Software Development

The Theoretical and Computational Biophysics Group maintains the following software development-related projects.

Computational Facility

The Theoretical and Computational Biophysics Group is a pioneer in the realm of high-performance computing. To meet our computational needs, we maintain a wide selection of computers divided into four main categories: compute power, visualization equipment, desktop workstations, and infrastructure. We also rely extensively on the nation's supercomputers.

The TCB Group is also dedicated to helping both the biomedical community, and the computational world as a whole, by sharing the knowledge developed while administering the group internally. This knowledge is shared in the user and sysadmin documentation libraries. Addititionally, source code can be found as part of the MDTools library.

VMD

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.

NAMD

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our tutorials show you how to use NAMD for biomolecular modeling.

BioCoRE

BioCoRE is a collaborative work environment for biomedical research, research management and training. A resource-centered platform, BioCoRE offers scientists, working together or alone, a seamless interface to a broad range of local and remote technologies such as discipline-specific and general tools, data, and visualization solutions. To harness and streamline collaborative capabilities across temporal and physical boundaries in research and training, BioCoRE builds on the transparent use of and communication between technological resources (hardware and software) and databases. BioCoRE features powerful yet easy-to-use tools, among them co-authoring papers and other documents, running applications on supercomputers, sharing molecular visualization over the Internet, notifying project team members of recent project changes by email, chatting, keeping a lab book, and other practical features.

MDTools is a collection of programs, scripts, and utilities we provide for researchers to make various modeling and simulation tasks easier, and to provide basic code and utilities which can be built up into larger toolsets. Each tool, script, or library is listed below and has its own separate distribution, documentation, etc. The programs in this collection are provided for the benefit of the research community, but are not officially supported unless otherwise stated. Each program may have a software license and/or citation suggestions which should be listed on its web page.

The structural biology software database contains programs which are thought to be of interest to researchers in the fields of structural biology, quantum chemistry, and bioinformatics. We encourage users to send the moderators new application submissions and feedback about the database. The source code for this web database system is freely available.