Databases for Modeling

Community Systems Biology Knowledgebase

BioCoDa - Biological Component Databank

Physiome Models

BioModels Database

CellML

Community Health Data Initiative

ModelDB for Neural Simulations - ModelDB provides an accessible location for storing and efficiently retrieving computational neuroscience models. Models can be coded in any programming language for any simulation environment.

PhysioNet - also provides members of the MSM community with free, secure, and reliable archival storage for their own data (see Sharing Data via PhysioNet)

VCellDB - a database of models developed by users of the Virtual Cell software. Over 500 of these models are publically accessible.

VIVO: Enabling National Networking of Scientists

Simtk.org – Simtk.org is a web platform that accelerates the development and dissemination of biocomputational software, models, and data. Its goal is to encourage and enable researchers to share their resources and knowledge. The site provides daily back-ups, download statistics, and numerous communications tools, such as wikis, mailing lists, discussion forums. Each project on the site also has its own subversion repository to enable collaborative software development. Explore the 600+ projects available on the site at http://simtk.org.

3D Virtual Cell Resource Catalog - The catalog is designed to enable the community to edit existing resources, add new resources and to rate and comment on the resources. Please log in to the website and add your resources. The 3DVC community catalog is a collaborative project between the 3DVC and the NIF (Neuroscience Information Framework). The initial existing resources in the 3DVC catalog were tagged from the NIF catalog as resources relating to the 3DVC Community. A special thanks to NIF for helping launch the catalog and providing supporting services; to Delsa.org for helping tag resources and to the working group members for hours of volunteer time and input. We encourage your participation by adding links to resources of interest to the 3DVirtual Cell Community as a first step to gathering and understanding the resources existing in our community.

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