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https://bioportal.bioontology.org/ontologies/NEMO/?p=summary

Ontology that describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive / behavioral) attributes, and data-level attributes (acquisition and analysis parameters). Its aim is to support data sharing, logic-based queries and mapping/integration of patterns across data from different labs, experiment paradigms, and modalities (EEG/MEG).

Proper citation: NEMO Ontology (RRID:SCR_003386) Copy   

•   Source: SciCrunch Registry

http://www.med.uc.edu/cardio_bio/

Our 24 faculty members approach the Research and Training in Cardiovascular Biology program from different subspecialties that include genetics, metabolism, development, cellular biology, systems biology, structural biology, biophysics, pharmacology, molecular biology, bioinformatics and biochemistry. While these subspecialties are clearly diverse, our faculty collaboratively leverages these areas toward the common goal of understanding cardiovascular disease from the gene all the way up to integrated organism function (systems biology). This diverse array of subspecialties provides a truly unique training environment that few centers can match. Another critical aspect of our training program is our steadfast commitment to a superior and nurturing training environment for our predoctoral trainees, postdoctoral trainees and clinician-scientists. Our training faculty are uniformly committed to monitoring our personnel for success in every way possible, to not only ensure their future placement in the academic ranks but to also build a stronger cardiovascular community around the country. The current National Institutes of Health-sponsored Research and Training in Cardiovascular Biology was instituted in 1978 by Arnold Schwartz, MD, PhD. This program has trained more than 120 scientists, who have pursued independent research careers and are holding prominent scientific positions worldwide. Our trainees have been distinguished as chairs of basic science departments, directors of centers or pharmaceutical companies, clinical directors and tenured faculty members in academic research. The overall emphasis continues to focus on integrative training and well-rounded knowledge of the fundamentals in biochemical, molecular, physiological and pharmacological underpinnings of cardiovascular disease. Dr. Schwartz has been a constant guiding force since the program was established. The University of Cincinnati, with Cincinnati Children's, has also developed a reputation as a leading center for the generation and analysis of genetically modified mouse models for interrogation of gene-disease relationships in the heart. This theme has been expanded to incorporate molecular genomics, proteomics and bioinformatics, as we continue to be among the leaders in the nation in molecular pathway analysis associated with single gene manipulations in the hearts of mice. Most faculty and trainees are using these approaches, but they are also well-versed in many other aspects of cardiovascular science, including excellence in basic physiology, pharmacology, biochemistry, structural biology and molecular biology. Thus, we are a rare conglomeration of faculty in which all aspects of cardiovascular biology are practiced, starting with cutting-edge molecular and genetic approaches, spanning more traditional cellular and whole animal approaches to build an integrated network of functional and disease-relevant data and extending to translational research incorporating cell therapy.

Proper citation: University of Cincinnati Research and Training in Cardiovascular Biology (RRID:SCR_003860) Copy   

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http://www.nih.gov/science/amp/alzheimers.htm

The Alzheimer's disease arm of the Accelerating Medicines Partnership (AMP) that will identify biomarkers that can predict clinical outcomes, conduct a large scale analysis of human AD patient brain tissue samples to validate biological targets, and to increase the understanding of molecular pathways involved in the disease to identify new potential therapeutic targets. The initiative will deposit all data in a repository that will be accessible for use by the biomedical community. The five year endeavor, beginning in 2014, will result in several sets of project outcomes. For the biomarkers project, tau imaging and EEG data will be released in year two, as baseline data becomes available. Completed data from the randomized, blinded trials will be added after the end of the five year studies. This will include both imaging data and data from blood and spinal fluid biomarker studies. For the network analysis project, each project will general several network models of late onset AD (LOAD) and identify key drivers of disease pathogensis by the end of year three. Years four and five will be dedicated to validating the novel targets and refining the network models of LOAD, including screening novel compounds or drugs already in use for other conditions that may have the ability to modulate the likely targets.

Proper citation: Accelerating Medicines Partnership - Alzheimers (RRID:SCR_003742) Copy   

•   Source: SciCrunch Registry

http://elementsofmorphology.nih.gov/

Data set of standardized terms used to describe human morphology including definitions of terms for the craniofacies in general, the major components of the face, and the hands and feet. This provides a uniform and internationally accepted terms to describe the human phenotype.

Proper citation: elements of morphology (RRID:SCR_003707) Copy   

•   Source: SciCrunch Registry

http://www.nih.gov/science/amp/autoimmune.htm

The autoimmune disease arm of the Accelerating Medicine Partnership (AMP), which aims to identify and validate the most promising biological targets of disease for new diagnostic and drug development, that is focused on rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). They seek to identify shared common flaws in inflammation, particularly those that are shared with a larger number of autoimmune disorders which can cause severe disability, greatly affect quality of life, and are associated with an increased risk of death. This project aims to reveal biomarkers and biological targets for drug development, matching existing drugs to patients with specific molecular profiles who are most likely to benefit. The research plan proposes a 5 year process. Year one will include startup activities such as validation of tissue acquisition processes and analytic technologies, and the development of operating procedures. The second year will focus on identification of disease specific pathways by comparing data from patients and healthy individuals. Years 3-5 will expand the scale to include comparisons of different subsets of patients with RA or lupus to allow molecularly based patient stratification for precise treatment. The final 12 months (2019) will also include preliminary target validation. The data will be made publicly available through an internet-based information portal.

Proper citation: Accelerating Medicines Partnership Autoimmune Diseases of Rheumatoid Arthritis and Lupus (RRID:SCR_003731) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/pmc/

Collection of full text archive of biomedical and life sciences journal literature at U.S. National Institutes of Health National Library of Medicine (NIH/NLM). With PubMed Central, NCBI is taking lead in preserving and maintaining open access to electronic literature. Value of PubMed Central, in addition to its role as an archive, lies in what can be done when data from diverse sources is stored in common format in single repository. All articles in PMC are free (sometimes on a delayed basis). Some journals go beyond free, to Open Access.

Proper citation: PubMed Central (RRID:SCR_004166) Copy   

•   Source: SciCrunch Registry

https://neurowiki.case.edu/

Curriculum materials for an Introduction to Neurobiology course for undergraduate and graduate students.

The course focuses on the analysis of neurons and neural circuits for behavior using the fundamental principles of neuroscience. From the online course syllabus, the 24 units that make up the course may be directly accessed. Each unit contains a reading, links to at least one simulation, and a problem set.

A list of all available simulations can be found here: https://neurowiki.case.edu/wiki/Simulations. * 25 simulations are written in JavaScript and will run in any browser.
Source code: https://github.com/CWRUChielLab/JSNeuroSim * Pre-compiled executables (Windows, Mac, Linux) are available for 1 desktop simulation, the Nernst Potential Simulator.
Source code: https://github.com/CWRUChielLab/Nernst Structure of the Course * Solving problems based on simulations of neuronal components, neurons, and simple circuits to understand how they work. * For advanced students, writing a neuroscience Wikipedia article, critical review, or grant, in stages.

Proper citation: NeuroWiki (RRID:SCR_004066) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/pdbe/

The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules.

Proper citation: PDBe - Protein Data Bank in Europe (RRID:SCR_004312) Copy   

•   Source: SciCrunch Registry

http://www.mprc.umaryland.edu/mbc.asp

The Maryland Brain Collection (MBC), a resource of the Maryland Psychiatric Research Center (MPRC), is dedicated to promoting research with brain tissue obtained post-mortem from individuals with schizophrenia or related disorders. The primary goal of the MBC is to provide high-quality tissue, along with comprehensive clinical information, for hypothesis-driven research. The MBC is not conceptualized as a Brain Bank with open access but is maintained and funded through collaborative research. The Maryland Brain Collection is managed by researchers at the Maryland Psychiatric Research Center (MPRC). MPRC scientists are dedicated to understanding the causes and improving the treatment of mental illness. The Maryland Brain Collection is associated with the Office of the Chief Medical Examiner for the State of Maryland and other donor sources. MPRC scientists collaborate with scientists from around the world to understand how abnormalities in brain tissue relate to mental illness. The purpose of the MBC is to study the following: Schizophrenia, Bipolar Disorder, Depression, Suicide/Teen suicide, Substance Abuse.

Proper citation: Maryland Brain Collection (RRID:SCR_004384) Copy   

•   Source: SciCrunch Registry

http://rarediseasesnetwork.epi.usf.edu/index.htm

The Rare Diseases Clinical Research Network (RDCRN) was created to facilitate collaboration among experts in many different types of rare diseases. Our goal is to contribute to the research and treatment of rare diseases by working together to identify biomarkers for disease risk, disease severity and activity, and clinical outcome, while also encouraging development of new approaches to diagnosis, prevention, and treatment. The Rare Diseases Clinical Research Network (RDCRN) is made up of 19 distinctive consortia that are working in concert to improve availability of rare disease information, treatment, clinical studies, and general awareness for both patients and the medical community. The RDCRN also aims to provide up-to-date information for patients and to assist in connecting patients with advocacy groups, expert doctors, and clinical research opportunities.

Proper citation: Rare Diseases Clinical Research Network (RRID:SCR_004372) Copy   

•   Source: SciCrunch Registry

http://tvmouse.compmed.ucdavis.edu/

Educational resource to introduce users to the anatomy, physiology, histology, and pathology of the laboratory mouse, with an emphasis on the Genetically Engineered Mouse (GEM). It provides access to histological images, scanned at high resolution and browsable through Zoomify, movie loops and animations derived from MRI, correlated MRI and histology. It has CNS data but is focused on the whole body, e.g., physiological data is available for the heart in the form of wave patterns, histology, CNS, pathology, magnetic resonance imaging, neoplasms; animation, virtual histology, mouse, correlated imaging, necropsy, whole mouse. It may be useful to neuroscientists by relating brain anatomy to the rest of the body. There is a movie illustrating necropsy of the mouse. A link to a compendium of histological slices of brain neoplasms is provided under the Image Archive link. There is a CNS link under construction for anatomical system, which presumably will include detailed CT imaging. This site still appears to be under construction.

Proper citation: Visible Mouse Project (RRID:SCR_002393) Copy   

•   Source: SciCrunch Registry

http://clinicaltrials.gov/

Registry and results database of federally and privately supported clinical trials conducted in United States and around world. Provides information about purpose of trial, who may participate, locations, and phone numbers for more details. This information should be used in conjunction with advice from health care professionals.Offers information for locating federally and privately supported clinical trials for wide range of diseases and conditions. Research study in human volunteers to answer specific health questions. Interventional trials determine whether experimental treatments or new ways of using known therapies are safe and effective under controlled environments. Observational trials address health issues in large groups of people or populations in natural settings. ClinicalTrials.gov contains trials sponsored by National Institutes of Health, other federal agencies, and private industry. Studies listed in database are conducted in all 50 States and in 178 countries.

Proper citation: ClinicalTrials.gov (RRID:SCR_002309) Copy   

•   Source: SciCrunch Registry

http://provean.jcvi.org/

A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.

Proper citation: PROVEAN (RRID:SCR_002182) Copy   

•   Source: SciCrunch Registry

http://mialab.mrn.org/software/eegift/index.html

Implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) EEG data. This MATLAB toolbox is compatible with MATLAB 6.5 and higher.

Proper citation: Group ICA Of EEG Toolbox (RRID:SCR_002478) Copy   

•   Source: SciCrunch Registry

http://www.cmhd.ca/genetrap/

Generate gene trap insertions using mutagenic polyA trap vectors, followed by sequence tagging to develop a library of mutagenized ES cells freely available to the scientific community. This library is searchable by sequence or key word searches including gene name or symbol, chromosome location, or Gene Ontology (GO) terms. In addition,they offer a custom email alert service in which researchers are able to submit search criteria. Researchers will receive automated e-mail notification of matching gene trap clones as they are entered into the library and database. The resource features the use of complementary second and third generation polyA trap vectors developed by the Stanford lab and the laboratory of Professor Yasumasa Ishida of the Nara Institute of Science and Technology (NAIST) in Japan to mutagenize murine embryonic stem (ES) cells. CMHD gene trap clones are distributed by the Canadian Mouse Mutant Repository(CMMR). Information about ordering, services, and pricing can be found on their web site (http://www.cmmr.ca/services/index.html)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: Centre for Modeling Human Disease Gene Trap Resource (RRID:SCR_002785) Copy   

•   Source: SciCrunch Registry

https://simtk.org

A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them. It serves as a repository for models that are published (as well as the associated code) to create a living archive of simulation scholarship. Simtk.org is organized into projects. A project represents a research endeavor, a software package or a collection of documents and publications. Includes sharing of image files, media, references to publications and manuscripts, as well as executables and applications for download and source code. Simulation tools are free to download and space is available for developers to manage, share and disseminate code.

Proper citation: Simtk.org (RRID:SCR_002680) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/foldvillin

An archive of hundreds of all-atom, explicit solvent molecular dynamics simulations that were performed on a set of nine unfolded conformations of a variant of the villin headpiece subdomain (HP-35 NleNle). It includes scripts for accessing the archive of villin trajectories as well as a VMD plug-in for viewing the trajectories. In addition, all starting structures used in the trajectories are also provided. The simulations were generated using a distributed computing method utilizing the symmetric multiprocessing paradigm for individual nodes of the Folding_at_home distributed computing network. The villin trajectories in the archive are divided into two projects: PROJ3036 and PROJ3037. PROJ3036 contains trajectories starting from nine non-folded configurations. PROJ3037 contains trajectories starting from the native (folded) state. Runs 0 through 8 (in PROJ3036) correspond to starting configurations 0 through 8 discussed in the paper in J. Mol. Biol. (2007) 374(3):806-816 (see the publications tab for a full reference), whereas RUN9 uses the same starting configuration as RUN8. Each run contains 100 trajectories (named clone 0-99), each with the same starting configuration but different random velocities. Trajectories vary in their length of time and are subdivided into frames, also known as a generation. Each frame contains around 400 configurational snapshots, or timepoints, of the trajectory, with the last configurational snapshot of frame i corresponding to the first configurational snapshot of generation i+1. The goal is to allow researchers to analyze and benefit from the many trajectories produced through the simulations.

Proper citation: Molecular Simulation Trajectories Archive of a Villin Variant (RRID:SCR_002704) Copy   

•   Source: SciCrunch Registry

http://hapmap.ncbi.nlm.nih.gov/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project.

Proper citation: International HapMap Project (RRID:SCR_002846) Copy   

•   Source: SciCrunch Registry

http://www.compucell3d.org/

Open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms. It uses Cellular Potts Model to model cell behavior.

Proper citation: CompuCell3D (RRID:SCR_003052) Copy   

•   Source: SciCrunch Registry

https://github.com/jefftc/changlab

Software system for performing bioinformatics analyses. System includes knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. Backwards-chaining rule-based expert system comprised of data model that can capture richness of biological data, and inference engine that reasons on knowledge base to produce workflows. Knowledge base is populated with rules to analyze microarray and next generation sequencing data.

Proper citation: BETSY (RRID:SCR_026239) Copy   

•   Source: SciCrunch Registry