Simbiome Resources

We have 92 entries from 99 different organizations.

ABAQUS - Abaqus, Inc., Simulia
Software suite for finite element analysis

ACTS Collection - Lawrence Berkeley National Laboratory, DARPA, NSF, NERSC, DOE - Department of Energy
Libraries for high performance scientific applications for parallel computers

Amber - Molecular Dynamics - Scripps Research Institute
Assisted model building with energy refinement

Amber Force Fields - Scripps Research Institute
molecular force fields for dynamics simulations

AutoCAD & Inventor - Autodesk, Inc.
CAD Software for 2D drawings and 3D solid modeling

Autolev - OnLine Dynamics, Inc.
Advanced symbolic manipulator for motion

B3C BioComputing Competence Centre - Istituti Ortopedici Rizzoli, Italy, SCS - SuperComputingSolutions
Development and commercialization of software for medical applications

BioPSE - Biomedical Problem Solving - University of Utah
Problem solving environment for modelling bioelectric field problems

BLAS - University of Tennessee, Oak Ridge National Lab
Basic Linear Algebra Subprograms

Boost C++ Libraries - Boost
Provides free peer-reviewed portable C++ source libraries

C3D - Motion Lab Systems, Inc.
File Format Reference

CATIA - Dassault Systems
CAD/CAE Software for 3D solid modeling, motion simulation, and FEA stress analysis

CGAL - Tel Aviv University, Utrecht University, Max-Planck-Institut für Informatik, ETH Zurich, Freie Universitat Berlin, Inria, GeometryFactory
Computational Geometry Algorithm Library

CHARMM - Harvard University
Program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations

Chime - Elsevier MDL, Inc., Symyx Technologies
Browser plug-in that renders 2D and 3D molecules directly within a Web page.

Chimera - University of California, San Francisco
Extensible, interactive molecular graphics program

Clipper - University of York
Improved Crystallographic Modeling

CNS - Crystallography & NMR System - Yale University
Macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy

CSD - Cambridge Structural Database - Cambridge University
The world repository of small molecule crystal structures

CTSim
The Open Source Computed Tomography Simulator

Dali - EMBL - Eurpean Bioinformatics Institute
Network service for comparing protein structures in 3D

DASSL - U.C Santa Barbara
Differential Algebraic System Solver

DelPhi - Columbia University
A Finite Difference Poisson-Boltzman Solver

Folding@Home Distributed Computing - Stanford University
Distributed Computing to Fold Proteins

GATE: PET SPECT - Swiss Center for Electronics and Microtechnology
GATE - Geant4 Simulation Application for Tomographic Emission

GRASP - Columbia University
Graphical Representation and Analysis of Structural Properties

GROMACS - Stockholm Bioinformatics Center, Stockholm University
Molecular Dynamics Simulation

Integrative Biomedical Computing (CIBC) - University of Utah
Collaborative Center for visualization and mathematical modeling in life sciences

ISB Data Resource - International Society of Biomechanics
International Society of Biomechanics Web Resource for Data

ISB Software Resources Repository - International Society of Biomechanics
Software Resources Repository for International Society of Biomechanics

ITK - Segmentation Toolkit - Kitware, Inc.
National Library of Medicine Insight Segmentation and Registration Toolkit

iTools - NIH, NAMIC, I2B2, MAGNet, NCBC, CCB, NCBO, Simbios, NCIBI
iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources

IUPS Physiome Project - International Union of Physiological Sciences
Computational framework for understanding human and other eukaryotic physiology

JMOL - Open Source
Open source molecule viewer written in Java.

Kinemage / KiNG - Duke University
Dynamic molecular scientific illustration presented as an interactive computer displays

Kinemage Protein Structures - Duke University
500 proteins used for the Ramachandran-plot distributions, with File ID {PDB code + chainID}

LAMMPS Molecular Dynamics Simulator - Sandia National Lab
Large-scale Atomic/Molecular Massively Parallel Simulator

LAPACK - University of Tennessee
Linear Algebra PACKage

Macromolecular Structure Database - EMBL - Eurpean Bioinformatics Institute
European project for the collection, management and distribution of data about macromolecular structures

Mathematica - Wolfram Research, Inc.
Symbolic Math Toolkit

MatLab - MathWorks, Inc.
Modeling and Analysis Platform

Metis - University of Minnesota
Serial Graph Partitioning

Modeller - University of California, San Francisco
Homology or comparative modeling of protein three-dimensional structures

MolDB - Yale University
Database of Macromolecular Movements

MPICH - Argonne National Laboratory
A Portable Implementation of MPI, the standard for message-passing libraries

MSC Software - MSC Software Corporation, Inc.
Enterprise Simulation Solutions

NAMD - University of Illinois
Parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems

NAST - Stanford University, Simbios
RNA structures with a coarse grained molecular dynamics and a knowledge based force field

NDB - Nucleic Acids Database - Rutgers University
Repository of three-dimensional structural information about nucleic acids

NSR National Simulation Resource - University of Washington
Collection of material of interest to biological modelers

OpenSim - Stanford University, Simbios
Software platform for neuromuscular simulations and model development

Paraview - Sandia National Lab, Kitware, Inc., LLNL
Parallel visualization application for large datasets

ParMetis - University of Minnesota
Parallel Graph Partitioning

PDB - Protein Databank - Rutgers University, University of California, San Diego
Public repository for molecular structures

Proshape - Stanford University, Duke University, University of California, Davis
Computational techniques for simulating, analyzing and visualizing protein structures

ProtoMol - University of Notre Dame
Framework for molecular dynamics simulations

Pubchem - NIH
Databases of the biological activities of small molecules

Pymol - DeLano Scientific LLC
Molecular graphics and modelling package

RasMol - Dowling College
Molecular Visualization Program

Robetta - University of Washington
Full-chain protein structure prediction server

ROSETTA - University of Washington
Software suite for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions

Rotamer Libraries - Duke University
Library of rotamers, low-energy side-chain conformations

S2S - Sequence to Structure - University Louis Pasteur
Framework to display, manipulate and interconnect RNA data from the sequence to the structure

SCWRL - Fox Chase Cancer Center
Prediction of protein side-chain conformations

SD/FAST - Parametric Technology Corporation, Inc.
Physically-based simulation of mechanical systems

Simbody - Stanford University, NIH, Simbios
SimTK Core API for mutibody dynamics

SIMM - MusculoGraphics, Inc.
Construction, modeling, animation, and analysis of three-dimensional musculoskeletal systems

Simtk.org - Stanford University, Simbios
Simtk.org, the software dissemination arm of Simbios, the NIH National Center for Physics-based Simulation on Biological Structures at Stanford University

Simulink - MathWorks, Inc.
Matlab Toolkit for Simulation and Model-Based Design

SimVascular - Stanford University, Simbios
Software for Cardiovascular Modeling and Simulation

SMILES Toolkit - Daylight, Inc.
Programming environment supporting molecular objects and the SMILES language

SOCR - UCLA
Statistics Online Computational Resource

Solid Edge - UGS, Inc.
CAD/CAE Software for 3D solid modeling

SolidWorks - SolidWorks Corporation
CAD/CAE Software for 3D solid modeling, motion simulation, and FEA stress analysis

Stanford NMBL Musculoskeletal Models - Stanford University, Simbios
Downloadable Models of various musculoskeletal systems

Super LU - Lawrence Berkeley National Laboratory
General purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations

SURFNET - University College London
Surfaces and void regions between surfaces from coordinate data supplied in a PDB file

The NSR Physiome Project - University of Washington
Quantitative Description of the Human Organism

The Visualization ToolKit - VTK - Kitware, Inc.
Open source, freely available software system for 3D computer graphics

TINKER - Washington University
Molecular modeling software for molecular mechanics and dynamics

toRNAdo - Stanford University, Simbios
Visualization tool for coarse grain (lumped) RNA structure models

UMFPACK - University of Florida
Routines for solving unsymmetric sparse linear systems

VMD - University of Illinois at Urbana-Champaign
displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting

WebMol - University of California, San Francisco
Java PDB viewer

Working Model - Design Simulation Technologies, Inc.
Easy-to-use 2D motion simulation tool

wwPDB - Worldwide Protein Data Bank - Rutgers University, University of California, San Diego
Worldwide Protein Data Bank

X-PLOR - Yale University
Crystallography Structure Determination

XPLOR-NIH - NIH
structure determination program which builds on the X-PLOR program

Yale Morph server - Yale University
2D and 3D animations of a plausible or semi-plausible pathway between two submitted protein subunit conformations