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Model Editor

PhysioDesigner 1.1 released

http://physiodesigner.org


PhysioDesigner is an open platform that supports multilevel modeling of physiological systems in the field of integrated life sciences and systems biology, including physiology and neuroscience. Users can combine and build mathematical models of biological and physiological functions on PhysioDesigner. Users can also integrate morphometric data on a model, which is used, for example, to define a domain in which partial differential equations are solved.

The models developed by PhysioDesigner are stored in PHML (Physiological Hierarchy Markup Language) format, which is an XML-based specification, to describe a wide variety of models of biological and physiological functions with a hierarchical structure. PHML fully inherits the specifications from 
insilicoML (ISML). PhysioDesigner can act as an editor and browser of the models written in PHML and ISML. It is also possible to import models written in CellML format and export models to CellML (some model expressions in PHML cannot be exported to CellML).

Another distinguishing feature of PhysioDesigner is that it provides a user function to create SBML-PHML hybrid models, which is a novel way to create multilevel physiological systems. In addition, morphological data can be integrated into the model.

Simulation of the models created by PhysioDesigner can be performed by the 
Flint simulator, which is developed concurrently with PhysioDesigner. Simulations also can be run in other ways. PhysioDesigner can export C++ and JAVA source codes including numerical integration solvers. Thus, users can easily perform simulations by compiling them. Finite element simulation for partial differential equations can be done by exporting a model in FreeFem++ format and running the script on FreeFem++.

PhysioDesigner is a successor to 
insilicoIDE (ISIDE), which was developed over the period from 2007 to 2011. Subsequently, all functions implemented on ISIDE were reimplemented on PhysioDesigner, and new functions were added. Details of the development history are here


posted 2015.01.01

PySB

PySB is a framework for building mathematical models of biochemical systems as Python programs. PySB abstracts the complex process of creating equations describing interactions among multiple proteins or other biomolecules into a simple and intuitive domain specific programming language (see example below), which is internally translated into BioNetGen or Kappa rules and from there into systems of equations. PySB makes it straightforward to divide models into modules and to call libraries of reusable elements (macros) that encode standard biochemical actions. These features promote model transparency, reuse and accuracy. PySB also interoperates with standard scientific Python libraries such as NumPy, SciPy and SymPy enabling model simulation and analysis. 

posted 2014.12.11

PhysioDesigner 1.0beta

PhysioDesigner is an open platform for supporting multilevel modeling of physiological systems in the field of integrated life-science and systems biology, including physiology, neuroscience and so on. Users can combine and build mathematical models of biological and physiological functions on PhysioDesigner. Users can also integrate morphometric data on a model, which is used, for example, to define a domain in which partial differential equations are solved. 

PhysioDesigner 1.0beta has been released. 

posted 2012.06.22

Edinburgh Pathway Editor

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). We support Windows, Mac and Linux:

http://epe.sourceforge.net/SourceForge/EPE.html

posted 2010.12.03

Omix

Omix is a highly customizable editor for manually drawing biochemical network diagrams. The software is equipped with extensive data visualization features. High quality vector graphics can be generated with Omix that are ideally suited for scientific presentation and publication.

http://www.13cflux.net/omix/

posted 2010.12.03

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

JDesigner

JDesigner is a graphical network editing tool developed by H. Sauro. It is tightly connected with Jarnac.

http://sys-bio.org/sbwWiki/sysbio/jdesigner

posted 2006.04.25

PaVESy

PaVESy is a pathway visualization and editing system.
http://pavesy.mpimp-golm.mpg.de/

posted 2006.04.25

SRS Pathway Editor

A pathway eduitor tool by Lion Bioscience AG.
http://www.lionbioscience.com/solutions/e20472/srspathwayeditor

posted 2006.04.25