CellDesigner 4.0
Category Cross-Omics>Pathway Analysis/Tools
Abstract CellDesigner is a structured diagram editor for drawing gene- regulatory and biochemical networks. The networks are drawn based on a 'process diagram', using the Systems Biology Graphical Notation (SBGN) system proposed by Kitano, and they are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. These networks are able to link with simulation and other analysis packages through the Systems Biology Workbench (SBW).
Products features/capabilities include:
CellDesigner supports simulation and parameter scans via integration with the SBML ODE Solver Library (SOSlib). By using CellDesigner, you can browse and modify existing SBML models with references to existing databases, and simulate/view its dynamics through its intuitive graphical interface.
The Process Diagram -- is a 'state transition' diagram. In the process diagram representation, each node represents the state of a molecule and its complex. Arrows represents state transitions among states of a molecule.
SBML compliant -- SBML is the computer-readable format for representing models of biochemical reaction networks in software. SBML is applicable to metabolic networks, cell-signaling pathways, regulatory networks, and many others. CellDesigner is SBML compliant software, making it easy to exchange data with other SBML compliant applications.
The SBML ODE Solver Library (SOSlib) -- is both a programming library and a command-line application for symbolic and numerical analysis of a system of ordinary differential equations (ODEs) derived from a chemical reaction network encoded in the Systems Biology Markup Language (SBML).
Direct integration with SBML ODE Solver via CellDesigner's Control Panel -- The “Control Panel” is designed to assist users to simulate directly from CellDesigner controlling the amounts and parameters of the Species under study. This feature enables you to specify the details of parameters, change amounts, conduct parameter searches, and conduct interactive simulations.
Linkage to SBW-powered Simulator modules -- The SBW is a modular, broker-based, message-passing framework for communication between applications that aid in research in systems biology. CellDesigner complies with SBW, which enables the seamless linkage to SBW-powered simulators.
Database Connections --
You can connect to various databases via Species Name or ID specified in the Notes of the components.
CellDesigner supports the connections to the following databases:
1) Via Species Name --
- a) DBGET - DBGET is an integrated database retrieval system for major biological databases.
- b) SGD - (Saccharomyces Genome Databse) - SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as bakers or budding yeast.
- c) iHOP - (Information Hyperlinked over Proteins) - A network of concurring genes and proteins which extends through the scientific literature touching on phenotypes, pathologies and gene function.
2) Via ID described in the Notes of the components --
- a) PubMed - is a service of the U.S. National Library of Medicine that includes over 17 million citations from MEDLINE (Medical Literature Analysis and Retrieval System Online) and other life science journals for biomedical articles back to the 1950s. PubMed includes links to full text articles and other related resources.
- b) Entrez Gene - is the gene-specific database at the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM), located on the campus of the US National Institutes of Health (NIH) in Bethesda, MD, USA.
3) Retrieve models from BioModels.Net - the BioModels Database is a data resource that allows biologists to store search and retrieve published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc.
CellDesigner can export images of your model in three (3) formats: 1) Portable Network Graphics (PNG); 2) Joint Photographic Experts Group (JPEG); or 3) Scalable Vector Graphics (SVG). And, these images can be exported to a Portable Document Format (PDF) file.
Major New Features in Version 4.0 include:
1) Enhanced Graphical Notation -- CellDesigner's Graphical Notation conforms to SBGN (Systems Biology Graphical Notation) proposal, such as Gene, Reactions, Protein Residues, Protein / Complex Status.
2) Plugin development framework. Develop your plugin in Eclipse (an open development platform), and you can call the plugin from the [Plugin] menu.
3) Macro Functions to provide the ability to draw the common parts of a model.
4) Enhanced KineticLaw Edit Dialog: Mathematical Markup Language (MathML) rendering in KineticLaw.
Note: KineticLaw is used to describe the rate at which the process defined by a given Reaction takes place.
5) Export Species/Reactions information including Notes into a Comma Separated Values (CSV) file.
6) Species ID Edit Dialog.
7) [Layout] menu: Automatic Layout function (using yFiles layout library).
8) Enhanced Edit Functions.
9) Layer Function to add comments / arrows on top of the models.
10) Database link to the 'Genome Network Platform' (a system biological approach to understanding the dynamic aspects of the transcription networks).
System Requirements
CellDesigner is implemented in Java, thus it runs on various platforms such as Windows, Linux, and MacOS X.
Manufacturer
- The Systems Biology Institute, Tokyo, Japan
- Tel: 81-3-5468-1661
- Fax: 81-3-5468-1664
- E-Mail: info@sbi.jp
- CellDesigner Inquiry: info@celldesigner.org
Manufacturer Web Site CellDesigner Organization
Price CellDesigner is freely available via the Web.
G6G Abstract Number 20159
G6G Manufacturer Number 102583