Developing Retinal Vascular ABM with Pericytes

Objective: Define a role for perivascular cells during developmental retinal angiogenesis in the context of endothelial cell Notch1-DLL4 signaling at the multicellular network level. Methods: The retinal vasculature is highly sensitive to growth factor m
Forum posts last week: 1

Vector Space Construction for the Microbiome

Project with the FDA as part of the UCSF-Stanford CERSI to predict drug metabolism by bacteria in the human gut. Prototyped on MetaCyc data using the mol2vec pipeline from Stefano Rensi. Work as part of student's masters thesis in Russ Altman's lab at Sta
Forum posts last week: 1
New members: 1

Virtual Prototyping for Prevention of Pressure Ulcers

This project aims to develop models i) to explore the etiology of pressure ulcers, and ii) to aid the design and evaluation of intervention strategies for their prevention.
New followers: 1

Grand Challenge Competition to Predict In Vivo Knee Loads

Provide a comprehensive data set with associated models that will enable researchers to validate musculoskeletal model estimates of muscle and joint contact forces in the knee.
Downloads last week: 35
Total downloads: 8,840

Muscle-actuated Simulation of Human Running

The purpose of this study was to determine how muscles contribute to propulsion (i.e., the fore-aft acceleration) and support (i.e., the vertical acceleration) of the body mass center during running.
Downloads last week: 19
Total downloads: 9,090

Lower Extremity EMG-driven Modeling with Automated Adjustment of Geometry

This project provides Matlab code for developing EMG-driven models of walking using scaled OpenSim lower extremity musculoskeletal models.
New download files: 1

Open Knee(s): Virtual Biomechanical Representations of the Knee Joint

Overall purposes of the project are: 1) To provide free access to three-dimensional finite element representations of the knee joint 2) Open development of knee models for collaborative testing and use
Downloads last week: 43
Total followers: 21
Total downloads: 9,994

Whole-Cell Computational Model of Mycoplasma genitalium

This project provides all code and data for the first "whole-cell" model of the entire life cycle of a living organism, Mycoplasma genitalium.
Downloads last week: 36
Total downloads: 15,156

Muscle Wrapping Over Multiple Smooth Surfaces

Provides high performance muscle wrapping for simulation of musculoskeletal dynamics.
New followers: 1

Simbody: Multibody Physics API

Simbody is useful for internal coordinate and coarse grained molecule modeling, large scale mechanical models like skeletons, and anything else that can be modeled as bodies interconnected by joints, acted upon by forces, and restricted by constraints.
Forum posts last week: 2
Total downloads: 3,322

Data-tracking optimization using collocation

This project contains a package that can be used to perform data-tracking optimization using collocation method. The codes and models are available. The tracking results for one subject during walking and running are also provided.
Downloads last week: 23

OpenMM

OpenMM includes everything one needs to run modern molecular simulations. It is extremely flexible with its custom functions, is open-source, and has high performance, especially on recent GPUs.
Downloads last week: 484
Forum posts last week: 22
Total followers: 34
Total downloads: 95,624

Platform for Dynamic Simulation and Control of Movement based on OpenSim&MATLAB

This project overcomes neuromusculoskeletal systems limitations of MATLAB®/Simulink® and robust design & control limitations of OpenSim through an interface between these two software packages that combines relevant strengths of each individual package.
New followers: 1

Matlab-Opensim Interfaces

Provides tools for using different aspects of Opensim within the Matlab environment, including command line pipelines as well as accessing the Opensim API directly. The main functionality has now been included as part of Opensim 3.0 with improved functionality (and will become more obsolete with Opensim 4.0). Please see the developer wiki for more information. Therefore this is being kept only as an archive, and users should see the documentation on interfacing Matlab with Opensim on the Opensim website (http://simtk-confluence.stanford.edu:8080/display/OpenSim/Scripting+with+Matlab). As such the forums etc will not be monitored.
New followers: 1
Total downloads: 3,207

SimVascular: Examples and Clinical Cases

Download examples and clinical case files for cardiovascular modeling and simulation compatible with SimVascular
Downloads last week: 42
Total downloads: 332