Model Editor

PNK 2e

The PNK (Petri Net Kernel) 2e is a software environment for the modeling and simulation of biological processes. It was developed as part of a M.Sc. project at the University of Edinburgh, UK. The software uses Stochastic Petri Nets (SPNs), a graphical representation of Markov Jump Processes.

http://page.mi.fu-berlin.de/%7Etrieglaf/PNK2e/index.html

posted 2006.04.25

CellDesigner

CellDesigner is a software suite for systems biology which enables grpahical editing of biological networks, simulation. It comply with SBML and SBGN, and can connect to SBW to utlize analysis packages.

http://celldesigner.org/

posted 2006.04.25

NetBuilder

NetBuilder is an interactive graphical tool for representing and simulating genetic regulatory networks in multicellular organisms. Developed by Maria Schilstra, Mark Robinson, and Chrystopher Nehaniv at University of Hartfordshare. SBML Compliant and SBW Enabled.

http://strc.herts.ac.uk/bio/maria/NetBuilder/

posted 2006.04.25

CADLIVE

CADLIVE is a system for constructing large-scale biological networks (metabolic and gene regulatory networks) using GUI (Graphic User Interface) and saving them as regulator reaction equations in a database in the format compatible to a simulator. It has been developed by H. Kurata at the Kyushu Institute of Technology together with staffs at Mitsui Knowledge Industry Co., Ltd.

http://kurata21.bse.kyutech.ac.jp/cadlive/

posted 2006.04.25

Bio Sketch Pad

Bio sketch Pad is an interactive tool for modeling and designing biomolecular and cellular networks with a simple, easy-to-use, graphical front end, leveraging powerful tools from control theory, hybrid systems, and software engineering.

http://www.cis.upenn.edu/biocomp/new_html/biosketch.php3

posted 2006.04.25

BioTapestry

BioTapestry is an interactive tool for building, visualizing, and simulating genetic regulatory networks. It is designed around the concept of a developmental network model, and is intended to deal with large scale models with consistency and clarity. It is capable of representing systems that exhibit increasing complexity over time, such as the genetic regulatory network controlling endomesoderm development in sea urchin embryos.
BioTapestry

posted 2006.04.25

BioUML

BioUML is Java framework for systems biology. 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 and simulations.

http://www.biouml.org/

posted 2006.04.25