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National Center for Multiscale Modeling of Biological Systems (MMBioS)

Ivet Bahar, Ph.D.
P41GM103712
Active

Center Overview

The National Center for Multiscale Modeling of Biological Systems (MMBioS) will develop tools to advance and facilitate cutting-edge research at the interface between high performance computing technology and the life sciences. Our overarching biological goal is the predictive multi-scale modeling of the spatiotemporal organization and evolution of neurosignaling systems and events. The advances made here will impact the research activities of a broad group of scientists, from molecular and structural biologists to cell and systems biologists. These advances will also facilitate the translation of basic tools to biomedical and clinical research by establishing and then disseminating a computational framework which integrates theory with experiment, and models with methods originating from different disciplines.

We are building on the unique state-of-the-art technology and methods at the forefront of molecular and cellular modeling that have been developed at our partner sites. Rapid advances in experimental technologies which are enabling the study of events ranging from single molecule dynamics to tissue level organization are also creating multi-scale modeling challenges. We will address these emerging challenges, including high performance computing, data storage and networking needs.

Resources

ResourceDescriptionSupported PlatformsSupported FormatsData TypeData Size (compressed)
AlignTK
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

AlignTK is an image alignment toolkit. It is designed for batch-oriented alignment of a large number of 2-D images in either 2 or 3-dimensions.  Although it has been applied most extensively to electron-microscopy (EM) images of neural tissue, the package can be used with arbitrary grayscale images.  Multiple image formats are supported.

Linux N/A N/A
ANM
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

ANM (Anisotropic network model) is a simple tool for predicting the collective motions of molecular systems introduced using Elastic Network Models (ENM) and normal mode analysis. The biomolecular system is represented as a network, or graph, the nodes of which are the residues and the springs are their interactions. The model helps elucidate the intrinsic dynamics of proteins and their complexes and make inferences on functional mechanisms.

Web-Based N/A N/A
BioNetGen
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

BioNetGen is software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks.

Linux, Mac OSX, Windows N/A N/A
CellBlender
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

CellBlender is a Blender addon for creation, simulation, visualization, and analysis of realistic 3D Cell Models. CellBlender leverages the full-featured 3D content creation capabilities of Blender to support a rich environment for the creation of simulation-ready, biophysically realistic models of the microscopic structure and biochemical function of cells.

CellBlender is fully functional with MCell and partially functional with SBML (http://sbml.org). We invite the computational cell biology community to contribute to the project, adding features and support...

Linux, Mac OSX, Windows N/A N/A
CellOrganizer
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

The CellOrganizer project provides tools for

  • learning generative models of cell organization directly from images
  • storing and retrieving those models in XML files
  • synthesizing cell images (or other representations) from one or more models

Model learning captures variation among cells in a collection of images. Images used for model learning and instances synthesized from models can be two- or three-dimensional static images or movies.

Linux, Mac OSX N/A N/A
GTKDynamo
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

GTKDynamo is free/open source software which, together with pDynamo, transforms PyMOL into a powerful interface for molecular modeling. The interface has been designed to facilitate determining reaction pathways in biological systems, specially using hybrid QC/MM (or QM/MM) methods. Pymol has been chosen as a graphical interface to pDynamo because it has a python API with wide documentation available.

Linux, Mac OSX N/A N/A
iGNM
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We present here an updated version, iGNM 2.0 http://gnmdb.csb.pitt.edu/, which covers more than 95% of the structures currently available in the Protein Data Bank (PDB). Advanced search and visualization capabilities, both 2D and...

Web-Based N/A N/A
MCell
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

MCell is a Monte Carlo reaction-diffusion simulator for modeling computational microphysiology in arbitrarily complex 3D spatial geometries.

As a modeling tool, MCell creates realistic simulations of cellular signaling in the complex 3fD subcellular microenvironment in and around living cells -- what we call cellular microphysiology. At such small subcellular scales the familiar macroscopic concept of concentration is not useful and stochastic behavior dominates. MCell uses highly optimized Monte Carlo algorithms to track the stochastic behavior of...

Linux, Mac OSX, Windows N/A N/A
ProDy
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

ProDy is a free and open-source Python package for protein structural dynamics and sequence evolution analysis. It is designed as a flexible and responsive API suitable for interactive usage and application development. NMWiz, a VMD plugin GUI, also accompanies ProDy for streamlining protein dynamics analysis calculations and enabling comparative visual analysis of experimental and theoretical data.
With ProDy, you can perform principal component analysis of heterogeneous X-ray structures, NMR models, and MD snapshots. Protein dynamics...

Linux, Mac OSX, Windows N/A N/A
WESTPA
National Center for Multiscale Modeling of Biological Systems (MMBioS)
NIGMS

WESTPA (the Weighted Ensemble Simulation Toolkit with Parallelization and Analysis) is an open-source software package that provides a high-performance framework for carrying out extended-timescale simulations of rare events with rigorous kinetics using the weighted ensemble algorithm of Huber and Kim (1996). The software also includes options for further enhancing the sampling efficiency through reassignment of weights according to either equilibrium or nonequilibrium steady state, and a plugin for using a weighted ensemble-based string method. The...

Linux, Mac OSX N/A N/A