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https://isi.edu/integration/people/chunnan/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 14, 2018. An XML-RPC client of a web-service server which provides the service to recognize named entities in the biomedical articles. It is Gene Mention Tagger (GMT) for Biological Text Mining.

Proper citation: AIIA-GMT (RRID:SCR_016397) Copy   

•   Source: SciCrunch Registry

https://hirnetwork.org/consortium/cmai

Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is developing innovative approaches to model basic aspects of human T1D immunobiology using novel in vivo and in vitro platforms.

Proper citation: HIRN Consortium on Modeling Autoimmune Interactions (RRID:SCR_016200) 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://www.trikinetics.com/

Data acquisition software for TriKinetics activity monitors. TriKinetics systems quantify animal movement over time, and can be used to measure behaviors such as circadian rhythm, sleep, longevity, social interaction, geotaxis, phototaxis, learning, and drug response in various species.

Proper citation: DAMSystems308 (RRID:SCR_016191) Copy   

•   Source: SciCrunch Registry

http://swarmsight.org/

Software for video analysis with modules to track insect antenna and proboscis movements. Its purpose is to assess the aggregate movement or activity levels of groups or swarms of animals.

Proper citation: SwarmSight (RRID:SCR_016451) Copy   

•   Source: SciCrunch Registry

https://unpaywall.org/

Database of free scholary articles. Content from over 50,000 publishers and repositories easy to find, track, and use. A website featuring web-based tools created and maintained by Impactstory, Inc.

Proper citation: Unpaywall (RRID:SCR_016471) 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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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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https://atcp.org/

The Ataxia Telangiectasia Children's Project, better known as the A-T Children's Project, was founded in late 1993 by a family in Florida with two young sons who have A-T. It is a public, tax-exempt, non-profit organization pursuant to Section 501(c)(3) of the Internal Revenue Code, and all gifts and donations to the Project are tax deductible. The A-T Children's Project was formed to raise funds through events and contributions from corporations, foundations and friends. These funds are then used to accelerate first-rate, international scientific research aimed at finding a cure and improving the lives of all children with ataxia-telangiectasia. - To encourage and support excellent laboratory research which will accelerate the discovery of a cure or possible therapies for ataxia-telangiectasia by: - awarding competitive research grants to top scientists using a peer-review board comprised of top scientists and physicians, - organizing and sponsoring workshops and symposiums in order to encourage cooperation among laboratories and to generate new research strategies, and - working with Congress and the National Institutes of Health to encourage the funding of active research on A-T by agencies of the U.S. government. - To improve the accurate and timely diagnosis of A-T patients by increasing public awareness and by educating physicians. - To develop and maintain an international patient registry of A-T patients with objective, neutral oversight, while leaving ultimate control in the hands of treating physicians, so that up-to-date clinical information about A-T patients can be obtained for researchers and so that when a treatment is developed, all patients can be reached through their physicians. - To support and oversee a clinical center and information clearinghouse at a top-rated, world-class medical center for the evaluation of A-T patients by a multidisciplinary team of specialists, and for the accumulation of experience in managing the many facets of A-T such as the ataxia, cancer and immune problems. - To develop quantitative endpoints for objectively measuring the progression rate and severity of the symptoms of A-T. - To maintain and enlarge a tissue/cell bank with objective, neutral oversight and control in order to ensure free access of existing and new researchers to A-T patient specimens. Sponsors: The A-T Children's Project is a non-profit organization that raises funds to support and coordinate first-rate biomedical research projects, scientific conferences and a clinical center aimed at finding a cure or life-improving therapies for ataxia-telangiectasia, a lethal genetic disease that attacks children, causing progressive loss of muscle control, immune system problems, and a strikingly high rate of cancer, especially leukemia and lymphoma.

Proper citation: Ataxia-Telangiectasia Childrens Project (RRID:SCR_001671) Copy   

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https://pmsf.org/

The Phelan-McDermid Syndrome Foundation, established in 2002, is a 501(c)3 nonprofit group that provides support services for those who have family members affected by 22q13 Deletion Syndrome / Phelan-McDermid Syndrome. It also raises money to further awareness of the syndrome through research and sponsoring an international conference every two years that brings together families, researchers and therapists. The Foundation facilitates connections between families through networking, communications and support services. We also build alliances with other rare diseases groups to expand our reach and exposure. The syndrome, which affects families worldwide, is a rare genetic occurrence and is the result of a damaged or missing protein on the 22nd chromosome. Our Foundation works with researchers who are looking into the cause and possible cure for the syndrome. PMSF's grants and fellowships program is intended to encourage research projects that will advance the development of treatments and cures for PMS. Our mission is to bring together everyone affected by 22q13 Deletion Syndrome/Phelan-McDermid Syndrome to help them through the challenges they face every day and to raise awareness in the medical and research communities.

Proper citation: Phelan-McDermid Syndrome Foundation (RRID:SCR_001707) Copy   

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http://tcag.ca/index.html

Service and training support for academic, government, and private sector scientists worldwide in genomics, including laboratory experimentation, statistical analysis, and comprehensive bioinformatics support, including large-scale genome comparisons, algorithm and tools development, and database curation, annotation and hosting. The Centre for Applied Genomics hosts a variety of databases related to ongoing supported projects: *Autism Chromosome Rearrangement Database *Cystic Fibrosis Mutation Database *The Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database *Database of Genomic Variants *The Chromosome 7 Annotation Project *Human Genome Segmental Duplication Database *Non-Human Segmental Duplication Database Healthy control DNA samples from the Ontario Population Genomics Platform are available. The Biobanking and Databasing Facility provides DNA extraction from lymphoblasts, fibroblasts and other cell types, archiving of white cell pellets, preparation and immortalization of cell lines, and comprehensive databasing and tracking of samples and/or cell lines within the facility.

Proper citation: TCAG (RRID:SCR_001840) Copy   

•   Source: SciCrunch Registry

http://www.ccmb.med.umich.edu/

The CCMB was created to facilitate interdisciplinary research in computational medicine and biology and to forge collaborative relationships with faculty across campus and the US. Computational medicine and bioinformatics, is an emerging field that pursues biological questions using advanced computational technology such as complex merged datasets and powerful computing clusters. The Center currently has three components: The Bioinformatics Graduate Program (BGP), The Collaborative Computing & Data Unit, and The Interdisciplinary Research Program. Faculty from all areas of campus are affiliated with the center. The Bioinformatics Graduate Program (BGP) trains masters and Ph.D-level scholars, and oversees the research computing for four faculty members with partial appointments in the program. The Bioinformatics Graduate Program currently has 24 doctoral and 11 master-level students. The Collaborative Computing & Data Unit provides expert support for large cluster computing -- a necessary component for doing research in computational medicine and biology. This core also works with the UM Medical School and Office of the Vice President for Research (OVPR) to address long-term deficits in computing needs across campus. Finally, The Interdisciplinary Research Program oversees several NIH and state-funded projects, the largest being the National Center for Integrative Biomedical Informatics, whose goal is developing tools to facilitate biomedical research. The IDR also provides support to faculty applying for interdisciplinary grants in all areas of bioinformatics research.

Proper citation: Center for Computational Medicine and Biology (RRID:SCR_001975) Copy   

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http://www.pdc.kth.se/

PDC operates leading-edge, high-performance computers on a national level. PDC offers easily accessible computational resources that primarily cater to the needs of Swedish academic research and education. PDC also takes part in major international projects to develop high-performance computing for the future and stay a leading national resource in parallel computing.

Proper citation: Royal Institute of Technology: PDC (RRID:SCR_001828) Copy   

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http://www.rrrc.us/

Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models.

Proper citation: Rat Resource and Research Center (RRID:SCR_002044) Copy   

•   Source: SciCrunch Registry

http://www.brainfacts.org/

A web portal that aggregates information and educational materials about the brain and brain diseases. Resources such as videos, key brain concepts, and hands-on activities may be used and shared with the public.

Proper citation: brainfacts.org (RRID:SCR_003514) Copy   

•   Source: SciCrunch Registry

http://clinicalinformatics.stanford.edu/projects/cdw.html

Research and development project at Stanford University to create a standards-based informatics platform supporting clinical and translational research. STRIDE consists of three integrated components: a clinical data warehouse, based on the HL7 Reference Information Model (RIM), containing clinical information on over 1.6 million pediatric and adult patients cared for at Stanford University Medical Center since 1995; an application development framework for building research data management applications on the STRIDE platform and a biospecimen data management system. STRIDE's semantic model uses standardized terminologies, such as SNOMED, RxNorm, ICD and CPT, to represent important biomedical concepts and their relationships. STRIDE receives clinical data for research use via HL7 feeds from both SUMC hospitals: Lucile Packard Children's Hospital and Stanford Hospital and Clinics. This clinical data is used to support a wide variety of translational research services including: * Anonymized Patient Research Cohort Discovery * Electronic Chart Review for Research * IRB-Approved Clinical Data Extraction * Biospecimen Data Management * Multimedia Research * Data Management and Research Registries STRIDE is a highly secure environment utilizing encryption, fine-grained access control, robust auditing and detailed data segregation. Additionally, STRIDE has a robust access control framework with well-defined access granting authorities and access control groups. Consequently STRIDE meets or exceeds the requirements of the HIPAA Privacy and Security regulations. Privacy protection is further enhanced by requiring IRB approval for all research projects using STRIDE clinical data. From a technology and standards perspective, STRIDE is hosted on the Oracle 11g database platform. STRIDE application software provides access to the web services of a three-tier infrastructures using SSL encryption with strong authentication. These programs are cross-platform, self-updating thick-client applications that provides a rich user interface for data entry, retrieval and review as well as image manipulation and annotation. STRIDE makes extensive use of XML technologies for representation of structured meta data, distributed systems technologies using JSON for secure remote communication between client and server, and Swing graphical interface components providing a rich widget-set as well as advanced imaging and graphing capabilities. Users of the STRIDE Research Desktop Client can perform rapid data entry into structured fields, compose complex queries, and interact securely with clinical, research and imaging data.

Proper citation: Stanford Translational Research Integrated Database Environment and Clinical Data Warehouse (RRID:SCR_003453) Copy   

•   Source: SciCrunch Registry

http://etoh.niaaa.nih.gov/

Portal to support researchers and practitioners searching for information related to alcohol research including links to a number of databases, journals, and Web sites focused on alcohol research and related topics. Also included is a link to the archived ETOH database, the premier Alcohol and Alcohol Problems Science Database, which contains over 130,000 records and covers the period from 1972 through 2003. Included in ETOH are abstracts and bibliographic references to journal articles, books, dissertation abstracts, conference papers and proceedings, reports and studies, and chapters in edited works. ETOH's scope reflects the multidisciplinary nature of the alcohol research field. The range of subject areas contained in ETOH includes: medicine, biochemistry, psychology, psychiatry, epidemiology, sociology, anthropology, treatment, prevention, education, accidents and safety, legislation, criminal justice, public policy, and health services research. The ETOH database is indexed with vocabulary from the Alcohol and Other Drug Thesaurus: A Guide to Concepts and Terminology in Substance Abuse and Addiction (AOD Thesaurus), Third Edition. More than 5,000 terms in the AOD Thesaurus are used as ETOH descriptors. The Databases/Resources section includes databases and resources for alcohol researchers and practitioners. It includes an introduction to the National Library of Medicine's PubMed and some sample searches on alcohol to run in the PubMed database; descriptions of and links to the various databases of the National Clearinghouse for Alcohol and Drug Information (NCADI); a selection of alcohol and other drug databases with their descriptions and links; links to peer-reviewed journals most often used by alcohol researchers; and links to a selection of Web sites pertinent to the substance abuse field.

Proper citation: Alcohol and Alcohol Problems Science Database (RRID:SCR_003768) Copy   

•   Source: SciCrunch Registry

http://www.brain.northwestern.edu/research/for-researchers/index.html

Tissue bank for collecting, cataloging and storing postmortem brain tissue samples from subjects with and without neurological disorders. Specimens are available for research on cognitive impairment, Alzheimer's, dementia and other disorders along with clinical data such as demographic information, health and family history and neuropsychological test scores. The bank provides services to distribute postmortem brain tissue and other samples to investigators for use in research that will provide qualitative and quantitative diagnostic information to physicians, families, and researchers.

Proper citation: Northwestern CNADC Tissue Bank / Neuropathology Core (RRID:SCR_013178) Copy   

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http://brain.ubc.ca/

Research facility for research on neurological and psychiatric disorders on the learning brain and the aging brain. The Centre utilizes a multidisciplinary approach to explore the causes and potential treatments of disorders like Alzheimer's disease, mental health and addiction, stroke and neurotrauma. The Centre focuses on translating research into patient care and therapies.

Proper citation: Djavad Mowafaghian Centre for Brain Health (RRID:SCR_013149) Copy   

•   Source: SciCrunch Registry

http://www.asia-spinalinjury.org

This website provides information about the American Spinal Injury Association. The mission of ASIA is to: (a) to promote and establish standards of excellence for all aspects of health care of individuals with spinal cord injury from onset throughout life. (b) to educate members, other healthcare professionals, patients and their families as well as the public on all aspects of spinal cord injury and its consequences in order to prevent injury, improve care, increase availability of services and maximize the injured individual''s potential for full participation in all areas of community life. (c) to foster research which aims at preventing spinal cord injury, improving care, reducing consequent disability, and finding a cure for both acute and chronic SCI. (d) to facilitate communication between members and other physicians, allied health care professionals, researchers and consumers.

Proper citation: American Spinal Injury Association (RRID:SCR_012977) Copy   

•   Source: SciCrunch Registry