CellML Tools

Category Cross-Omics>Pathway Analysis/Tools

Abstract The CellML team is committed to providing freely available tools for creating, editing, and using CellML models.

Information regarding tools being developed internally is provided and external projects developing tools which utilize the CellML format are also provided.

1) Application Programming Interface (API) Specifications and Implementations -- The manufacturer has defined an official CellML API. This API provides an interface that applications can use to manipulate and process CellML documents. The interfaces are designed to be independent of any programming language, platform, or vendor, and are expressed in the OMG Interface Definition Language (IDL).

It addresses both CellML 1.0 and CellML 1.1. The manufacturer has also produced an implementation of this specification in C++. This API can be accessed either directly from your C++ program, or from any language for which a CORBA language mapping is available.

2) Model Databases --

The Physiome Model Repository (PMR) - PMR is a Plone product (Plone is a ready-to-run content management system) designed to facilitate model upload, storage, curation, and download. It allows information about models to be viewed, and the original model to be downloaded. The Physiome Model Repository software is used to run the official CellML Model Repository.

BioModels.net - The BioModels.net project is an international effort to (a) define agreed-upon standards for model curation, (b) define agreed- upon vocabularies for annotating models with connections to biological data resources, and (c) provide a free, centralized, publicly-accessible database of annotated, computational models in structured formats.

3) Complete CellML Environments -- These are tools which provide a "full service" in regard to CellML model editing and use. They will typically include at least model editing and simulation capabilities and will possibly include such extras as model validation, creation, and visualization tools.

Physiome CellML Environment (PCEnv) - PCEnv is an open source tool environment being developed at the Auckland Bioengineering Institute. It makes use of the CellML DOM API and the CellML Context in order to tie everything together (and allow it to work with other tools that are Not solely targeted at PCEnv).

One extension will allow integration and replace mozCellML. PCEnv is built on top of the Mozilla platform. PCEnv v0.4 has recently been released and supports model editing, simulation and results visualization.

Cellular Open Resource (COR) - COR is a Microsoft Windows environment for cellular modeling that is built around CellML (except for reactions and metadata which are Not supported).

COR is currently being developed and maintained by Dr Alan Ganey in the Mechano-Electric Feedback lab at the University of Oxford.

4) Other Modeling Environments -- Modeling environments differ from the CellML environments above in that they are Not based entirely on CellML but rather offer various levels of support for utilizing CellML. These environments provide tools for the support of general mathematical modeling as well as interfaces specific for certain areas of biological modeling.

JSim - JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim's primary focus is in physiology and biomedicine; however its computational engine is quite general and applicable to a wide range of scientific domains.

JSim models may inter-mix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim also imports the SBML and CellML model archival formats.

JSim is developed by the National Simulation Resource at the University of Washington, Department of Bioengineering.

Virtual Cell (VCell) - VCell is developed at the National Resource for Cell Analysis and Modeling (NRCAM) located at the University of Connecticut Health Center. It is a tool to build models and run simulations of cellular processes, including the modeling of reactions, diffusion, membrane transport, flow, and electrical potential & currents.

VCell has the facilities for compartmental and spatial simulations (1-, 2- , and 3-dimensional) on analytical or image-based geometries. It provides a collaborative working environment via a shared database and interoperability through the use of various data formats (including SBML and CellML).

insilicoIDE - The insilicoIDE is developed at the Center for Advanced Medical Engineering and Informatics at Osaka University. It is a tool to browse, build and run simulation models of physiological dynamics.

It can import models in the CellML format for exploring the hierarchical structure of the models, editing, modifying, networking the models, and for simulating the dynamics of the models.

5) Validation Tools -- These tools focus on the validation of CellML model documents and the models they describe.

XML validation - Standard XML validation of CellML documents provides a good first stop in model validation. There are several choices here:

a) CellML 1.0 DTD (written by Warren Hedley, Auckland Bioengineering Institute).

b) CellML 1.0 XML Schema (written by Autumn Cuellar, Auckland Bioengineering Institute) - This is the simplest version of a CellML Schema possible. It completely leaves out all elements outside the CellML namespace.

c) CellML 1.1 XML Schema (written by Andrew Miller, Auckland Bioengineering Institute) - This is a CellML 1.1 Schema. It imports additional W3C defined schema definitions for content, MathML and XLink. A Java program which loads the schema and validates a list of documents is also available.

d) RELAX NG schema for CellML 1.0 (written by Jonathan Cooper, University of Oxford) - also requires the MathML RELAX NG schema. Jonathan developed these as part of his validation tool suite, PyCml.

PyCml - As part of the Integartive Biology project, Jonathan Cooper has been working on a validator tool suite for CellML 1.0. It is written in Python, and uses the RELAX NG and Schematron validation languages where appropriate. PyCml can be obtained and there is a web-based validation service available under the CellML page for the eDiaMoND project.

6) Simulation Tools -- In addition to the simulation abilities of the above tool suites there are also some simulation specific tools available.

API Generator for ODE Solution (AGOS) - AGOS is a tool developed at FISIOCOMP, Universidade Federal de Juiz de Fora, Brazil. It provides an on-line tool that automatically builds up an object-oriented C++ class library that allows its users to manipulate and numerically solve Initial Value Problems based on ODE systems described by the CellML and MathML standards.

CellMLSimulator - This is a tool built on top of the C Code Generation Service (CCGS) from the CellML API implementation. It uses the CellML simulation and graphing metadata to decide what simulations need to be performed using the models specified in the metadata and then (optionally) produces the described plots. CellMLSimulator is an open source application developed by David Nickerson.

Cell Electrophysiology Simulation Environment (CESE) - CESE is a Java framework for performing computational electrophysiological simulations.

7) Miscellaneous Utilities -- Various tools that fit none of the above categories.

CellML 1.1 to CellML 1.0 - CellML 1.1 to CellML 1.0 is a simple C++ file written by Jonathan Cooper based on the CellML API. It can be used to faciliate the conversion of a CellML 1.1 model into a CellML 1.0 model.

CellML 1.0 to CellML 1.1 - In a similar (but opposite!) style, David Nickerson has produced a tool which can be used to "decompose" a CellML 1.0 model into a CellML 1.1 hierarchy of components. This process also extracts model boundary and initial conditions embedded in the original model into new top level components in the 1.1 model hierarchy.

CellML2Dot - CellML2Dot is a tool developed by David Nickerson which reads CellML models (1.0 and 1.1) and writes out various configurable parts of the model as dot files suitable for use with the Graphviz (and compatible) graph visualization software.


MathML display helper - A set of files that gets you started if you want to display some MathML in a web page.

MathML Renderer (written by Autumn Cuellar, Auckland Bioengineering Institute) - an XSLT transform that converts the CellML subset of MathML to a LaTeX file. Save the file to your local hard drive and run with any XSLT processor.

Equation Extractor for Viewing (written by Warren Hedley, Auckland Bioengineering Institute) - an XSLT transform that extracts the MathML from a CellML document and formats it in semi-Presentation MathML.

Scripts -

MatLab2CellML (written by Steven Niederer, Auckland Bioengineering Institute) - a Perl package containing Eqn2Cellml which generates CellML code from an equation written in a single line MATLAB format. Eqn2CellML requires a single string input and returns a single string output.

System Requirements



Manufacturer Web Site Auckland Bioengineering Institute, CellML Tools

Price Contact manufacturer.

G6G Abstract Number 20294

G6G Manufacturer Number 102852