Modeling Resources

Kirschner and Linderman Labs

Modeling Methods and Tools: Ordinary Differential Equations (several non-linear types, all continuous, determistic approaches) and Agent-based Model (stochastic, discrete approach)

Software Development: Languages and Tools: C++/C OOP, JAVA

Software Sharing Programs: MATLAB codes and documentation for shareware analysis tools created by our group.

SBML format of Models: To make our models "sharing-friendly", we have prepared SBML format for the models in the papers in the following link that are derived from this study:

The Schnell Lab

Model Repositories:

Software Tools:

The Schloss Lab

Software Technology: MOTHUR is a bioinformatics program for analyzing microbial communities. The MOTHUR project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. In February 2009 we released the first version of mothur, which had accelerated versions of the popular DOTUR and SONS programs. Since then we have added the functionality of a number of other popular tools including s-libshuff, TreeClimber (i.e. the parsimony test), UniFrac, distance calculation, visualization tools, a NAST-based aligner, and many other features.

Data and Design Resources

The Luker Lab

Imaging Technology: The Center for Molecular Imaging houses state-of-the-art instruments for multi-modality imaging in cell-based assays and living mice. Available instruments include IVIS bioluminescence/fluorescence systems, 7 and 9.4T Varian MRI systems, and microPET/SPECT/CT instruments. The facility includes dedicated housing facilities for animals undergoing longitudinal imaging studies. The Center has advanced image analysis programs for co-registering multi-modality imaging data sets and extracting quantitative parameters on a voxel-wise basis.