NPACI Tools for Biological Sciences

Medicine

GENESIS (GEneral NEural SImulation System) is a general purpose simulation platform which was developed in CalTech to support the simulation of neural systems ranging from complex models of single neurons to simulations of large networks made up of more abstract neuronal components (http://www.bbb.caltech.edu:80/GENESIS)

Neuroscience M-cell simulator (http://www.mcell.cnl.salk.edu,
http://www.npaci.edu/enVision/v15.3/modeling.html)

Brain data project including Neurosimulator
(http://www.npaci.edu/enVision/v15.3/refining.html,
http://www.npaci.edu/enVision/v14.4/ns_federating.html,
http://www.npaci.edu/envision/v14.4/ns_refining.html )

Stress computations in biology using finite-element analysis (http://www.npaci.edu/envision/v15.3/keaveny.html)

Molecular Biology

Protein Data Bank Contains over 11,000 3-D models of proteins and nucleic acids. It includes LIMA (Ligand Matching server)
(http://www.rcsb.org/pdb,
http://www.npaci.edu/envision/v15.2/legion.html,
http://www.npaci.edu/envision/v15.4/ondrechen.html,
http://www.npaci.edu/envision/v14.4/ie_molsci.html,
http://www.npaci.edu/envision/v14.4/rcsb_pdb.html,
http://www.scripps.edu/pub/olson-web)

Biological Data Representation & Query This project is creating methods for high-performance querying of molecular biology sequence and structure databases http://www.sdsc.edu/pb

Molecular dynamics simulation of protein folding
(http://www.npaci.edu/Alpha/ProteinFolding,
http://www.npaci.edu/envision/v15.4/proteinfolding.html,
http://www.npaci.edu/envision/v15.4/choe.html,
http://www.npaci.edu/envision/v14.4/sac_amber.html)

Biology workbench 3.2 allows to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools (NCSA) (http://workbench.sdsc.edu)

Nucleic acid database, with information on known DNA structures (http://ndb.sdsc.edu)

Microstructure Image-Based Collaboratory (MIBC) remote analysis of microbiological images ( http://www-ncmir.ucsd.edu/MIBC/index.html)

Enhanced Biological Imaging for refining electron microscopy results: This project seeks to enhance reconstruction in electron microscopy and the computing environment to support it. This work will facilitate atomic-level structure determination of non-crystallizable systems (http://www.npaci.edu/Thrusts/MS/imaging.html)

MEME: a tool for discovering motifs (repeatedly occurring sequence patterns) in a group of related DNA or protein sequences. (http://www.sdsc.edu/MEME/meme/website)

NBCR: The National Biomedical Computation Resource. A collection of projects and resources related to molecular modeling and studying molecular dynamics on parallel computers, DNA pattern matching, parallel image reconstruction from High Voltage Electron Microscope data, etc. (http://nbcr.sdsc.edu/nbcr.html)

Telescience project: Remote control of microscopy and tomography including database image analysis (http://www.npaci.edu/Alpha/Telescience,
http://www.npaci.edu/envision/v15.4/telescience.html)

Cholesterol-membrane interactions
(http://www.npaci.edu/online/v4.4/smondryev.html)

Telemicroscopy: Visualization of 3D cellular structures with an electron microscope connected to SDSC supercomputer (http://www-ncmir.ucsd.edu/CMDA)

CMS Molecular Biology Resource: Directory of Internet resources on biochemistry, bioinformatics and biotechnology (http://www.sdsc.edu/ResTools/cmshp.html)

Bioinformatics: Processing biological data collection, e.g. Human Genome Project data (http://www.npaci.edu/Alpha/Bioinformatics,
http://www.npaci.edu/envision/v15.4/bioinformatics.html)

MICE: Molecular Interactive Collaborative Environment: a web-based tool developed at SDSC, which allows researchers at
different locations to visualize synchronously complex models of molecular structure. (http://MICE.sdsc.edu)