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http://bioportal.bioontology.org/

Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services.

Proper citation: BioPortal (RRID:SCR_002713) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/rna-viz-proto

A software application for animating and visualising RNA and other macromolecular structures. Users are able to use their intuition to interactively refold RNA structures and produce morphs from one structure to another. It allow researchers to explore and manipulate molecular structures Imported from BiositeMaps registry, to better understand structure:function relationships, folding pathways, and molecular motion.

Proper citation: ToRNADo (RRID:SCR_002706) Copy   

•   Source: SciCrunch Registry

http://simbios.stanford.edu/index.html

Simbios is the NIH Center for physics-based Simulation of Biological Structures. Simbios provides infrastructure, software, and training to help biomedical researchers understand biological form and function as they create novel drugs, synthetic tissues, medical devices, and surgical interventions. Simbios is investigating a wide scale of biological structures - from molecules to organisms. Driving biological problems include RNA folding, protein folding, myosin dynamics, cardiovascular dynamics, and neuromuscular biomechanics. Investigators interested in collaborating with Simbios can apply for NIH funding. To encourage collaboration in building accurate biological models and simulations, Simbios also provides the biomedical community with https://simtk.org, a free, secure, distributed, development system for projects. Projects may include models, software, data, documentation, publications, and graphics and have automatic backups and off-site storage. Projects may be public or private and have project-specific mailing lists, forums, bug & feature databases, news, blogs, and source-code repositories. Simbios is developing and disseminating the SimTK core simulation toolkit, (simtk.org/home/simtkcore). SimTK core is open-source software developed by experienced professionals. The software includes advanced capabilities for modeling the geometry and physics of biological systems. To ensure utility and accuracy, the software and training material is being developed and tested in close collaboration with biomedical scientists. Simbios has developed OpenSim, an application for advanced neuromuscular modeling that uses the SimTK toolkit, and is making it openly available at simtk.org/home/opensim. Simbios also publishes the Biomedical Computation Review, a magazine devoted to the science and tools in biocomputation, aimed at the community which encompasses the diverse biocomputation disciplines. To help researchers find high quality software and tools Simbios has also establishes the Simbiome an inventory of high-quality commercial and academic bio-simulation tools. Simbios has recurring openings for postdoctoral researchers.

Proper citation: Simbios (RRID:SCR_004320) Copy   

•   Source: SciCrunch Registry

http://web.stanford.edu/group/barres_lab/brain_rnaseq.html

Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain.

Proper citation: Brain RNA-Seq (RRID:SCR_013736) Copy   

•   Source: SciCrunch Registry

https://maria.stanford.edu/index.php

Web multimodal recurrent neural network tool designed to predict HLA-II (Human Leukocyte Antigen class II) peptide ligand presentation. It uses cell HLA alleles, peptide sequences, and source genes to evaluate antigen presentation. Used for predicting the likelihood of antigen presentation from a gene of interest in the context of specific HLA class II alleles.

Proper citation: MARIA (RRID:SCR_028673) Copy   

•   Source: SciCrunch Registry

http://www.pharmgkb.org/

Database and central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes. PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. PharmGKB is part of the NIH Pharmacogenomics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. A selected subset of data from PharmGKB is accessible via a SOAP interface. Downloaded data is available for individual research purposes only. Drugs with pharmacogenomic information in the context of FDA-approved drug labels are cataloged and drugs with mounting pharmacogenomic evidence are listed.

Proper citation: PharmGKB (RRID:SCR_002689) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/simtkcore

SimTK Core is one of the two packages that together constitute SimTK, the biosimulation toolkit from the Simbios Center. The other major component of SimTK is OpenMM which is packaged separately. This SimTK Core project collects together all the binaries needed for the various SimTK Core subprojects. These include Simbody, Molmodel, Simmath (including Ipopt), Simmatrix, CPodes, SimTKcommon, and Lapack. See the individual projects for descriptions. SimTK brings together in a robust, convenient, open source form the collection of highly-specialized technologies necessary to building successful physics-based simulations of biological structures. These include: strict adherence to an important set of abstractions and guiding principles, robust, high-performance numerical methods, support for developing and sharing physics-based models, and careful software engineering. Accessible High Performance Computing We believe that a primary concern of simulation scientists is performance, that is, speed of computation. We seek to build valid, approximate models using classical physics in order to achieve reasonable run times for our computational studies, so that we can hope to learn something interesting before retirement. In the choice of SimTK technologies, we are focused on achieving the best possible performance on hardware that most researchers actually have. In today''s practice, that means commodity multiprocessors and small clusters. The difference in performance between the best methods and the do-it-yourself techniques most people use can be astoundingeasily an order of magnitude or more. The growing set of SimTK Core libraries seeks to provide the best implementation of the best-known methods for widely used computations such as: Linear algebra, numerical integration and Monte Carlo sampling, multibody (internal coordinate) dynamics, molecular force field evaluation, nonlinear root finding and optimization. All SimTK Core software is in the form of C++ APIs, is thread-safe, and quietly exploits multiple CPUs when they are present. The resulting pre-built binaries are available for download and immediate use. Audience: Biosimulation application programmers interested in including robust, high-performance physics-based simulation in their domain-specific applications.

Proper citation: SimTKCore (RRID:SCR_008268) Copy   

•   Source: SciCrunch Registry

http://www-ssrl.slac.stanford.edu/content/science/ssrl-smb-program

Biomedical technology research center that operates as a integrated center with three primary areas (or cores) of technological research and development and scientific focus: macromolecular crystallography (MC), X-ray absorption spectroscopy (XAS) and small-angle X-ray scattering/diffraction (SAXS) . Central to the core technological developments in all three areas is the development and utilization of improved detectors and instrumentation, especially to be able to take maximum advantage of the high brightness of SSRL?s third-generation synchrotron X-ray storage ring (SPEAR3). A primary focus is the use of enhanced computing and data management tools to provide more user-friendly, real-time and on-line instrumentation control, including full remote access for crystallography, data reduction and analysis.

Proper citation: SSRL Structural Molecular Biology (RRID:SCR_009000) Copy   

•   Source: SciCrunch Registry

http://opensim.stanford.edu

OpenSim is an open-source software system that lets users develop models of musculoskeletal structures and create dynamic simulations of movement. The software provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through multi-institutional collaboration. The underlying software is written in ANSI C++, and the graphical user interface (GUI) is written in Java. OpenSim technology makes it possible to develop customized controllers, analyses, contact models, and muscle models among other things. These plugins can be shared without the need to alter or compile source code. Users can analyze existing models and simulations and develop new models and simulations from within the GUI.

Proper citation: OpenSim (RRID:SCR_002683) Copy   

•   Source: SciCrunch Registry

https://webprotege.stanford.edu

Web based platform for editing biomedical ontologies. Web application for editing OWL 2 ontologies. Open source, lightweight, web based ontology editor implemented in Java and JavaScript using OWL API and Google Web Toolkit. For users who do not wish to host their ontologies on Stanford servers, WebProtégé is available as Web app that can be run locally using Servlet container such as Tomcat.

Proper citation: WebProtege (RRID:SCR_024627) Copy   

•   Source: SciCrunch Registry

https://openmm.org/

Software toolkit to run modern molecular simulations. It can be used either as a standalone application for running simulations, or as a library that enables accelerated calculations for molecular dynamics on high-performance computer architectures.

Proper citation: OpenMM (RRID:SCR_000436) Copy   

•   Source: SciCrunch Registry

http://snyderome.stanford.edu/

Data set generated by personal omics profiling of Dr. Michael Snyder at Stanford University. It combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. The analysis revealed various medical risks, including type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions.

Proper citation: iPOP (RRID:SCR_008991) Copy   

•   Source: SciCrunch Registry