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http://emsci.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A clinical spinal cord injury network that provides a database of clinical assessment data from spinal cord injured patients. The EMSCI assessment scheme currently consists of the so called core sets: neurological (ISNCSCI), functional (10MWT, 6MWT, TUG, WISCI2) measurements and independence measures (SCIM3). Additional assessments are: neurophysiology (MEP, SSEP, NCV), pain, hand function and an urodynamics.

Proper citation: European Multicenter Study about Spinal Cord Injury (RRID:SCR_003720) Copy   

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https://med.inria.fr/

Software tool as multi platform medical image processing and visualization software. Functionalities include 2D/3D/4D image visualization, image registration, diffusion MR processing and tractography, filtering.

Proper citation: medInria (RRID:SCR_001462) Copy   

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https://repository.niddk.nih.gov/network/110

Network that brings together clinical centers with expertise in caring for patients with chronic hepatitis B virus (HBV) infection to conduct research in order to better understand the physiological effects of the disease and develop effective treatment strategies with the currently available therapies. The web site is designed to inform the public of the research activities conducted by the Hepatitis B Research Network. It is also a portal to support communications for their researchers and participants in their studies. The Hepatitis B Research Network is currently seeking patients for a multi-center prospective study of the natural history of chronic hepatitis B. Within the next few months treatment trials for various patients with chronic hepatitis B will also begin enrolling patients. Details of the entry criteria for these studies can be obtained from the clinical centers outlined on the website's map.

Proper citation: Hepatitis B Research Network (RRID:SCR_001531) Copy   

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http://www.neuroanatomy.wisc.edu/

Training materials including Web edition modules of the neuroanatomy coursebooks used by first-year medical students at the University of Wisconsin Medical School (UWMS), videos, and images. Topics include spinal cord, brain stem, Cerebellum, Thalamus, Cranial Nerves and National Board Review practice questions.

Proper citation: UW-Madison Neuroscience Resources (RRID:SCR_001649) Copy   

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http://psychiatry.ucsd.edu/index.html

The Department of Psychiatry at the University of California, San Diego is one of the most innovative and productive academic departments of psychiatry in the country. The guiding principle in this development has been that the educational and research programs of a psychiatry department must be at the cutting edge and encompass and integrate the most current innovations in the field with those approaches from the past which have proven to be valid and effective. The department has a strong commitment to the dynamic understanding of an individual's current social context and feelings, and past behaviors and experiences. We believe we have created one of the best available integrations of the biopsychosocial approaches to understanding normal and abnormal human behavior. By design, a rich diversity of scientific and clinical strategies are represented within the department, but the core organizing ethic of our educational and training programs is a profound commitment to our patients well being. It is the department's conviction that clinical psychiatry can only be learned in the context of meaningful interaction and contact with patients. The Residency Training Program is developmental in nature, appropriately challenging the residents at each level as they move from intensively supervised beginners to autonomous, confident, skilled clinicians and colleagues at graduation. The training occurs within the department's ambiance of collegiality, enthusiasm, openness of communication, intellectual and scientific rigor, and spirit of inquiry, which characterize our highly productive and energetic faculty. The UCSD faculty represent a virtual who's who of world-class basic and clinical scientists and clinicians, all of whom are available and participate in our residents training and experiences. The tradition at UCSD, both on the general campus and within the School of Medicine, is that of academic excellence. The department shares in this tradition and expects it from its faculty, trainees, and students. The goal of the residency program is to develop highly competent psychiatric physicians and leaders who are comprehensively trained in the most up-to-date diagnostic and treatment techniques which have proven effective for the full spectrum of mental disorders.

Proper citation: University of California at San Diego Department of Psychiatry (RRID:SCR_001931) Copy   

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http://bioinformatics.aecom.yu.edu/index.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Primary informatics resource for joint research efforts of the Albert Einstein College of Medicine and Montefiore Medical Center to facilitate the study and understanding of biological processes, clinical disorders, pathologic abnormalities, and the relationships among them, using a wide variety of informatics techniques, applications, and user training. Their services include: * Collaboration on research design to enable effective data management throughout all phases of a project * Provision of management capability for large volumes of data generated by microarrays and related technologies * Provision and supports a software toolchest for data capture, retrieval, and analysis * Design and implementation of custom interfaces to incorporate existing or separately designed databases into the central data management architecture * Support for data management for the Biorepository, to enhance specimen storage, identification, and linkage with clinical data * Ensuring conformity of data elements and structures to national standards via participation in standards organizations, facilitating intramural and extramural collaboration * Providing individualized support to end-users with bioinformatics training needs * Serving as a bioinformatics liaison to other research institutes and organizations * Providing data management support for clinical research * Providing a common, secure repository for clinical, experimental, and biosample storage data

Proper citation: Einstein-Montefiore ICTR Research Informatics Core (RRID:SCR_003451) Copy   

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http://hivdb.stanford.edu/

The Stanford University HIV Drug Resistance Database is a curated public database designed to represent, store, and analyze the different forms of data underlying HIVs drug resistance. HIVDB has three main types of content: (1) Database queries and references, (2) Interactive programs, and (3) Educational resources. Database queries are designed primarily for researchers studying HIV drug resistance. The interactive programs and educational resources are designed for both researchers and those wishing to learn more about HIV drug resistance. 1.DATABASE QUERY AND REFERENCE PAGES Genotype-Treatment Correlations This Genotype-Treatment section of the database links to 15 interactive query pages that explore the relationship between treatment with HIV-1 antiretroviral drugs (ARVs) and mutations in HIV reverse transcriptase (RT), protease, and integrase. There are five types of interactive query pages: Treatment Profiles (Protease and RT inhibitors) Mutation Profiles (Protease and RT mutations) Detailed Treatment Queries (Protease, RT, and integrase inhibitors) Detailed Mutation Queries (Protease, RT, and integrase mutations) Mutation Prevalence According to Subtype and Treatment Genotype-Phenotype Correlations The main page of the Genotype-Phenotype Correlations section links to four interactive query pages: three dynamically updated data summaries and one regularly updated downloadable dataset. Drug Resistance Positions Query for levels of resistance associated with known drug resistance mutations Detailed Phenotype Queries Queries for levels of resistance associated with individual mutations or mutation combinations at all positions of protease, RT, and integrase Patterns of Drug Resistance Mutations Downloadable Reference Dataset Genotype-Clinical Correlations This part of the database has two main sections: Clinical Trials Datasets Summaries of Clinical Studies References This part of the database has two main sections: one with summaries of the data from each of the references in HIVDB and one in which every primate immunodeficiency virus sequence in GenBank is annotated according to its presence or absence in HIVDB. Studies in HIVDB GenBank <=> HIVDB New Submissions Approximately every three months, the New Submissions section lists the studies that have been entered into HIVDB. The study title links to the introductory page of the study in the References section. Database Statistics (http://hivdb.stanford.edu/pages/HIVdbStatistics.html) 2. INTERACTIVE PROGRAMS HIVDB has seven main interactive programs. 1. HIVdb Program Mutation List Analysis Sequence Analysis HIVdb Output Sierra Web Service Release Notes Algorithm Specification Interface (ASI) 2. HIValg Program 3. HIVseq Program 4. Calibrated Population Resistance (CPR) tool 5. Mutation ARV Evidence Listing (MARVEL) 6. ART-AiDE 7. Rega HIV-1 Subtyping tool Three programs in the HIV Drug Resistance Database share a common code base: HIVseq, HIVdb, and HIValg. HIVseq accepts user-submitted protease, RT, and integrase sequences, compares them to the consensus subtype B reference sequence, and uses the differences as query parameters for interrogating the HIV Drug Resistance database (Shafer, D Jung, & B Betts, Nat Med 2000; Rhee SY et al. AIDS 2006). The query result provides users with the prevalence of protease, RT and integrase mutations according to subtype and PI, nucleoside RT inhibitor (NRTI), non-nucleoside RT inhibitor (NNRTI), and integrase inhibitor (INI) exposure. This allows users to detect unusual sequence results immediately so that the person doing the sequencing can check the primary sequence output while it is still on the desktop. In addition, unexpected associations between sequences or isolates can be discovered by immediately retrieving data on isolates sharing one or more mutations with the sequence. There are three ways in which the HIVdb program can be used: (i) entering a list of protease and RT mutations, (ii) entering a complete sequence containing protease, RT, and/or integrase, and (iii) using a Web Service. HIVdb is an expert system that accepts user-submitted HIV-1 pol sequences and returns inferred levels of resistance to 20 FDA-approved ARV drugs including 8 PIs, 7 NRTIs, 4 NNRTIs, and - with this update - one INI. In the HIVdb system, each HIV-1 drug resistance mutation is assigned a drug penalty score and a comment; the total score for a drug is derived by adding the scores of each mutation associated with resistance to that drug. Using the total drug score, the program reports one of the following levels of inferred drug resistance: susceptible, potential low-level resistance, low-level resistance, intermediate resistance, and high-level resistance. HIValg is designed for users interested in comparing the results of different algorithms or who are interested in comparing and evaluating existing and newly developed algorithms. The ability to develop new algorithms that can be run on the HIV Drug Resistance Database depends on the Algorithm Specific Interface (ASI) compiler (Shafer & Betts JCM 2003). Submission of Sequences and Mutations For each of the three programs, sequences can be entered using either the Sequence Analysis Form or the Mutation List form. 3. EDUCATIONAL RESOURCES HIVDB contains several regularly updated sections summarizing data linking RT, protease, and integrase mutations and antiretroviral drugs (ARVs). These sections include (i) tabular summaries of the major mutations associated with each ARV class, (ii) detailed summaries of the major, minor, and accessory mutations associated with each ARV, (iii) the comments used by the HIVdb program, (iv) the scores used by the HIVdb program, (v) clinical studies in which baseline drug resistance mutations have been correlated with the virological response (clinical outcome) to a specific ARV, (vi) mutations that can be used for drug resistance surveillance, and (vii) a two-page PDF handout. 1. Drug Resistance Summaries Tabular Drug Resistance Summaries by ARV Class Detailed Drug Resistance Summaries by ARV Drug Resistance Mutation Comments Used by the HIVdb Program Drug Resistance Mutation Scores Used by the HIVdb Program Genotype-Clinical Outcome Correlation Studies 2. Surveillance Drug-Resistance Mutation List Section 3. PDF Handout Grant Support 1. National Institute for Allergy and Infectious Diseases (NIAID, NIH): Online HIV Drug Resistance Database (PI: Robert W. Shafer, MD, 1R01AI68581-01A1), 04/01/06 - 3/31/11 2. National Institute for Allergy and Infectious Diseases (NIAID, NIH) supplement to the grant Identification of Multidrug-Resistant HIV-1 Isolates (PI: Robert W. Shafer, MD, AI46148-01): Supplement provided 1999-2005. 3. NIH/NIGMS Program Project on AIDS Structural Biology Program Project: Targeting Ensembles of Drug Resistant Protease Variants (PI: Celia Schiffer, PhD, University of Massachusetts): 2002-2007 4. University-wide AIDS Research Program (CR03-ST-524). Community collaborative award: Optimizing Clinical HIV Genotypic Resistance Interpretation: Principal Investigators: Robert W. Shafer, MD and W. Jeffrey Fessel MD (Kaiser Permanente Medical Care Program): 2004-2005 5. Stanford University Bio-X Interdisciplinary Initiative: HIV Gene Sequence Analysis for Drug Resistance Studies: A Pharmacogenetic Challenge Principal Investigators: Robert W. Shafer, MD and Daphne Koller, Ph.D. (Computer Science): 2000-2002

Proper citation: Stanford University HIV Drug Resistance Database (RRID:SCR_006631) Copy   

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http://www.research.va.gov/programs/tissue_banking/als/

A human tissue bank that collects, processes, stores and gives out research specimens for future scientific studies. Presently, the VABBB is obtaining neurologic tissue specimens from Veterans who suffer from amyotrophic lateral sclerosis (ALS) and other illnesses that affect Veterans, along with relevant clinical data, essential for research. Currently, neither the cause nor prevention of ALS is known. Medical researchers are currently examining environmental, toxic, genetic, traumatic, medical, and occupational influences as possible contributors to the development and progression of ALS. Veterans have a higher risk of developing ALS compared with non-Veterans; however, the reasons for this higher risk are currently unknown. Any Veteran with ALS in the U.S. may enroll in the VABBB.

Proper citation: VA Biorepository Brain Bank (RRID:SCR_006546) Copy   

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https://www.iscaconsortium.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 22, 2022. A rapidly growing group of clinical cytogenetics and molecular genetics laboratories committed to improving quality of patient care related to clinical genetic testing using new molecular cytogenetic technologies including array comparative genomic hybridization (aCGH) and quantitative SNP analysis by microarrays or bead chip technology. They improve clinical care by providing a large publicly available database and forum where clinicians and researchers can share knowledge to expedite the understanding of copy number variation (CNV) in an abnormal population. The ISCA database contains whole genome array data from a subset of the ISCA Consortium clinical diagnostic laboratories. Array analysis was carried out on individuals with phenotypes including intellectual disability, autism, and developmental delay. Efforts of the Consortium include: # Clinical Utility: The ISCA Consortium has made recommendations regarding the appropriate clinical indications for cytogenetic array testing (Miller et al. AJHG 2010, PMID: 20466091). Currently, discussions are focused on pediatric applications for children with unexplained developmental delay, intellectual disability, autism and other developmental disabilities. A separate committee has been developed to address appropriate cancer genetic applications (http://www.urmc.rochester.edu/ccmc/). # Evidence-based standards for cytogenomic array design: The Consortium will develop recommendations for standards for the design, resolution and content of cytogenomic arrays using an evidence-based process and an international panel of experts in clinical genetics, clinical laboratory genetics (cytogenetics and molecular genetics), genomics and bioinformatics. This design is intended to be platform and vendor-neutral (common denominator is genome sequence coordinates), and is a dynamic process with input from the broader genetics community and evidence-based review by the expert panel (which will evolve into a Standing Committee with international representation). # Public Database for clinical and research community: It is essential that publicly available databases be created and maintained for cytogenetic array data generated in clinical testing laboratories. The ISCA data will be held in dbGaP and dbVar at NCBI/NIH and curated by a committee of clinical genetics laboratory experts. The very high quality of copy number data (i.e., deletions and duplications) coming from clinical laboratories combined with expert curation will produce an invaluable resource to the clinical and research communities. # Standards for interpretation of cytogenetic array results: Using the ISCA Database, along with other genomic and genetics databases, the Consortium will develop recommendations for the interpretation and reporting of pathogenic vs. benign copy number changes as well as imbalances of unknown clinical significance.

Proper citation: ISCA Consortium (RRID:SCR_006168) Copy   

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

Archive of aggregated information about sequence variation and its relationship to human health. Provides reports of relationships among human variations and phenotypes along with supporting evidence. Submissions from clinical testing labs, research labs, locus-specific databases, expert panels and professional societies are welcome. Collects reports of variants found in patient samples, assertions made regarding their clinical significance, information about submitter, and other supporting data. Alleles described in submissions are mapped to reference sequences, and reported according to HGVS standard.

Proper citation: ClinVar (RRID:SCR_006169) Copy   

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https://gitlab.com/SimonHTausch/HiLive

Software tool for performing read mapping that maps Illumina HiSeq sequencer read alignments when they are produced. Used in Next Generation Sequencing in time critical, clinical applications.

Proper citation: HiLive (RRID:SCR_016134) Copy   

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https://github.com/HicServices/RDMP/wiki

Software toolkit which automates the loading, storage, linkage and provision of data sets. It also cleans, transforms and documents provenance meta-data and domain knowledge to make data sets “research ready”.

Proper citation: Research Data Management Platform (RRID:SCR_016268) Copy   

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https://sleepdata.org/

System for sharing sleep data. Organization portal that aggregates, harmonizes, and organizes sleep and clinical data from individuals studied as part of cohort studies or clinical trials and provides suite of tools to facilitate data exploration and data visualization. National Heart, Lung, and Blood Institute resource designed to provide big data resources to sleep research community.

Proper citation: National Sleep Research Resource (NSRR) (RRID:SCR_016576) Copy   

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http://cahub.cancer.gov/about/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. A national center for biospecimen science and standards to advance cancer research and treatment. It was created in response to the critical and growing need for high-quality, well-documented biospecimens for cancer research. The initiative builds on resources already developed by the NCI, including the Biospecimen Research Network and the NCI Best Practices for Biospecimen Resources, both of which were developed to address challenges around standardization of the collection and dissemination of quality biospecimens. caHUB will develop the infrastructure for collaborative biospecimen research and the production of evidence-based biospecimen standard operating procedures.

Proper citation: caHUB (RRID:SCR_009657) Copy   

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http://code.google.com/p/neurological-disease-ontology/

An ontology for the representation of the range of clinical and basic science aspects of neurological diseases. ND has a broad scope that includes neurological diseases as well as their associated signs, symptoms, diagnoses, pathologies, etiologies, processes, treatments, and any other aspect of a neurological disease that is or can be encountered in the course of clinical practice or medical research. ND is being built in accordance with the OBO Foundry principles. It is an extension of the Ontology for General Medical Science (OGMS) as well as the Basic Formal Ontology (BFO). ND aims to develop classes utilizing both textual and axiomatized definitions to describe and formalize relations between instances of classes both within the ontology itself as well as between ND and external ontologies such as the: Gene Ontology (GO), Cell Ontology (CL), Protein Ontology (PRO), Chemical Entities of Biological Interest (ChEBI), and Ontology for Biomedical Investigations (OBI).

Proper citation: Neurological disease ontology (RRID:SCR_010284) Copy   

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http://code.google.com/p/ogms/

An ontology based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop (Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.

Proper citation: Ontology for General Medical Science (RRID:SCR_010384) Copy   

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http://www.cvm.ncsu.edu/ccmtr/

The mission of the CCMTR is to promote scientific discovery and facilitate its clinical application to achieve the goal of improving the health of animals and humans. The needs of the patients direct the emphasis of basic research, patient samples provide the critical resource to investigate the basis of disease, and patient participation in clinical studies is required to generate the evidence needed to apply new drugs, vaccines and technology to the broader patient population. Initiatives at the Center are designed to develop the multidisciplinary teams necessary to bring an idea from the lab to the patient. The Center is home to service cores that provide advanced technology, collect and store clinical patient samples, and perform clinical trials to validate new medical interventions. North Carolina State University''s College of Veterinary Medicine (CVM) is a dynamic community whose members are dedicated to preparing veterinarians and veterinarian scientists while advancing animal and human health from the cellular level through entire ecosystems.

Proper citation: Center for Comparative Medicine and Translational Research (RRID:SCR_008299) Copy   

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http://www.rad.upenn.edu/sbia/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. A section of the Penn department of radiology, it is devoted to the development of computer-based image analysis methods and their application to clinical research studies. Image analysis methodologies include image registration, segmentation, population-based statistical analysis, biophysical modeling of anatomical deformations, and high-dimensional pattern classification. Clinical research studies spans a variety of clinical areas and organs, and they include brain diseases such as Alzheimer's disease and schizophrenia, evaluation of treatment effects in large clinical trials, diagnosis of cardiac diseases, and diagnosis prostate, breast and brain cancer. SBIA also performs small animal imaging research aiming to understand brain development in mouse models. It has multiple resources which can be accessed by researcher.

Proper citation: SBIA (RRID:SCR_013628) Copy   

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https://sbpdiscovery.org/tag/neuroscienceandagingresearchcenter/

Center that translates basic science discoveries into new treatments to extend lifespan and to combat degenerative disorders associated with aging or development. Their researchers are discovering the etiological pathways as well as small-molecule and stem cell-based treatments to address the clinical unmet need of these patients. The Center uses a team based approach to apply their expertise in stem cells to develop therapies for new treatments for stroke and Parkinson's disease. They are also performing high-throughput screens to identify new molecules to protect the synapses of nervesthe connections between nerves that mediate movement, memory and cognition for Alzheimer's, Parkinson's and autism. By studying the links between Down syndrome and Alzheimer's disease, they are exploring new treatments to improve cognition in both disorders. Their collaborations with clinical partners enable them to test new discoveries in human trials, with a goal to improve the lives of patients and families affected by neurodegenerative disease and aging disorders.

Proper citation: Sanford-Burnham Neuroscience and Aging Research Center (RRID:SCR_001688) Copy   

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https://radiology.duke.edu/research/centers-and-shared-resources/center-advanced-magnetic-resonance-development

Research facility of the Department of Radiology at the Duke University Medical Center (DUMC) providing access to a whole-body, commercially manufactured 3 Tesla (Trio, Siemens Medical Systems) MR Imaging and Spectroscopy System with full research capability. The Center is fully equipped to perform clinical and research MR imaging or spectroscopy studies on humans or large animals. A full range of monitoring, anesthesia, RF coil development, computer and instrumental control facilities as well as MR research technologists and physics/chemistry consultation are available to Department of Radiology researchers and their collaborators.

Proper citation: CAMRD (RRID:SCR_001713) Copy   

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