT

:: MORE INFORMATION

Citation

The Systems Biology Research Tool: evolvable open-source software
Jeremiah Wright and Andreas Wagner
BMC Systems Biology 2008, 2:55

SYCAMORE 2016 – Systems Biology Computational Analysis and Modeling Research Environment

SYCAMORE 2016

:: DESCRIPTION

SYCAMORE is a system that provides you with a faciliated access to a number of tools and methods in order to build models of biochemical systems, view, analyse and refine them, as well as perform quick simulations.

::DEVELOPER

SYCAMORE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Jun 15;24(12):1463-4. doi: 10.1093/bioinformatics/btn207. Epub 2008 May 7.
SYCAMORE–a systems biology computational analysis and modeling research environment.
Weidemann A1, Richter S, Stein M, Sahle S, Gauges R, Gabdoulline R, Surovtsova I, Semmelrock N, Besson B, Rojas I, Wade R, Kummer U.

Lynx v3.0 – Integrated Systems Biology Platform

Lynx v3.0

:: DESCRIPTION

Lynx is a database and knowledge extraction engine for integrative medicine

::DEVELOPER

Somaye Hashemifar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

Sulakhe D, Xie B, Taylor A, D’Souza M, Balasubramanian S, Hashemifar S, White S, Dave UJ, Agam G, Xu J, Wang S, Gilliam TC, Maltsev N.
Lynx: a knowledge base and an analytical workbench for integrative medicine.
Nucleic Acids Res. 2016 Jan 4;44(D1):D882-7. doi: 10.1093/nar/gkv1257. Epub 2015 Nov 20. PMID: 26590263; PMCID: PMC4702889.

Edinburgh Pathway Editor 3.0a13 – Visual Editor for Systems Biology

Edinburgh Pathway Editor 3.0a13

:: DESCRIPTION

EPE (Edinburgh Pathway Editor) is a visual editor for Systems Biology. It allows you to draw Graphical Notations commonly used in Systems Biology. In particular it supports Systems Biology Graphical Notations (SBGN).

::DEVELOPER

SynthSys (formerly CSBE)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

Edinburgh Pathway Editor

:: MORE INFORMATION

Citation:

A. Sorokin, K. Paliy, A. Selkov, O. V. Demin, S. Dronov, P. Ghazal, I. Goryanin
The pathway editor: a tool for managing complex biological networks
IBM Journal of Research and Development , Nov. 2006 ,Volume: 50 Issue:6 ,p561 – 573

BioUML 0.9.10 – Open Source Java Framework for Systems Biology

BioUML 0.9.10

:: DESCRIPTION

BioUML is open source integrated Java platform for building virtual cell and virtual physiological human. It spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts (R, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data.

::DEVELOPER

BioUML Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

 BioUML

:: MORE INFORMATION

Citation

Adv Exp Med Biol. 2012;736:235-45. doi: 10.1007/978-1-4419-7210-1_13.
A modular model of the apoptosis machinery.
Kutumova EO1, Kiselev IN, Sharipov RN, Lavrik IN, Kolpakov FA.

SemanticSBML 2.0 – Annotation Checking& Merging of Systems Biology Models

SemanticSBML 2.0

:: DESCRIPTION

SemanticSBML create, check, annotate, merge SBML (System Biology Markup Lanugage) models. The program includes a graphical user interface as well as a console interface that can process batch jobs.

Semantic annotations can be used to define – among other things – the biochemical meaning of model elements. The tool semanticSBML is made to handle such annotations. It helps you to edit them and to check and merge your models.

::DEVELOPER

semanticSBML team at Humboldt University Berlin

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SemanticSBML

:: MORE INFORMATION

Citation

For citing semanticSBML, please refer to: Krause F, Uhlendorf J., Lubitz T., Schulz M., Klipp E., Liebermeister W. (2010),
Annotation and merging of SBML models with semanticSBML,
Bioinformatics 26 (3), 421-422, doi:10.1093/bioinformatics/btp642.

SBSI 1.4.5 – Systems Biology Software Infrastructure

SBSI 1.4.5

:: DESCRIPTION

SBSI (Systems Biology Software Infrastructure) is a suite of software applications and libraries with the following aims:

  • To provide access to parallelized algorithms for computationally challenging tasks such as parameter optimisation.
  • To enable registered users to run these algorithms on their models and data, using HPC machines.
  • To provide access for users with varying levels of computational modelling experience.

There are three main software components in SBSI: SBSINumerics, SBSIVisual and SBSIDispatcher.

SBSINumerics contains a configurable, parallelized command line application for running parameter estimations.

SBSIVisual is a desktop application, that provides easier access to SBSINumerics functionality for non-programmers, and can display results, run simulations, and interact with systems biology databases.

SBSIDispatcher is a middleware component, that can deploy and manage SBSINumerics procedures on backend servers.

::DEVELOPER

SBSI Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

SBSI

:: MORE INFORMATION

Citation

SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology.
Adams R, Clark A, Yamaguchi A, Hanlon N, Tsorman N, Ali S, Lebedeva G, Goltsov A, Sorokin A, Akman OE, Troein C, Millar AJ, Goryanin I, Gilmore S.
Bioinformatics. 2013 Mar 1;29(5):664-665. Epub 2013 Jan 17.

Morpheus 2.0 RC2 – Modeling Environment for Multiscale and Multicellular Systems Biology

Morpheus 2.0 RC2

:: DESCRIPTION

Morpheus is a modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. It allows rapid development of multiscale models in biological terms and mathematical expressions rather than programming code. Its graphical user interface supports the entire workflow from model construction and simulation to visualization, archiving and batch processing.

::DEVELOPER

IMC group

:: SCREENSHOTS

Morpheus

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 Morpheus 

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 1;30(9):1331-2. doi: 10.1093/bioinformatics/btt772. Epub 2014 Jan 17.
Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology.
Starruß J1, de Back W, Brusch L, Deutsch A.

3Omics – Web based Systems Biology Visualization tool

3Omics

:: DESCRIPTION

3Omics is a one-click web tool for visualizing and rapidly integrating multiple inter- or intra-transcriptomic, proteomic, and metabolomic human data.

::DEVELOPER

3Omics team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Syst Biol. 2013 Jul 23;7:64. doi: 10.1186/1752-0509-7-64.
3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data.
Kuo TC1, Tian TF, Tseng YJ.