Products created by the Schnell Lab

Model Repositories

 

AggModd

 

AggMod is an online model repository of mathematical models of protein aggregation.  It provides free and open access to models derived from the published, peer-reviewed papers.  Each model is implemented and curated in Berkeley Madonna, a software for the modeling and analysis of dynamic systems.

 

The Brehm Center Systems Biology Model Repository

 

The Brehm Center Systems Biology Model Repository is a database of mathematical models of diabetes and obesity for use in the basic science and clinical research.  The repository provides free and open access to models derived from the published, peer-reviewed papers. The models are implemented and curated in Berkeley Madonna, a software for the modeling and analysis of dynamic systems.  To facilitate model sharing among systems biologists, model codes are also available for other simulation programs.

 

 

Web services

 

Disorder Atlas

 

Disorder Atlas is a web-based service that facilitates the interpretation of intrinsic disorder predictions using proteome-based descriptive statistics. This service is also equipped to facilitate large-scale systematic exploratory searches for proteins encompassing disorder features of interest, and further allows users to browse the prevalence of multiple disorder features at the proteome level. Disorder Atlas is freely available for non-commercial users. Individuals seeking to use Disorder Atlas for commercial purposes should contact Dr. Santiago Schnell.

 

Disorder Atlas was partially supported by the University of Michigan Protein Folding Diseases Initiative and the University of Michigan Medical School Research Discovery Fund.

 

 

Software Tools

 

MIKANA

 

MIKANA is a Method for Inferring Kinetics and Network Architecture of biochemical reactions.  MIKANA infers biochemical pathway mechanisms from time course data using global nonlinear modeling techniques to identify elementary reaction steps which constitute the pathway.  The Schnell Lab developed this tool in collaboration with Dr. Edmund Crampin (University of Melbourne) and Dr. Patrick McSharry (University of Oxford).

 

MIKANA was partially supported by the National Science Foundation (Awards IIS-0513701 and IIS-0852743).

 

Network WorkBench

 

Network WorkBench is a large-scale network analysis, modeling and visualization toolkit for biomedical, social science and physics research.  Dr. Santiago Schnell was part of the leading team supervising the development of Network WorkBench.  The other leading members of the project team were: Katy Börner (Indiana University School of Library and Informatics Science), Albert-László Barabási (Department of Physics, Northeastern University), Alessandro Vespignani (Department of Physics, Northeastern University), Stanley Wasserman (Department of Statistics, Indiana University) and Eric Wernert (Indiana University Information Technology Services).

 

This project was supported in part by the National Science Foundation (Award IIS-0513650).

The Schnell Lab, University of Michigan Medical School

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