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http://www.ks.uiuc.edu/

The Theoretical and Computational Biophysics Group (TCBG), an NIH Resource for Macromolecular Modeling and Bioinformatics, was founded by Professor Klaus Schulten in 1989 and is located at the Beckman Institute of the University of Illinois at Urbana-Champaign (UIUC). The group is led by Professor Klaus Schulten (Physics, Biophysics, Chemistry) with Professors Laxmikant Kale (Computer Science), Zaida Luthey-Schulten (Chemistry) and Alek Aksimentiev (Physics), and with the Resource''s assistant director Dr. Emad Tajkhorshid (Biophysics). Research and development activities of the TCBG center on the structure and function of supramolecular systems in the living cell, and on the development of new algorithms and efficient computing tools for structural biology. :The TCBG brings the most advanced molecular modeling, bioinformatics, and computational technologies to bear on questions of biomedical relevance. We extend, refine and deliver these technologies in response to experimental progress and emerging needs of the wide biomedical research community. We magnify the impact of our work through direct collaboration with experimental researchers, the distribution of cutting-edge and user-friendly software, and via extensive training, service, and dissemination efforts. :cell, algorithm, simulation software, membrane potential, genome, molecule, ion channel, chromatin, Image Processing software, data Data visualization software, simulation software; Membrane Biophysics, Mechanobiology, Nanoengineering, Bioenergetics, Neurobiology, Molecular Dynamics, cellular membrane, osmotic pressure, proteins (use protein), Gatekeeper Protein, membrane, mechanosensitive channel of small conductance (MscS), Visual Molecular Dynamics (VMD), Quantum Biology, quantum chemistry, Molecular Dynamics Simulator, Nanoscale Imaging, cellular membrane tension, bacterial cell, electron paramagnetic measurements, computer modeling, atomic detail, computational microscope, Lipoproteins [high density lipoproteins (HDL)], Petascale Computing, Macromolecular Modeling, Bioinformatics, supramolecular systems, living cell, algorithms (use algorithm), computing tools, structural biology, molecular modeling, computational technologies, membrane proteins, structural information, molecular visualization, Molecular modeling tools, structural information, bioinformatics databases, molecular dynamics simulations, interactive modeling, collaborations, theoretical, experimental researchers, light energy, electrical membrane potentials (use membrane potential, add term as syn), synthesis of ATP, photosynthetic systems, storage and control of genetic information, classical and quantum dynamical motion of biopolymers, numerical experiments, non-equilibrium statistical mechanics, elasticity theory, theory of disordered systems, collaborative environment, Software Development, cells (use cell), molecular graphics viewer, static and dynamic structures, DNA sequencing, genomes (use genome), direct manipulation and observation, single molecules (use molecule), bioenergetic proteins, nanotechnology, steered/interactive molecular dynamics, dissemination, coarse-graining methods, residue-based and shape-based coarse graining, CG, polymeric systems, Computational Environment, Training, Workshops, Tutorials, Case Studies, Classes, research, Highly Cited, compute power, visualization equipment, desktop workstations, lipid bilayers, allow passage of ions across the membrane (use ion channel), mechanotransduction, membrane tension, 3-D graphics, built-in scripting, animating, analyzing, ideal DNA interbasepair helical parameters, plugin, nucleosomes, antialiasing, depthcueing, Molecular Representations, analysis and Data visualization software (use Image Processing software, and data Data visualization software, add terms as syn.), computer simulations (use simulation software), photosynthetic systems, computational clusters :

Proper citation: Theoretical and Computational Biophysics Group (TCBG) (RRID:SCR_013598) Copy   

•   Source: SciCrunch Registry

http://www.ibdbiom.eu/

The Inflammatory Bowel Disease Biomarkers Consortium (IBD-BIOM) addresses the need to improve our understanding of inflammatory bowel disease (IBD) through new biomarkers into molecular dysfunctions that give rise to IBD. The biomarkers targeted by the consortium will be translated into early-detection clinical diagnostic tests for IBD patients.

Proper citation: Inflammatory Bowel Disease Biomarkers Consortium (IBD BIOM) (RRID:SCR_013710) Copy   

•   Source: SciCrunch Registry

http://c-path.org/programs/msoac/

The Multiple Sclerosis Outcome Assessments Consortium (MSOAC) is a public-private partnership which aims to accelerate the development of new therapies for MS by generating new tools for measuring outcomes in clinical trials. It is collecting, standardizing, and analyzing data about MS with the goal of qualifying new measures of disability for the disease. MSOAC is the newest of the eight consortia of Critical Path Institute (C-Path), a nonprofit organization that is dedicated to accelerating drug development by delivering on the mission outlined by FDA''''s critical path initiative.

Proper citation: Multiple Sclerosis Outcome Assessments Consortium (MSOAC) (RRID:SCR_013712) Copy   

•   Source: SciCrunch Registry

http://www.fnih.org/work/research-partners/osteoarthritis-biomarkers-project

The Osteoarthritis Biomarkers Project (OABP) is a consortium designed to identify and classify biological markers of progression of knee osteoarthritis. Their goal is to advance the ability to predict the individual risk of developing severe OA and to monitor progression of OA.

Proper citation: Osteoarthritis Biomarkers Project (OABP) (RRID:SCR_013714) Copy   

•   Source: SciCrunch Registry

https://cananolab.nci.nih.gov/caNanoLab/

Data sharing portal designed to facilitate information sharing across international biomedical nanotechnology research community to expedite and validate use of nanotechnology in biomedicine.

Proper citation: Cancer Nanotechnology Laboratory (caNanoLab) (RRID:SCR_013717) Copy   

•   Source: SciCrunch Registry

http://goldminer.arrs.org/home.php

An image repository that provides access to published, peer-reviewed medical images from biomedical journals.

Proper citation: ARRS GoldMiner (RRID:SCR_013716) Copy   

•   Source: SciCrunch Registry

https://www.delaneycare.org/index.php

The Collaboratory of AIDS Researchers for Eradication (CARE) is a consortium of scientific experts in the field of HIV latency from several U.S. and European academic research institutions as well as Merck Research Laboratories working together to find a cure for HIV.

Proper citation: Collaboratory of AIDS Researchers for Eradciation (CARE) (RRID:SCR_013681) Copy   

•   Source: SciCrunch Registry

http://www.ccrm.ca/

The Centre for Commercialization of Regenerative Medicine''s (CCRM) is an industry consortium that aims to accelerate the application of regenerative medicine to clinical practice. Stakeholder in the consortium include the pharmaceutical, devices, reagents, tools, biomaterials and cell therapeutic companies.

Proper citation: Centre for Commercialization of Regenerative Medicine (CCRM) (RRID:SCR_013683) Copy   

•   Source: SciCrunch Registry

http://www.functionalglycomics.org/static/consortium/consortium.shtml

The Consortium for Functional Glycomics (CFG) serves to combine the expertise and glycomics resources to reveal functions of glycans and glycan-binding proteins (GBPs) that impact human health and disease. The CFG offers resources to the community free of charge, including glycan array screening services, a reagent bank, and access to a large glycomics database and data analysis tools.

Proper citation: Consortium for Functional Glycomics (CFG) (RRID:SCR_013689) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/NEOMARK3

Ontology that describes the medical information necessary for early detection of the oral cancer reoccurrence extracted from the NeoMark Project.

Proper citation: Neomark Oral Cancer Ontology version 3 (RRID:SCR_010375) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/NEOMARK4

Ontology that describes the medical information necessary for early detection of the oral cancer reoccurrence extracted from the NeoMark Project.

Proper citation: Neomark Oral Cancer Ontology version 4 (RRID:SCR_010376) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/NEUMORE

Ontology of neural functional motor recovery.

Proper citation: Neural Motor Recovery Ontology (RRID:SCR_010377) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/NMOSP

Species ontology that adopts and integrates relevant portions of available taxonomies as needed based on the species and strain terms represented in the current release of NeuroMorpho.Org (72 terms as of the 5.7 release) and any future additions. When a NeuroMorpho.Org term is mapped with an external resource, its entire lineage (ancestors and descendants) is added to the NeuroMorpho.Org species ontology. The resulting 1,340 terms of this initial version of the ontology come for 65% from the NCBI taxonomy (24 NeuroMorpho.Org species/strain terms mapped), 30% from the Rat Gene Database (1 term mapped), and altogether 5% from NIFSTD (7 terms mapped), MeSH (2 terms mapped), ITIS (1 term mapped), and custom-added concepts (41 terms mapped, largely mouse strains from Jackson Labs).

Proper citation: NeuroMorpho.Org species ontology (RRID:SCR_010378) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/PSIMOD

Ontology consisting of terms that describe protein chemical modifications, logically linked by an is_a relationship in such a way as to form a direct acyclic graph (DAG). The PSI-MOD ontology has more than 45 top-level nodes, and provides alternative hierarchical paths for classifying protein modifications either by the molecular structure of the modification, or by the amino acid residue that is modified.

Proper citation: Protein Modification Ontology (RRID:SCR_010412) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/QUDT

Collection of ontologies that define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. The goal of the QUDT ontology is to provide a unified model of, measurable quantities, units for measuring different kinds of quantities, the numerical values of quantities in different units of measure and the data structures and data types used to store and manipulate these objects in software. This OWL schema is a foundation for a basic treatment of units.

Proper citation: QUDT (RRID:SCR_010416) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/OMIT

Ontology to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans'' various diseases and biological processes (usually through miRs'' respective target genes). OMIT has reused and extended a set of well-established concepts from existing bio-ontologies, e.g., Gene Ontology, Sequence Ontology, Protein Ontology, NCBI Organism Taxonomy, Human Disease Ontology, Foundational Model of Anatomy, and so forth.

Proper citation: Ontology for MicroRNA Target Prediction (RRID:SCR_010387) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ROLEO

Ontology in the domain of role classification that aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles.

Proper citation: Role Ontology (RRID:SCR_010420) Copy   

•   Source: SciCrunch Registry

http://inlab.ibfm.cnr.it/PET_template.php

This is a place holder for this tool. The documentation is not yet available (documented 5/30/2014).

Proper citation: Dementia-specific FDG PET Template for SPM analyses (RRID:SCR_010465) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/IDO

Ontologies designed as a set of interoperable ontologies that will together provide coverage of the infectious disease domain. At the core of the set is a general Infectious Disease Ontology (IDO-Core) of entities relevant to both biomedical and clinical aspects of most infectious diseases. Sub-domain specific extensions of IDO-Core complete the set providing ontology coverage of entities relevant to specific pathogens or diseases. Please note: The ontology metrics displayed by BioPortal do not distinguish IDO-developed terms from terms imported from other ontologies.

Proper citation: Infectious Disease Ontology (RRID:SCR_010345) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ICECI

A system of classifications to enable systematic description of how injuries occur. It is designed especially to assist injury prevention. It was originally designed for use in settings in which information is recorded in a way that allows statistical reporting--for example, injury surveillance based on collection of information about cases attending a sample of hospital emergency departments. It has also been found useful for other purposes. For example, it has been used as a reference classification during revision of another classification, to record risk-factor exposure of children in a cohort study, as the basis for special-purpose classifications and in a growing number of other ways.

Proper citation: International Classification of External Causes of Injuries (RRID:SCR_010348) Copy   

•   Source: SciCrunch Registry