Core 1 | Core 2 | Core 3 | Core 4 | Core 5 | IP | Services | Doc | Award Period: III| II | I
| Core 1: Integrative Modeling of Subcellular Processes: Application to Synaptic Activity and Pharmaceutical Discovery | ||
| APBS | Adaptive Poisson-Boltzman Solver. This code allows the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. | [Download] [Documentation] [Related] |
| PDB2PQR Server | This server enables a user to convert PDB files into PQR files. PQR files are PDB files where the occupancy and B-factor columns have been replaced by per-atom charge and radius. | [Download] [Documentation] [Related] |
| APBS Command | This software is a graphical user interface module for Vision that simplifies the setup of APBS calculations and enhances the analysis of the results of such calculations. It also has a Web Service interface to APBS. | [Download] [Documentation] [Related] |
| iAPBS |
iAPBS is a C/Fortran interface to APBS, fast and powerful Poisson-Boltzmann equation solver. This interface enables access to most of APBS capability from within any C or Fortran code. In addition to the reference implementation, iAPBS/CHARMM and iAPBS/Amber modules are also available. These modules extend CHARMM and Amber functionality with APBS routines for electrostatic calculations. Work on iAPBS/NAMD module is in progress. |
[Download] [Documentation] [Related] |
| FETK | a collection of parallel adaptive multilevel finite element software libraries and tools for solving PDE’s and IE’s. | [Download] [Documentation] [Related] |
| SMOL | A solver for the popular Smoluchowski diffusion equation for diffusion events considering the electrostatic interactions between solvent and solutes. Both steady-state and time-dependent SMOL equations are included. | [Download] [Documentation] [Related] |
| FERBE | Collections of software for interpreting umbrella sampling, steered MD and single-molecule force spectroscopy experiments | |
| Core 2: Data Integration and Analytic Tools for Molecular Sequences | ||
| Biological Networks | a bioinformatics software platform for visualizing molecular interaction networks, data integration, and data query using graph query engine. Frontend to PathSys II. Regineered PathSys for biological association graphs. | [Download] [Documentation] [Related] |
| Influenza Database | access to heterogeneous information that are of value to researchers in epidemiology, virology and vaccine development | |
| CMDB | Continuity model database for cardiac cells, with support for cellML and SBML models, currently accessible through Continuity’s model editor | |
| Core 3. Structurally and Functionally Integrated Modeling of Cell and Organ Biophysics | ||
| Continuity 6 | a computational tool for continuum problems in bioengineering and physiology, especially those related to cardiac mechanics and electrocardiology research. In addition to continuum modeling, Continuity 6.0 has facilities for least-squares fitting of parametric models to experimental measurements from diverse sources including gross anatomy, histomorphology, 3-D medical imaging, and physiological and biomechanical testing. | [Download] [Documentation] [Related] |
| Core 4. Creating Visualization Environments for Multi-Scale Biomedical Modeling | ||
| AutoDock | is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. | [Download] [Documentation] [Related] |
| MGLTools | Python Molecular Viewer (PMV), Visual Programming Environment, including NetworkEditor (Vision) and AutoDockTools, which provides a GUI for setting up and running docking calculations using AutoDock (ADT) | [Download] [Documentation] [Related] |
| Core 5. Grid Computing and Analysis for Multi-scale Biomedical Applications | ||
| GAMA | complete GSI credential management and integration solution tailored for use in the emerging CyberInfrastructure through web portals or web service-based clients | [Download] [Documentation] [Related] |
| Opal | SOAP-based web service interface for programmatic access to applications such as APBS, GAMESS, QMView, and other NBCR applications. | [Download] [Documentation] [Related] |
| Gemstone | “grid enabled molecular science through online networked environments”, aka, GEMSTONE, is designed as a rich client built on the Mozilla engine and supports dynamic integration of GUI elements specified by Web Servies. | [Download] [Documentation] [Related] |
| Pydusa, aka, myMPI++ | a Python module which contains calls to many of the important MPI routines and enables mixing of Python, C, and Fortran MPI programs | [Download] [Documentation] [Related] |
| Rock’n Rolls | Rolls are RPM packages configured for automatic (re)deployment to Rocks-based clusters. | [Download] [Documentation] [Related] |
| My WorkSphere |
My WorkSphere is a portal environment based on GridSphere, with customized portlets supporting a range of essential daily activities in biomedical research. This environment utilizes software developed by the National Biomedical Computation Resource (NBCR), and other projects such as NCMIR, BIRN, GEON, Rocks, and other open source efforts from a number of international projects such as Gfarm, CSF4, and APAC. |
[Related] |
| Cell Centered DataBase (CCDB) | one of the first Internet databases for cellular imaging data, makes 3D microscopic imaging data available to the structural biology and neuroscience communities. This database houses structural and protein distribution information derived from confocal, multiphoton, and electron microscopy, including correlated microscopy. | |
| TxBR | Transform Based Back-Projection algorithm that seeks improvements in tomograms and corrects distortions. TxBR produces data sets suitable for further tomographic segmentation and reconstruction.TxBR is accessible through the Telescience portal as part of a suite of tomographic reconstructiontools that are grid-enabled . | |
| Telesciene Portal | The Telescience Portal, the interface for the Telescience Project, consolidates access for controlling instruments remotely, managing data, and controlling batch jobs with a single login and password. The Portal walks the user through the complex process of remote data acquisition via Telemicroscopy; Globus-enabled parallel tomographic reconstruction; advanced visualization, segmentation, and data processing tools; and transparent deposition of data products into federated libraries of cellular structure. TxBR, G-tomo are accessible from the Telescience portal. | |
| GAMESS | This code allows one to carry out quantum chemical computations for small to medium size molecular systems, including a variety of options for structure, property and dynamics. | [Download] [Documentation] [Related] |
| QMView | This software is a graphical user interface that simplifies set up and analysis of quantum mechanical computations using GAMESS. | [Download] [Documentation] [Related] |
| Integrative Projects | ||
| Avian Flu Grid | This project aims to use the grid and high performance computing infrastructure to develop a model for global collaboration in the fight against the pandemic threat of Avian flu and other emerging infectious diseases. Currently the project focuses on the Hemagglutinin and Neuraminidase proteins from Avian and Human flu viruses in order to understand the mechanism of host selectivity and drug resistance. Through a global partnership forged over the PRAGMA grid development activities, we now aim to build a scalable, global, and open knowledge environment for developing novel inhibitors to avian flu. In addition, by involving scientific researchers with grid developers, database developers, and leveraging tools and resources from member institutes, we intend to deliver both grid computing tools and data management and sharing capabilities that are tested through cutting edge scientific research, and formulate sustainable models of data sharing and drug discovery through international collaboration. |
[Related] |
| SMOL+ | Reconstructions of the 3 dimensional microanatomy of the mouse ventricular myocyte from normal and failing hearts. In a gene targeted model of congestive heart failure, there are substantial alterations in the 3 dimensional architecture of the transverse tubular system. To explore the relationship between t-tubule structure and excitation-contraction coupling, we developed a multiscale finite element model of a single t-tubule and the surrounding half-sarcomeres. The results suggest that heterogeneous distribution of L-type calcium channels along the t-tubules may be important for synchrony of intracellular transients. New anatomical reconstructions of myocyte microanatomy and numerical methods will enable this multiscale analysis to be extended to the whole cell scale. The software component will be released as part of the SMOL package, with mesoscale modeling as the newly added features. | [Related] |
| Biomedical Community Services | ||
| Grid computing resources | see User Services | |
| Training & Dissemination | see Community Portal | |
| MAST | Motif Alignment & Search Tool (Bailey, U. Queensland) | |
| MEME | Multiple EM for Motif Elicitation | [Download] [Documentation] [Related] |
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MetaMEME
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Meta-MEME is a software toolkit for building and using motif-based hidden Markov models of DNA and proteins. The input to Meta-MEME is a set of similar protein sequences, as well as a set of motif models discovered by MEME. Meta-MEME combines these models into a single, motif-based hidden Markov model and uses this model to search a sequence database for homologs. (Noble, U. Washington) | |
| MCAST | Searching a sequence database for a cluster of hits to query motifs. | |
| Gist | Support Vector Machine (SVM) classification algorithm. | |
| Euler | Genomic DNA fragment assembly tool (Pevzner, UCSD) | |
| ABA | The portal for the A-Bruijin Aligner for multiple alignment of sequences with repeated and shuffled elements. | |
| GRIMM | Genome Rearrangements In Man and Mouse (Tesler, UCSD) | |
| MGR | Multiple Genome Rearrangements | |
| HAP | a haplotype analysis system which is aimed in helping geneticists perform disease association studies (Eleazar, UCLA). | |
| Award Period II (5/1/1999 – 4/30/2004) | ||