eagle-i eagle-i Network Shared Resource Repositoryeagle-i Network Shared Resource Repository
See it in Search

Stanford University

Summary:

Stanford University is one of the world's leading research universities. Stanford is known for its entrepreneurial character, drawn from the legacy of its founders, Jane and Leland Stanford, and its relationship to Silicon Valley. Research and teaching stresses interdisciplinary approaches to problem solving. Areas of excellence range from the humanities to social sciences to engineering and the sciences. Stanford is located in California's Bay Area, one of the most intellectually dynamic and culturally diverse areas of the nation.

Affiliations:

Resources:

Databases

  • Collagen Database ( Database )

    This project contains the supplementary materials for the cited publication on molecular dynamics simulations of collagen type I.

    Keywords: collagen, fibrous proteins, osteogenesis imperfecta

  • Neuromuscular Models Library ( Database )

    "Welcome to the neuromuscular models library! The goal of this site is to provide a resource for students, researchers, and clinicians to access, use, test, and develop models. The majority of models in this library are for use with OpenSIM (which you can download free through simtk.org) and/or SIMM. Please take a look and enjoy.

    Please respect your fellow modelers.
    In using these models we ask that you respect the hard work of your fellow researchers by citing their work appropriately. When you go to the Download section you will be directed to individual project pages for each model which contain all of the files and documentation. Please carefully review the publications and cite the references in your future papers, presentations, grant applications, etc.

    Have a model to contribute?
    Do you have a model which you would like to make available through this library? Providing others with access to your models can stimulate future studies, provide a foundation for young researchers, and maximize the impact of your model. It’s easy to set up a project page to post your model. This will allow you to track who is using your model and be in contact with them. Please consider contributing! The project administrators can help you post your model, so please contact us if you would like to get started."

    Keywords: computational model, neuromuscular model

  • RiboWEB: The Ribosomal Experimental Knowledge Base ( Database )

    Riboweb is a knowledge base with information about ribosomal structure data. Riboweb contains a summary of biochemical and biophysical measurements made on the 30S (and to some degree 50S) subunit up to approximately the year 2000. It generally contains local measures (cross-linking, protection) as opposed to global measures of structure (e.g. EM, crystallography).

    Keywords: ribosome

Software

  • Adaptively Sampled Particle Fluids ( Software )

    This project presents geometric feature-size based adaptive sampling algorithms for Lagrangian particle fluids. This adaptive sampling strategy allows using smaller (and thus more) particles in geometrically complex regions, while less particles are used for thick flat fluid volumes. Additionally, a novel distance-based particle surface definition is implemented which hides the particle granularity and allows dynamic resampling near the fluid-air interface. The code is implemented in C++ and should compile on linux.

  • AlloPathFinder ( Software )

    "This project contains the AlloPathFinder application that allows users to compute likely allosteric pathways in proteins. The underlying assumption is that residues participating in allosteric communication should be fairly conserved and that communication happens through residues that are close in space.

    The initial application for the code provided was to study the allosteric communication in myosin. Myosin is a well-studied molecular motor protein that walks along actin filaments to achieve cellular tasks such as movement of cargo proteins.

    It couples ATP hydrolysis to highly-coordinated conformational changes that result in a power-stroke motion, or ''walking'' of myosin. Communication between a set of residues must link the three functional regions of myosin and transduce energy: the catalytic ATP binding region, the lever arm, and the actin-binding domain. We are investigating which residues are likely to participate in allosteric communication pathways."

    Keywords: allosteric communication, allostery

  • Amber/Sander plus OpenMM ( Software )

    This project provides additions to the Amber Software suite providing Amber users with a Amber (Sander) compatible interface to OpenMM. This will allow Amber users to explore OpenMM to run GPU accelerated Molecular Dynamics using their existing (Sander) input files. OpenMM's emphasis is on hardware acceleration.

    it provides a consistent API along with significantly enhanced performance on a variety of GPUs. Exciting benchmarks, showing the power of OpenMM are included on the Downloads page under "README_SPEED.txt".

    Keywords: AMBER, OpenMM, Sander

  • Anatomicaly-based 3D models of the middle ear and the inner ear ( Software )

    The OtoBiomechanics Group at Stanford is developing three-dimensional and multiscale bio-computational models of the middle ear and the inner ear and their applications to understanding disease processes and interventions.

    This project is a collection of code that simulates the biomechanics of the cochlea and the middle ear. At the core is FAST4. This is a program for calculating axisymmetric shells of revolution. FAST4 uses asymptotic methods for calculations, which are orders of magnitude faster than other methods including the finite element approach. The interface to FAST4 is built using MATLAB or Mathematica.

  • Biomechanics of Growth Directory ( Software )

    This project provides a simple but yet very illustrative tool how changes in the mechanical environment effect biological structure, density and volume. The simulation is based on three dimensional geometrically nonlinear finite elements. The code is developed in matlab and very basic. The project has been developed and used in class (ME337, "Mechanics of Growth").

    Keywords: computational biomechanics, finite element, growth model

  • Biomedical Computation Review ( Software )

    Holds the code that runs the Biomedical Computation Review website and database.

    Keywords: BCR, biomedical, computation, magazine

  • BlurLab -- 3D Simulated Microscopy Software Package ( Software )

    and the ability to simulate FRAP experiments. The software provides a platform for adjusting and saving these simulated images, as well as a number of helpful, semi-automated features to make image simulation easy and less error prone. Keywords: convolution, fluorescence, FRAP, function, image, microscopy, noise, point, resolution, simulation, spread, TIRF the ability to view scenes in wide-field and TIRF, and perform Z-slicing simulations of mean and fully stochastic photobleacing inclusion of thermal, shot and custom noise spectra BlurLab is an easy to use platform for generating simulated fluorescence microscopy data for use in mechanistic modeling visualization, image comparison, and hypothesis testing. The software accepts the 3D positions, intensities and labels of fluorescing objects that are produced by an underlying mechanistic model and transforms them into high quality simulated images. The program includes full 3D convolution with realistic (or even measured) point spread functions

  • BPPalign: Aligning RNA secondary structure probabilities to discover new motifs ( Software )

    This tool provides basic scripts to run the partition executable RNAstructure on hundreds of homolog sequences from RFAM, and to then visualize the results by averaging across these matrices. Examples from purine-binding and double glycine-binding riboswitches are included.

    Keywords: Boltzmann, Motif discovery, Riboswitch, RNAstructure

  • C2A (Coarse to Atomic) ( Software )

    This work uses a knowledge-based approach to instantiate full atomic detail into coarse grain templates of RNA 3D structures. Any atom-based coarse-graining scheme can be used as input for our method. The result is a full atomic structure.

  • C3D Extraction Toolbox ( Software )

    This toolbox is of benefit to musculoskeletal modellers in the field of biomechanics/bioengineering to assist extracting kinematic, kinetic, and EMG information directly from a C3D file for Matlab manipulation or for input to OpenSim biosimulation software. The scripts can be configured for any laboratory configuration. This software is free without warranty but I do ask for acknowledgement if used in publications. Free download is available with documentation and two examples included. Main features of this script include: Custom markerset extraction Foot-plate detection algorithm Kinetic extraction (ground reaction forces / moments) Center of pressure calculation Transformation to customizable model coordinate system Custom EMG acquisition & processing tools XML file production (for OpenSim) Lab customizable The scripts require Motion Labs C3D Server software (freeware) and XML Toolbox (Marc Molinari)(freeware) which is included with the script download. Also requires Matlab 2008 or greater (32 bit only) with the Signal Processing Toolbox. Additional C3D software may be useful and these are available at http://www.c3d.org/c3dapps.html. Review the included manual for version updates and additions. Please inform me of bugs / suggestions to improve as this will be an ongoing project.

    Keywords: c3d, extract, gait, opensim, simulation

  • Cardiovascular Model Repository ( Software )

    The geometric models in this repository are collected from on-going and past research projects in the Cardiovascular Biomechanics Research Laboratory at Stanford University. The geometric models are mostly built from imaging data of healthy and diseased individuals. For each of the models, a short description is given with a reference. Click on the model image for a larger image of the model. The geometric models are in VTK PolyData XML .vtp format.

    You are free to download the geometric models and use them provided that you properly reference the source. The models are part of the academic output of the researcher cited and should be referred to as such. Permission is granted to use these models for research purposes, but for commercial use please contact the director of the Cardiovascular Biomechanics Research Laboratory, Charles A. Taylor (taylorca@stanford.edu).

    Keywords: aneurysm, arteriofemoral bypass, cardiovascular simulation, image-based geometric modeling, SimVascular, stent, VTK, .vtp format

  • Chand's Simulations ( Software )

    "This project is intended to serve as a repository for software I develop for physics-based simulation of human motion, as part of the work in the Neuromuscular Biomechanics Lab."

  • Clustering Algorithms for Massively Parallel Architectures Including GPU Nodes ( Software )

    The CAMPAIGN projects goals are to modularize and parallelize clustering algorithms and explore new clustering approaches, with special concentration on running on GPUs. This project s results are intended, among others, to be used with the FEATURE project at Stanford.

    Keywords: clustering

  • Competing metabolic pathways control viral frameshifting and host resistance ( Software )

    This project includes Matlab scripts that simulate the competition between the ISC and TUS pathways in E. coli and link this competition to lambda phage infection. A simulation of non-competitive interactions between the ISC and TUS pathways is provided as a control.

    Keywords: competitive inhibition, computational model, Escherichia coli, lambda phage, systems biology, viral infection

  • Discrete Center Hierarchies ( Software )

    Many applications require repeated computation of proximity information of a set of moving points. The discrete center hierarchy data structure allows the maintenance of such information.

  • EMG-informed Computed Muscle Control for Dynamic Simulations of Movement ( Software )

    This project is an EMG-informed control plug-in that interfaces with OpenSim to provide robust estimates of muscles activation patterns.

    Keywords: Dynamic simulation, EMG, musculoskeletal biomechanics, neuromuscular control, neuromuscular simulation

  • FEATURE ( Algorithmic software suite )

    "FEATURE is a suite of automated tools that examine biological structures and produce useful representations of the key biophysical and biochemical features of these structures that are critical for understanding function. The utility of this system extends from medical/pharmaceutical applications (model-based drug design, comparing pharmacological activities) to industrial applications (understanding structural stability, protein engineering)."

    Keywords: bayesian inference, calcium binding sites, functional sites, function annotation, protein microenvironments, structural bioinformatics, support vector machine

  • Finite element method for nonlinear solid mechanics with discontinuous Galerkin ( Software )

    "The library is written in C,C++, and Fortran. Thus far, it has only been tested on a linux cluster consisting of 92 Intel processors. For use of this library, the user must create a C++ driver application that will supply C style arrays containing the mesh data for the biological model. These include the standard connectivity, coordinate, and boundary data arrays. These can be given in the form of a conforming finite element mesh, since the library has a utility that will convert this data into a discontinuous finite element mesh. The user will need to decide the most appropriate way to analyze the results. Presently there is a utility that will create output files for the TecPlot visualization package."

  • ForceBalance : Automatic Optimization of Force Fields ( Software )

    ForceBalance is a force field optimization software package. It improves the accuracy of force fields by automatically tuning the force field parameters to match supplied reference data from experimental measurements and high-level calculations. The main goal of ForceBalance is to advance the force field development process by applying a highly general and systematic procedure with explicitly specified input data and optimization algorithms, paving the way to higher accuracy force fields, improved reproducibility, and well-defined scopes of validity and error estimation for the parameters. The optimization framework is highly versatile in terms of both the force field and the reference data; virtually any force field belonging to any software can be optimized, and the reference data can include experimental measurements and/or high-level quantum computations. Users of this program are highly encouraged to contact me (Lee-Ping) for more information!

    Keywords: balance, force field, gromacs, openmm, optimization, parameterization, potential

  • HiTRACE: High-Throughput Robust Analysis for Capillary Electrophoresis ( Software )

    This project contains the HiTRACE software that allows users to accurately and automatically perform key quantitative analysis tasks involved in high-throughput capillary electrophoresis (CE) of nucleic acids. CE has become a workhorse technology underlying high-throughput experimental methods such as high-speed genome sequencing and large-scale footprinting for nucleic acid structural inference. Despite the wide availability of CE-based equipment, there remain challenges in leveraging the full power of CE for quantitative analysis of RNA and DNA structure. We developed HiTRACE in order to address this issue. See Preprint for more information.

    Keywords: alignment, capillary electrophoresis, peak fitting

  • HP35 Contact Formation Predictions ( Software )

    We provide a set of predictions for the Villin mutant HP35-NLE-NLE.

    Keywords: protein folding

  • Integrated Flux Balance Analysis Model of Escherichia coli ( Software )

    This project includes several MATLAB scripts that simulate E. coli central metabolism and the effects of single gene deletions on metabolism using 3 approaches -- iFBA, rFBA, and ODE. The project also includes several MATLAB scripts that simulate biochemical networks using 1) integrated flux balance analysis (iFBA) -- a combined FBA, boolean regulatory, and ODE approach; 2) regulatory flux balance analysis (rFBA); and 3) ordinary differential equations (ODE). Additionally, the project includes several MATLAB and php scripts for visualizing metabolic simulations.

    Keywords: central carbon metabolism, computational model, diauxic growth, Escherichia coli, flux-balance analysis, growth model, systems biology

  • LAPACK linear algebra library (with BLAS) ( Software )

    "This project is the SimTK Core implementation of the extremely reliable, high speed linear algebra package LAPACK and the underlying BLAS library on which LAPACK is built. We make use of ATLAS to generate "hand tuned" BLAS kernels for a variety of hardware platforms, including multiprocessors, using a variety of operating systems including Windows, Mac, and Red Hat Linux. We pre-build on all these platforms and make the binaries available as a single shared library which can be conveniently used by any program. This means that users who are not experts in high performance scientific computation can nonetheless use the fastest linear algebra methods available for their machines.

    Our download page provides libraries that are specifically tuned for your hardware platform -- come and get 'em. The project also provides example programs, documentation and regression tests."

    Keywords: BLAS, linear algebra

  • Lepton Mathematical Expression Parser ( Software )

    Lepton ("lightweight expression parser") is a small C++ library for parsing, evaluating, differentiating, and analyzing mathematical expressions.

    Keywords: expression, function, parser

  • LiFFT: Likelihood-based Fits of Footprinting Transitions ( Software )

    This analysis tool will allow researchers to analyze their entire footprinting dataset, without filtering out noisy lanes and residues, or heuristic normalization, by employing a likelihood-based model fitting approach. This methodology allows for the rigorous estimation of parameters and parameter confidence intervals, to fit footprinting data to real physical models.

    Keywords: RNA footprinting data analysis

  • LoopTK: Protein Loop Kinematic Toolkit ( Software )

    "Analyzing the motion of flexible protein loops is becoming increasingly important in understanding the various roles that proteins play in human body. LoopTK is a C++ based object-oriented toolkit which models the kinematics of a protein chain and provides methods to explore its motion space. In LoopTK, a protein chain is modeled as a robot manipulator with bonds acting as arms and the dihedral degree of freedoms acting as joints.

    LoopTK is designed specifically to model the kinematics of protein loops, but it can be used to analyze the motion of any part of the protein chain. LoopTK provides methods for sampling the conformation space of protein loops as well as the self motion space of a loop. Example applications for LoopTK include x-ray crystallography, homology modeling, and drug design.

    LoopTK was developed in close collaboration with the Joint Center for Structural Genomics (JCSG) at the Stanford Linear Accelerator Center. Now a part of the JCSG's protein structure determination process, loopTK models missing protein fragments into experimental data (http://smb.slac.stanford.edu/XpleoServer/Xpleo.jsp).

    This material is based upon work supported by the National Science Foundation under Grant No. 0443939. Any opinions, findings, and conclusions or recommendations expressed in the above material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation."

    Keywords: protein 3d structure, protein chain, protein kinematics, protein loop, protein modeling

  • Lower Extremity Model ( Software )

    This project holds all the files necessary for a SIMM-based musculoskeletal model of the human lower-extremity which can also be easily imported and used in OpenSIM. In order to respect the time and effort put in by the original developers please carefully read accompanying publications and cite appropriate references in future work. The links to the left contain all the files (Downloads) and documentation (Documents) related to the model. Please cite the following paper: - Delp, S.L., Loan, J.P., Hoy, M.G., Zajac, F.E., Topp E.L., Rosen, J.M.: An interactive graphics-based model of the lower extremity to study orthopaedic surgical procedures, IEEE Transactions on Biomedical Engineering, vol. 37, pp. 757-767, 1990.

    About the model: Originally developed in DATE by Scott Delp to examine how surgical changes in musculoskeletal geometry and muscle architecture affect muscle force and joint motion this model uses seven segments and seven degrees-of-freedom to represent the human lower extremity. The model is about 1.8m tall and has the strength of a young, adult male. Muscle lines of action for forty-three muscle-tendon actuators are based on their anatomical relationships to three-dimensional surface representations of bones. A model for each actuator was formulated to compute its isometric force-length relation. The kinematics of the lower extremity were specified by modeling the hip, knee, ankle, subtalar, and metatarsophalangeal joints. Thus, the force and joint moment that each muscle-tendon actuator develops can be computed for any body position. The joint moments calculated with the model compare well with experimentally measured isometric joint moments.

  • MemtestG80 and MemtestCL: Memory Testers for CUDA- and OpenCL-enabled GPUs ( Software )

    MemtestG80 and MemtestCL are a software-based testers to test for "soft errors" in GPU memory or logic for NVIDIA CUDA-enabled or OpenCL-enabled (of any manufacturer) GPUs. They use a variety of proven test patterns (some custom and some based on Memtest86) to verify the correct operation of GPU memory and logic. They are useful tools to ensure that given GPUs do not produce "silent errors" which may corrupt the results of a computation without triggering an overt error. Haque IS and Pande VS. Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU. In Proceedings of 10th IEEE/ACM International Conference on Cluster, Cloud, and Grid Computing (CCGrid 2010), pp 691-696.

    Keywords: gpu, memory, reliability, testing

  • Molmodel: SimTK molecular modeling API ( Software )

    "Molmodel is a programmer’s toolkit for building reduced-coordinate, yet still all-atom, models of large biopolymers such as proteins, RNA, and DNA. You control the allowed mobility. By default, Molmodel builds torsion-coordinate models in which bond stretch and bend angles are rigid while bond torsion angles are mobile. But you can rigidify or free any subsets of the atoms, such as the rigid benzene ring shown here.

    Molmodel is a C++ API for biochemist-friendly molecular modeling that extends the Simbody API to simplify construction of high-performance articulated models of molecules. All of the Simbody API is available when using Molmodel and Simbody must be installed and functioning in order to use Molmodel. See https://simtk.org/home/simbody for more information. Read the Simbody User’s Guide for background, installation instructions, and examples.

    Molmodel can produce models with dramatically fewer degrees of freedom than a typical molecular model, yet the reduced set of coordinates is still a fully nonlinear basis for molecular motions of any size. Structural searches and optimizations benefit from a much reduced search space, Monte Carlo moves can achieve much higher acceptance rates, and dynamics can proceed with much larger step sizes due to the lower natural frequencies produced by larger moving bodies. Because all the atoms are still present, conventional force fields and implicit solvent models can be used for energy and force computations, and Molmodel can use OpenMM (https://simtk.org/home/openmm) to accelerate those calculations. Alternatively, Molmodel is flexible enough to allow you to design your own force fields. Physics-based, knowledge-based, and special-purpose potentials can be designed and incorporated into your Molmodel model.

    While reduced coordinate models have been used succesfully for a variety of purposes (they are ubiquitous in NMR structure refinement, for example), research is needed to determine the best way to model a given molecular system for the particular study at hand. Both the physical properties of a molecular system of interest, and the particular investigation being performed will influence the best choice of model. The point of Molmodel is to enable you or users of your software to perform those studies by providing making it easy to create molecular models with mobility only where you choose to allow it, and then to easily revise those choices.

    Molmodel, Simbody, and OpenMM are components of the open source biosimulation toolkit SimTK, developed and supported by the NIH-funded Center for Physics-Based Simulation of Biological Structures at Stanford (http://simbios.stanford.edu). Molmodel was developed originally for SimTK by Christopher Bruns and Michael Sherman, with major contributions from Peter Eastman and Samuel Flores.

    NOTE: Prior to the 2.2 release, binaries of Molmodel were bundled with other SimTK Core modules. Those can still be found in the Downloads section of the SimTKcore project, at http://simtk.org/home/simtkcore."

    Keywords: molecular dynamics

  • MSMExplorer: A Visualization Application for Markov State Models for Folding ( Software )

    A java-based visualization application for Markov State Models for folding simulations. The programs is designed as a gui interface for viewing and interacting with MSMs constructed by MSMBuilder. SOURCE CODE NOTICE: for up-to-date source code access please visit: http://github.com/brycecr/msmexplorer Similarly, Up-to-date distributions can be downloaded from https://github.com/brycecr/msmexplorer/downloads but periodic major releases (considered "stable") will still be uploaded to simtk. In the Documents section of this site, you'll find an illustrated Reference and Tutorial PDF and a short tutorial video.

    Keywords: Folding, GUI, Markov state model, Phase space, protein folding, Visualization

  • Muscle function of overground running across a range of speeds ( Software )

    This project is a repository of overground running data (3.5m/s 5.2m/s, 7.0m/s and 9.0m/s) along with a working musculoskeletal model to perform simulations and derive the function of individual muscles.

    Keywords: dataset, muscle function, running, sprinting

  • NA_thermo ( Software )

    NA_thermo is a small archive of primer design and nucleic acid thermodynamic scripts used by the Das lab at Stanford for high-throughput RNA synthesis and design.

    Keywords: RNA, DNA, high-throughput

  • NAST ( Software )

    August 2010 UPDATE
    New Releases (1.0) of NAST and C2A are available!
    Lots of exciting new features, detailed in the new manual NastTutorial.v4.pdf (under the "Downloads" button on the left).
    C2A has been separated from NAST, please download and install separately from the C2A project page: simtk.org/home/c2a.

    *****
    Feb 2010 UPDATE 2 - If you are running C2A on a molecules that contains an "end" piece of length 1, please see the wiki for special instructions for fixing a bug that affects you
    *****

    *****
    Feb 2010 UPDATE 1 - Special instructions for running NAST with very large RNA molecules (>1000 nucleotides) are posted on the wiki
    *****


    *****
    Nov 09 UPDATE - NAST is now available on most unix/pc/mac platforms. Please read the instructions posted on the wiki for details.
    *****

    NAST (Nucleic Acid Simulation Toolkit) is a knowledge-based coarse-grained tool for modeling RNA structures. It produces a diverse set of plausible 3D structures that satisfy user-provided constraints based on:

    1. primary sequence
    2. known or predicted secondary structure
    3. known or predicted tertiary contacts (optional)

    Additionally, NAST can use residue-resolution experimental data (e.g. hydroxyl radical footprinting) to filter the generated decoy structures.

    NAST uses an RNA-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate large numbers of plausible 3D structures that satisfy the constraints given on the secondary and tertiary structure. It then filter these structures based on agreement to the experimental data (if available). This results in a model of the molecule which satisfies all the known residue-resolution data.

    TO USE NAST: Please read the README file under the downloads section.

    Keywords: Coarse grained, Knowledge-based, RNA

  • NMBL Image to Model Pipeline ( Software )

    The NMBL Pipeline is a version of NAMIC's (www.na-mic.org) 3D Slicer, adapted to the needs of the Neuromuscular Biomechanics Lab (NMBL) at Stanford University. Slicer is an open-source software tool for performing a diverse array of medical image processing activities within one freely available, easily extensible kit. NMBL Pipeline is intended to coincide with NAMIC's Slicer, and is developed along with 3D Slicer in full collaboration with NAMIC. The differences between NMBL Pipeline and Slicer will be minimal, and probably will include the absence of some of Slicer's modules in NMBL Pipeline, and perhaps some differences in default value settings. This project will continue to be developed for use by NMBL and other members of the general Slicer user community.

    I intend to use SimTK.org in exactly those ways that are intended: namely to make my software available to SimTK users and provide users with documentation, while the users are encouraged to provide feedback to me for improvements.

    Keywords: Image registration, Image segmentation, Mesh generation

  • OpenMM ( Software )

    "OpenMM is a library which provides tools for modern molecular modeling simulation. As a library it can be hooked into any code, allowing that code to do molecular modeling with minimal extra coding.

    Moreover, OpenMM has a strong emphasis on hardware acceleration, thus providing not just a consistent API, but much greater performance than what one could get from just about any other code available.

    VISITING SCHOLAR PROGRAM: An opportunity for individuals to visit Stanford University for a four-week period to advance their OpenMM projects. Applications for this year are no longer being accepted. To learn more about the program, visit http://simbios.stanford.edu/OpenMMVisitingScholar.htm

    AVAILABILITY: See the download section for our latest preview release. A roadmap of future releases can be found on the Wiki.

    MAILING LIST: Sign up for the OpenMM-news mailing list to receive updates about the project. (Click on Advanced -> Mailing Lists)

    NEED HELP? Check out the discussion forums under Public Forums and the material from our workshops under Downloads. If you're new to molecular dynamics, check out the Wiki and OpenMM Zephyr.

    CITING OPENMM: Any work that uses OpenMM should cite the papers listed on the Publications page."

  • OpenMM Software Suite ( Software )

    The OpenMM Software suite encompasses several essential software tools for molecular simulations: OpenMM: a library providing tools for modern molecular modeling simulation. It can be easily hooked into any code, and has a strong emphasis on hardware acceleration, thus providing not just a consistent API, but superior performance. PyOpenMM: a python API that wraps the OpenMM library, for those preferring to code in python. AMBER-compatible front end to OpenMM, designed for AMBER users that would like to enjoy the speed of OpenMM. MSMBuilder: analyze and combine data generated by molecular dynamics runs. MSM Builder provides a means to parallelize OpenMM runs across multiple GPUs OpenMM Zephyr: a user-friendly, easy to use, molecular simulation application, with OpenMM accelerated Gromacs inside, for studying molecular dynamics of proteins, RNA, and other molecules.

    Keywords: GPU, Molecular Dynamics

  • OpenSim ( Software )

    "OpenSim is a freely available, user extensible software system that lets users develop models of musculoskeletal structures and create dynamic simulations of movement.

    Find out how to join the community and see the work being performed using OpenSim at opensim.stanford.edu.

    Access all of our OpenSim resources at the new Support Site.

    Watch our Introductory Video get an overview of the OpenSim project and see how modeling can be used to help plan surgery for children with cerebral palsy."

    Keywords: muscle-driven simulation, musculoskeletal biomechanics, neuromuscular simulation

  • OpenSim 3D World Objects Library ( Software )

    We have developed a library of 3D world objects which appear as colored solid bodies in OpenSim. The objects are formatted with color, texture, and correct geometries. We hope these objects both provide a visual context for simulations and also serve as a tool to analyze interactions of objects with musculoskeletal models.

    Keywords: 3D, Objects, opensim, visual, World

  • OpenSim Motion and Simulation Data ( Software )

    A repository of motion data from experiments and simulations, contributed by members of the OpenSim community. Please respect your fellow OpenSim Users. In using these data we ask that you respect the hard work of your fellow researchers by citing their work appropriately. When you go to the Download section you will be directed to individual project pages for each model which contain all of the files and documentation. Please carefully review the publications and cite the references in your future papers, presentations, grant applications, etc. Have data to contribute? Do you have simulation or motion data which you would like to make available through this library? Providing others with access to your data can stimulate future studies, provide a foundation for young researchers, and maximize the impact of your work. Its easy to set up a project page to post your work. This will allow you to track who is using your data and be in contact with them. Please consider contributing! If you would like to have your project included on this site, please contact Jennifer Hicks, listed as one of the Project Leads. No guarantees about quality, correctness or support are provided by the SimTK team or OpenSim team. Use at your own risk.

    Keywords: experimental data, OpenSim, Simulations

  • OpenSim Utilities ( Software )

    A repository of tools written by members of the OpenSim community to support their usage of the software. Please respect your fellow OpenSim Users. In using these utilities we ask that you respect the hard work of your fellow researchers by citing their work appropriately. When you go to the Download section you will be directed to individual project pages for each model which contain all of the files and documentation. Please carefully review the publications and cite the references in your future papers, presentations, grant applications, etc. Have a utility to contribute? Do you have a utility which you would like to make available through this library? Providing others with access to your tools and utiities can stimulate future studies, provide a foundation for young researchers, and maximize the impact of your work. Its easy to set up a project page to post your work. This will allow you to track who is using your utilities and be in contact with them. Please consider contributing! If you would like to have your project included on this site, please contact Jennifer Hicks, listed as one of the Project Leads. No guarantees about quality, correctness or support are provided by the SimTK team or OpenSim team. Use at your own risk.

    Keywords: extensions, OpenSim, plugins, software tools, utilities

  • PAPER Accelerates Parallel Evaluations of ROCS ( Software )

    PAPER is a program to calculate optimal molecular overlays, based on the Gaussian model of molecular shape (as used, for example, in OpenEye ROCS). It accelerates large screening experiments by evaluating multiple overlays in parallel on NVIDIA GPUs.

  • PROTEAND ( Software )

    "PROTEAND generates interactive graphical representations that highlight uncertainty in atomic coordinates. It represents structural uncertainty in three ways: (1) The traditional way: The program shows a collection of structures as superposed and overlapped stick-figure models. (2) Ellipsoids: At each atom position, the program shows an ellipsoid derived from a three-dimensional Gaussian model of uncertainty. This probabilistic model provides additional information about the relationship between atoms that can be displayed as a correlation matrix. (3) Rigid-body volumes: Using clouds of dots, the program can show the range of rigid-body motion of selected substructures, such as individual alpha helices."

  • Protein Mechanica Coarse-Grained Molecular Motor Modeling Application ( Software )

    This project is an interactive application that allows users to generate structurally realistic models of molecular motor conformations. Coarse-grained models of molecular structures are constructed by combining groups of atoms into a system of arbitrarily shaped rigid bodies connected by joints. Contacts between rigid bodies enforce excluded volume constraints, and spring potentials model system elasticity. This simplified representation allows the conformations of complex molecular motors to be simulated interactively, providing a tool for hypothesis building and quantitative comparisons between models and experiments.

    Keywords: coarse-grained molecule modeling, Molecular simulation, protein kinematics

  • Sam's Simulations ( Software )

    This project is intended to serve as a repository for software developed for physics-based simulation of human motion, as part of the work in the Neuromuscular Biomechanics Lab.

    Keywords: full-body model, muscle-driven simulation, musculoskeletal biomechanics, neuromuscular simulation, running

  • scexpress: A visual aid to examine expression patterns within single cells ( Software )

    We have designed SC Express, a bioinformatics tool that produces a three-dimensional shape that is reflective of the expression patterns of a single cell. The software package accepts tab delimited text files containing the relevant gene expression data and provides a graphical user interface that enables facile comparison of any two individual cell types on the same screen.

    Keywords: single cell expression

  • Simbody: SimTK multibody dynamics API ( Software )

    This project is a SimTK toolset providing general multibody dynamics capability, that is, the ability to solve Newton's 2nd law F=ma in any set of generalized coordinates subject to arbitrary constraints. (That's Isaac himself in the oval.) Simbody is provided as an open source, object-oriented C++ API and delivers high-performance, accuracy-controlled science/engineering-quality results.

    Simbody uses an advanced formulation of rigid body mechanics to provide results in Order(n) time for any set of n coordinates. This can be used for internal coordinate modeling of molecules, or for coarse-grained models based on larger chunks. It is also useful for large-scale mechanical models, such as neuromuscular models of human gait, robotics, avatars, and animation. Simbody can also be used in real time interactive applications for biosimulation as well as for virtual worlds and games.

    This toolset was developed originally for SimTK by Michael Sherman at the Simbios Center at Stanford, with major contributions from Peter Eastman and others. Simbody descends directly from the public domain NIH Internal Variable Dynamics Module (IVM) facility for molecular dynamics developed and kindly provided by Charles Schwieters. IVM is in turn based on the spatial operator algebra of Rodriguez and Jain from NASA's Jet Propulsion Laboratory (JPL), and Simbody has adopted that formulation.

    NOTE: Prior to the 2.2 release, binaries of Simbody were bundled with other SimTK modules in the SimTKcore project. Those can still be found at http://simtk.org/home/simtkcore, Downloads page.

    Keywords: articulated body, coarse-grained molecule modeling, constrained motion, internal coordinates, mechanical simulation, mechanics, molecular dynamics, multibody dynamics, rigid body, simtk core, skeletal mechanics, torsion coordinates

  • SIML: a fast SIMD implementation of LINGO chemical similarities ( Software )

    SIML ("Single-Instruction, Multiple-LINGO") is a library containing implementations of a fast SIMD algorithm for calculating the LINGO chemical similarity metric (described in an upcoming publication). This method, currently implemented for x86 CPUs (non-vectorized) and NVIDIA GPUs, is several times faster than existing LINGO implementations for the CPU, and two orders of magnitude faster when run on a GPU.

    Keywords: chemical similarity, GPU

  • SimTK Core Toolset (obsolete project) ( Software )

    Prior to June, 2011 this project was used to distribute the Simbios-developed Simbody and Molmodel packages in the SimTK biosimulation toolkit. These are now distributed separately from the Simbody and Molmodel projects (https://simtk.org/home/simbody, https://simtk.org/home/molmodel). Please use those projects instead of this one.

    The other major component of SimTK is the GPU-accelerated molecular dynamics package OpenMM, see https://simtk.org/home/openmm if you are interested.

    The text below refers to the pre-June, 2011 packaging and has been superseded as described above.

    SimTK Core subprojects This SimTK Core project collects together all the binaries needed for the various SimTK Core subprojects. These include Simbody, Molmodel, Simmath (including Ipopt), Simmatrix, CPodes, SimTKcommon, and Lapack. See the individual projects for descriptions.

    SimTK overview
    SimTK brings together in a robust, convenient, open source form the collection of highly-specialized technologies necessary to building successful physics-based simulations of biological structures. These include: strict adherence to an important set of abstractions and guiding principles, robust, high-performance numerical methods, support for developing and sharing physics-based models, and careful software engineering.

    Accessible High Performance Computing
    We believe that a primary concern of simulation scientists is performance, that is, speed of computation. We seek to build valid, approximate models using classical physics in order to achieve reasonable run times for our computational studies, so that we can hope to learn something interesting before retirement. In the choice of SimTK technologies, we are focused on achieving the best possible performance on hardware that most researchers actually have. In today's practice, that means commodity multiprocessors and small clusters.

    The difference in performance between the best methods and the do-it-yourself techniques most people use can be astounding—easily an order of magnitude or more. The growing set of SimTK Core libraries seeks to provide the best implementation of the best-known methods for widely used computations such as:
    Linear algebra, numerical integration and Monte Carlo sampling, multibody (internal coordinate) dynamics, molecular force field evaluation, nonlinear root finding and optimization. All SimTK Core software is in the form of C++ APIs, is thread-safe, and quietly exploits multiple CPUs when they are present.

    The resulting pre-built binaries are available for download and immediate use.

    Citation: Any work that uses SimTK Core (including Simbody) should cite the following paper: Jeanette P. Schmidt, Scott L. Delp, Michael A. Sherman, Charles A. Taylor,Vijay S. Pande, Russ B. Altman, "The Simbios National Center: SystemsBiology in Motion", Proceedings of the IEEE, special issue on Computational System Biology. Volume 96, Issue 8:1266 - 1280. (2008)

    Keywords: omputational algorithms, high-performance, linear algebra, numerical integration, numerical methods, optimization

  • SimTK, the Simbios biosimulation ToolKit ( Software )

    "SimTK, the Simbios biosimulation toolkit, provides a robust, high-performing, open-source collection of technologies that are valuable for building applications that employ physics-based simulations of biological structures. It is well-suited for applications in a wide variety of domains from molecules to whole organisms.

    Accessible High Performance Computing
    The growing set of SimTK libraries offers the best implementation of the best-known methods for widely used computations. With it, we enable valid models to be built using classical physics while simultaneously providing the best possible performance on commonly available hardware, such as commodity multiprocessors with high-performance GPUs and small clusters."

  • SStructView Applet ( Software )

    This is the SStructViewApplet by Ramon Felciano.

    Keywords: domain graphics, RNA secondary structure

  • SUNDIALS: Suite of nonlinear differential algebraic solvers ( Software )

    This project provides a high performance, cross platform implementation of SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers).
    Which consists of the following modules:
    CVODE for solving ordinary differential equations using a variable order implicit solver
    CVODES ODE solver with sensitivity analysis
    IDA solves differential algebraic equations
    KINSOL solves nonlinear algebraic systems

  • Thermodynamics and Kinetics of Biomolecular Folding ( Software )

    SimTK RNA_Fold project aims to understand the accurate folding pathways of RNA molecules. Free energy landscape of RNA folding will be studied for all atom model or physical based coarse graining model. Replica exchange Molecular Dynamics, simulated tempering and other sampling methods will be used to enhance sampling. Folding@Home distributed computing will be used due to its big computing power.

    Keywords: RNA, rna folding

  • Tim's OpenSim Utilities ( Software )

    This project site is concerned with extending the functionality of OpenSim through the use of scripting tools and plugins. Click on the downloads link to browse the set of freely available OpenSim tools for download.

    Previously delivered interactive webinars demonstrating the use of the Pseudo-Inverse Induced Acceleration plugin for OpenSim (IndAccPI).

    Keywords: matlab, OpenSim, plugin

  • Torso + Lower Extremity Model ( Software )

    This project contains an OpenSIM model file that includes a torso segment in addition to the lower extremity. The model contains 23 degrees of freedom and 92 muscle-tendon actuators. The joint between the torso and the pelvis is represented by a ball-and-socket joint. In order to respect the time and effort put in by the original developers please carefully read accompanying publications and cite appropriate references in future work. The links to the left contain all the files (Downloads) and documentation (Documents) related to the model. Please cite the following paper: - Delp, S.L., Loan, J.P., Hoy, M.G., Zajac, F.E., Topp E.L., Rosen, J.M.: An interactive graphics-based model of the lower extremity to study orthopaedic surgical procedures, IEEE Transactions on Biomedical Engineering, vol. 37, pp. 757-767, 1990.

    About the model: The lower-extremity portion of the model was originally developed by Scott Delp to examine how surgical changes in musculoskeletal geometry and muscle architecture affect muscle force and joint motion. With the addition of the torso segment this model has 23 degrees of freedom and 92 muscle actuators. The model is about 1.8m tall and has the strength of a young, adult male. Muscle lines of action are based on their anatomical relationships to three-dimensional surface representations of bones. A model for each actuator was formulated to compute its isometric force-length relation. The kinematics of the lower extremity is specified by modeling the lumbar, hip, knee, ankle, subtalar, and metatarsophalangeal joints.

  • VA-BATTS: Stresses in bone sections with inhomogeneous material properties ( Software )

    A new software tool to calculate bending, axial, torsional, and transverse shear stresses within bone cross sections having inhomogeneous material properties.

  • VA-Squish: Determining Cartilage Linear Biphasic constants from Indentation test ( Software )

    ***New Release - version 2.1: please update***

    Indentation testing is commonly used to test cartilage material properties. Using a linear biphasic material model, the determination of three material constants (aggregate modulus, Poisson's ratio, and permeability) from the test results requires an optimization or curve-fitting approach to determine a solution that best matches the experimental creep or stress-relaxation data.

    The VA-Squish project developed a fast and easy way (using MATLAB) to calculate the best-fit bi-phasic constants, based on input from a standardized indentation test. This method involves creating a multi-dimensional Cartilage Interpolant Response Surface (CIRS) map from a large number of solutions obtained from finite element analyses and then searching this surface map for the closest solution. CIRS maps were generated for a range of different testing conditions.

    Response surface files have been generated for a specific set of test conditions. It is recommended that anyone who is considering performing tests choose a test setup and testing parameters that exactly match one for which a response surface exists. These are given in the downloads section of this website and are listed in Table 2 of the VA-Squish User Guide.

    Flat, porous indenter contact has been modeled as both frictionless and with a coefficient of static friction. The improved model which incorporates friction is a more accurate model of the experimental conditions. Additionally, the new release, v2.0, includes an improved mesh which is double biased through the radius and biased through the thickness.

    Keywords: Biphasic material properties, Cartilage, Indentation testing

  • ViewCommonPaths Application ( Software )

    The ViewCommonPaths program helps to simultaneously visualize a set of numeric sequences that have the same start and end elements by drawing them into a common directed acyclic graph (DAG). In particular, ViewCommonPaths helps to simultaneously visualize a set of allosteric communication paths with the same start and end residues. Given a set of allosteric paths (each a sequence of residues), ViewCommonPaths creates a DAG from the set of individual pathways and allows a quick visual analysis of these pathways and the relationships among the residues along these paths.

    Keywords: allosteric communication, allosteric communication paths, computational modeling, directed acyclic graph, multiple sequence alignments, protein residues

  • VTK Mac with Java Support ( Software )

    Using Java with VTK on Mac OS X 10.3 and higher is basically broken. This project aims to correct these problems and provide a version of VTK on the Mac where Java (and C++) can be used. This code is based on the latest VTK 4.2 stable release. The changes made to VTK here have been submitted to the VTK organization, but these have not yet been integrated into their code repository. Also, the changes will probably never make it to their 4.2 code base, so we will provide this code until the next stable release of VTK comes out with proper Java Mac support.

    Java VTK support on the Mac uses Cocoa. Tcl and Python wrappers currently do not work with Cocoa, so they are not supported with this modified version of VTK. Java and C++ are supported.

  • xerces-c ( Software )

    Project for headers and binaries of xerces-c tools for parsing xml files.


Web Links:

Last updated: 2013-10-01T12:29:19.934-05:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016