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.
http://malthus.micro.med.umich.edu/MSM/shareware

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: http://malthus.micro.med.umich.edu/MSM/sbml

Model Repositories:

• AggModd - An aggregation reaction mechanism model repository
  http://aggmod.ccmb.med.umich.edu
• The Brehm Center Systems Biology Model Repository - A diabetes and obesity mathematical model repository
  http://sitemaker.umich.edu/diabetes.models

• MIKANA - An algorithm to infer kinetics and mechanism of complex reactions from time course data
  http://sitemaker.umich.edu/schnell.lab/mikana
• Network Workbench - A large-scale network analysis, modeling and visualization toolkit for biomedical, social science and physics research
  http://sitemaker.umich.edu/schnell.lab/network_workbench

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.
http://www.mothur.org

Software Technology: Source code for the chemo-mechanical evolution of a stress fiber-focal adhesions system.
http://sitemaker.umich.edu/compphys/software&config=nUxkqkTEE9wIgvPUrZzdH0

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.
http://www.med.umich.edu/cmi

Main Website: http://www.bme.umich.edu/labs/mnmbiotech

Core Facilities Section: The Micro/Nano/Molecular Biotechnology Lab is equipped with soft lithography (SLF), cell culture (CCF), micromachining, and microscopy facilities. More information is available at...
http://www.bme.umich.edu/labs/mnmbiotech/facilities.php