Karr Lab :: Resources

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.

Second generation whole-cell models and whole-cell modeling tools

For users
- Model and tools
- Data
- Interactive tutorials
- Documentation
For developers
- Source code
- Python packages
- Data packages
- Docker images
- Builds
- Test results
- Test coverage

First generation whole-cell models and whole-cell modeling tools

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.
WholeCellKB
Web-based software for creating model organism databases for whole-cell models. Implemented in Python using the Django framework.
WholeCellSimDB
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.
WholeCellViz
Web-based software for exploratory data analysis of whole-cell simulations. Implemented in JavaScript using jQuery, flot, and three.js.

Integrated models (precursor to whole-cell models)

Integrated flux-balance analysis (iFBA)
Provides MATLAB code and results for a computational model of E. coli which integrates an ordinary differential equation model of central carbon metabolism, a flux-balance analysis model of all of metabolism, and a Boolean model of transcriptional regulation.

NetworkPainter

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.

MATLAB utilities

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.

Instructional materials

WholeCell.org

Central hub for information about whole-cell modeling.

An introduction to whole-cell modeling

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.

Graduate fellowships information

Collection of information about graduate fellowships and sample applications.

Courses

2019 Whole-cell modeling summer school

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

Past courses

2017 Whole-Cell Modeling Summer School
2016 Whole-Cell Modeling Summer School
2016 Whole-Cell Modeling Summer Workshop
2015 Whole-Cell Modeling Standards Workshop