Models, Tools & Databases

Models, Tools & Databases


3D GranSim

GranSim is a hybrid agent-based computational model (ABM) that describes the formation and function of a granuloma during Mycobacterium tuberculosis infection in the lung.

A Gestalt inference model for auditory scene segregation

The auditory stream segregation model leverages the multiplexed and non-linear representation of sounds along an auditory hierarchy and learns local and global statistical structure naturally emergent in natural and complex sounds.

Digital Lung

The lung model integrates mechanics and cell models.

Dynamic Regularity Extraction (D-REX) Model

The D-REX model is designed for exploring the computational mechanisms in the brain involved in statistical regularity extraction from dynamic sounds.


GranSim, the Agent-based model (ABM) describing tuberculosis (TB) granuloma formation and function in the lung, was developed based on four basic concepts: an environment (section of the lung parenchyma), agents (immune cells), ABM rules that govern the agents and their interactions, and the time

Innate Immune Response Agent-based Model (IIRABM)

The Innate Immune Response Agent-Based Model (IIRABM) is a two-dimensional abstract representation of the human endothelial-blood interface.  This abstraction is designed to model the endothelial-blood interface for a traumatic (in the medical sense) injury, and does so by representing this inter

Multiscale Imaging-based Cluster Analysis (MICA) - bridging individual and population scales of the human lungs

MICA is an imaging clustering analysis method that employs imaging-based metrics at local and global scales of the human lungs constructed from 3D computed tomography (CT) lung images to identify homogeneous subgroups, known as clusters, in healthy, asthma and COPD populations.

Multiscale Model for Functionalized Nanocarrier Targeting for Drug Delivery

Multiscale Model of Platelet in Blood Flow

We will use an integrated Dissipative Particle Dynamics (DPD) and Coarse Grained Molecular Dynamics (CGMD) approach that allows platelets to continuously change their shape and synergistically activate by a biomechanical transductive linkage chain, interact with other blood constituents an

Neuroanatomic Propagation of ALS within the Spinal Cord

Amyotrophic lateral sclerosis (ALS) is the most common Motor Neuron Disease. It is a progressive neurodegenerative disease that affects motor neurons in the brain and the spinal cord.

Nutritional immunity lung model

Multiscale model that allows the study of the effect of host-centric perturbations of iron metabolism during the very early stages of infection

Open Knee(s): virtual biomechanical representations of the knee joint

This resource is a project website to provide free access to three-dimensional finite element representations of the knee joint and open development of knee models for collaborative testing and use.

Physics-based mass action dynamics of central metabolism including regulation and thermodynamics

This is a physics-based model of central metabolism of Neurospora crassa, a filamentous fungi, in which physiologically reasonable rate constants are inferred from data and physical principles.

Reference Models for Multi-Layer Tissue Structures

This resource is the project website to provide fundamental data, open and freely accessible databases of tissue mechanical and anatomical properties, models of multi-layer tissue structures of musculoskeletal extremities.

Reproducibility in simulation­-based prediction of natural knee mechanics

This project aims for understanding the influence of modelers’ approaches and decisions (essentially their art) throughout the lifecycle of modeling and simulation.


Data and Model Sharing Group

Data and Model Sharing

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Data and Model Sharing Group

Human Neocortical Neurosolver

Magneto- and electro-encephalography (MEG/EEG) non-invasively record human brain activity with millisecond resolution providing reliable markers of healthy and disease states.

OpenSim: easy-to-use, extensible software for modeling, simulating, controlling, and analyzing the musculoskeletal system

OpenSim is a software platform for modeling humans, animals, robots, and the environment, and simulating their interaction and movement. OpenSim has a graphical user interface (GUI) for visualizing models and generating and analyzing simulations.

Prediction of metabolite concentrations, rate constants and post-translational regulation

This tool consists of Jupyter notebooks, contained in the Supplementary Information to the linked article, for a new approach to modeling the mass action kinetics of metabolism. The central metabolism of Neurospora crassa, a filamentous fungi, is used for demonstration purposes.

scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data

scEpath is an approach that calculates energy landscapes and probabilistic directed graphs in order to reconstruct developmental trajectories.

SoptSc: Cell lineage and communication network inference via optimization for single-cell transcriptomics.

Implementation of pattern recognition algorithms and visualization tools for similarity and communication between cells and populations of cells.

StochSS: an integrated development environment for simulation of biochemical networks

Discrete stochastic simulation has become an important and widely-used tool for modeling of biological systems at the molecular scale.


EDGAR Electrocardiographic Imaging Database

The Experimental Data and Geometric Analysis Repository (EDGAR) is a free, web-based repository hosted by the SCI Institute at the University of Utah.

Neurospora crassa Pathway-Genome Knowledgebase

This is a Biocyc genome-scale model of Neurospora crassa, with on-going curation including metabolism, regulation, and genome, adopted from the original work by Dreyfuss, Zucker, et al. (

Reference in vivo data for anatomy and mechanics of multi-layer tissue structures

Data to understand the mechanics of multi-layer tissue structures of the limbs, particularly of the lower and upper legs and arms. Anatomical and mechanical data were collected on extremities of 100 adult subjects (50 male, 50 female) from the general population.

SPARC Portal

The SPARC Portal provides interactive access to a growing collection of data, maps, and computational studies generated by researchers funded through the