Models, Data and Tools
All of our models, data and tools are freely available open-source with detailed tutorials, examples, and documentation via the links below.
- Whole-cell model of Mycoplasma genitalium
First whole-cell model of the bacterium M. genitalium. Includes MATLAB simulation code, training data, and MATLAB code for analysis of whole-cell simulations.
Web-based software for creating model organism databases for whole-cell models. Implemented in Python using the Django framework.
Database for storing and retrieving whole-cell simulations. Implemented in Python using the Django framework, h5py, and MySQL. Includes a web-based user interface developed using flot.
Graphical user interface for easily creating signaling network diagrams animated with biomolecular data. Exports signaling diagrams to various formats including Flash. Provides all ActionScript and PHP code.
Utilities for representing N-dimensional sparse matrices; representing chemical formulae; reading and writing .mat files; differencing .mat files and struct; querying MySQL databases; logging unit test results; and generating coverage reports.
A primer on whole-cell modeling including the fundamentals of cell modeling, software engineering, scientific communication, and funding whole-cell modeling research. Includes detailed tutorials and coding exercises.
Collection of information about graduate fellowships and sample applications.
7-day school on whole-cell modeling featuring didactic lectures and hands-on tutorials.
- Location: Center for Regulatory Genomics, Barcelona, Spain
- Date: April 7-13 2019