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Software for managing geochemical data created by individual geochronology laboratory. Designed for flexibility and extensibility, so that it can be tailored to the needs of individual analytical labs that manage wide variety of data. Database set up for metadata tracking.
Proper citation: Sparrow-data (RRID:SCR_024432) Copy
https://cran.r-project.org/web/packages/DrugSim2DR/
Software R package to predict drug functional similarity to drug repurposing.
Proper citation: DrugSim2DR (RRID:SCR_024564) Copy
https://github.com/bioinfo-center-pasteur-fr/toppred
Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins.
Proper citation: toppred (RRID:SCR_024385) Copy
https://github.com/paulgeeleher/pRRophetic
Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data,
Proper citation: pRRophetic (RRID:SCR_024417) Copy
https://github.com/bartongroup/yanosim
Software tool as read simulator for nanopore DRS datasets.
Proper citation: Yanosim (RRID:SCR_024363) Copy
https://github.com/chaoszhang/A-pro
Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy.
Proper citation: ASTRAL-Pro (RRID:SCR_024520) Copy
CNBC is joint venture of University of Pittsburgh and Carnegie Mellon University. Our center leverages the strengths of the University of Pittsburgh in basic and clinical neuroscience and those of Carnegie Mellon in cognitive and computational neuroscience to support a coordinated cross-university research and educational program of international stature. In addition to our Ph.D. program in Neural Computation, we sponsor a graduate certificate program in cooperation with a wide variety of affiliated Ph.D. programs.
Proper citation: Center for the Neural Basis of Cognition (RRID:SCR_002301) Copy
http://www.radiology.ucsf.edu/cind
Biomedical technology research center that develops and validates new imaging methods for detecting brain abnormalities in neurodegenerative diseases, including Alzheimer's disease, vascular dementia, frontotemporal dementia, Parkinson's disease, as well as epilepsy, depression, and other conditions associated with nerve loss in the brain. As people around the globe live longer, the impact of neurodegenerative diseases is expected to increase further with dire social and economical consequences for societies if no effective treatments are developed soon. The development at CIND is aimed to improve magnetic resonance imaging (MRI). The ultimate goal of the scientific program is to identify imaging markers that improve accuracy in diagnosing neurodegenerative diseases at early stages, achieve more reliable prognoses of disease progression, and facilitate the discovery of effective treatment interventions. In addition to addressing the general needs for studying neurodegenerative diseases, another focus of CIND concerns brain diseases associated with military service and war combat, such as post traumatic stress disorder (PTSD), brain trauma, gulf war illness and the long-term effects of these conditions on the mental health of veterans. The symbiosis between CIND and the Veterans Administration Medical Center in San Francisco makes this program uniquely suited to serve military veterans.
Proper citation: Center for Imaging of Neurodegenerative Diseases (RRID:SCR_001968) Copy
http://www.duke.edu/web/gpcr-assay/index.html
Describes data from and access to permanent cell lines containing beta-arrestin fluorescent protein biosensors. This assay Bank provides plasmids, cells lines, and resulting data to the NIDA/NIH funded research community in order to better understand and combat addiction.
Proper citation: Addiction Research GPCR Assay Bank (RRID:SCR_002895) Copy
Group of 10 academic laboratories provide pancreatic islets of cGMP-quality to eligible investigators for use in FDA approved, IRB-approved transplantation protocols in which isolated human islets are transplanted into qualified patients afflicted with type 1 diabetes mellitus; optimize the harvest, purification, function, storage, and shipment of islets while developing tests that characterize the quality and predict the effectiveness of islets transplanted into patients with diabetes mellitus; and provide pancreatic islets for basic science studies. The centers are electronically linked through an Administrative and Bioinformatics Coordinating Center (ABCC). The ABCC manages a system with objectively defined criteria that establishes the order of priority for islet distribution. It also provides database and other informatics to track the utilization of pancreata and all distributed clinical grade islets for transplant and basic research, and supports the Islet Cell Resource Centers Consortium so that the research community has a single entry point to the program. Qualified researchers from domestic institutions may request islets by submitting a written application to the director of the ABCC. The ICRs will distribute Islets as appropriate for either clinical or basic science protocol use to eligible investigators who have received a favorable review and subsequent approval by the ICR Steering Committee (SC). The Administrative and Bioinformatics Coordinating Center (ABCC) manages the distribution according to a priority list. The ABCC will give preference to investigators who have peer-reviewed, NIH-funded research support.
Proper citation: Islet Cell Resource Centers (RRID:SCR_002806) Copy
Collaborative project to bring together biochemical pathway databases and research communities focused on plant metabolism. Used to build broad network of plant metabolic pathway databases. Central feature of PMN is PlantCyc, comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.
Proper citation: Plant Metabolic Network (RRID:SCR_002888) Copy
Biomedical technology research center designed to advance basis and clinical aspects of tissue engineering, to provide training for investigators and dissemination of scientific findings and new techniques. Expertise and facilities are focused on research, problem solving and training for biomedical community through integrated systems approach to challenges in tissue engineering. Mission for TERC is to engineer human tissues for medical impact. Includes Functional human tissue grafts: human tissues for application in regenerative medicine;Human disease models in vitro: in vitro models of human disease to provide new experimental tools to understand progression of disease, effects and mechanisms of drug action; Biological materials research: bioengineering tools for cell biology studies in context of tissue development, regeneration and disease.
Proper citation: Tissue Engineering Resource Center (RRID:SCR_000103) Copy
https://www.ontario.ca/page/ministry-research-innovation-and-science
Ministry that supports research, commercialization and innovation taking place across Ontario through a range of programs and services like the Ontario Research Fund, Innovation Demonstration Fund and Ontario Venture Capital Fund.
Proper citation: Ontario Ministry of Research and Innovation; Ontario; Canada (RRID:SCR_000989) Copy
http://neuroscience.berkeley.edu/
Portal for UC Berkeley's neuroscience research center. The group focuses on interdisciplinary collaboration between neuroscientists and members of UC Berkeley programs in engineering, chemistry, statistics, and computation. It also runs the neuroscience PhD program.
Proper citation: Helen Wills Neuroscience Institute (RRID:SCR_001991) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Project Halo is a staged, long-range research effort by Vulcan Inc. towards the development of a Digital Aristotlea reasoning system capable of answering novel questions and solving advanced problems in a broad range of scientific disciplines and related human affairs. The project focuses on creating two primary functions: a tutor capable of instructing and assessing students in those subjects, and a research assistant with broad, interdisciplinary skills to help scientists and others in their work. Vulcan began work towards this ambitious vision in 2003 with the Halo Pilot a six-month effort to investigate the feasibility of creating a scientific knowledge base capable of answering novel questions from the AP (1st year college level) chemistry test. Three teams SRI International, Cycorp, and Ontoprise developed knowledge bases, for a limited section of an AP-chemistry syllabus, that were able to correctly answer 40 to 50 percent of the associated questions from the AP test. Since 2004, Project Halo has worked to improve these systems, with an emphasis on enabling knowledge entry by domain experts, instead of specialists in artificial intelligence software. In 2004, Vulcan began the development of Automated User-Centered Reasoning and Acquisition System (AURA), by SRI, that enables domain experts (graduate students in Biology, Chemistry, and Physics) to enter knowledge from introductory science textbooks. In 2006, an evaluation of AURA showed that students could create AURA knowledge bases that correctly answered 40 percent of the questions on a limited AP exam. In 2008, the next evaluation demonstrated an improvement of that score to 70 percent correct. In parallel, Project Halo has sponsored Ontoprise to develop semantic extensions to MediaWiki, the software that Wikipedia runs on. Ontoprise has developed a set of Semantic MediaWiki (SMW)+ extensions to MediaWiki that provide a community-based environment for authoring ontologies and creating semantically enhanced wikis. SMW+ has been widely used and is being applied in project management, enterprise collaboration and knowledge management, business intelligence, and the management of large terminology sets. In 2007, Vulcan began a new effort, Halo Advanced Research (HalAR), to address the difficult knowledge representation and reasoning (KR) challenges that prevent the realization of Digital Aristotle. This effort has produced a new semantic rule language and reasoning system, Semantic Inferencing on Large Knowledge (SILK), which includes major advances, including for default and higher-order reasoning over the web.
Proper citation: Project Halo (RRID:SCR_000136) Copy
Embryonic stem cell distribution unit that distributes material arising within European Conditional Mouse Mutagenesis Program consortium, currently targeting vectors and ES cells. Upon user request EUCOMM grow targeting vectors from glycerol stocks and prepare vector DNA. Identity of vector is verified by restriction mapping. Upon user request EUCOMM thaw, expand and re-freeze several aliquots of desired ES cell clone. Standard controls include PCR based assay. Upon additional request EuMMCR unit develops genotyping PCR, which can be used to genotype chimeric mice that may be generated using those ES cell clones.
Proper citation: EuMMCR (RRID:SCR_001506) Copy
Repository of biospecimen and phenotype data collected from Crohn's disease and ulcerative colitis cases and controls recruited at six sites throughout North America that are available to the scientific community. Phenotyping is performed using a standardized protocol, and lymphoblastoid cell lines are established for each subject. Phenotype data for each subject are collected by the Consortium's Data Coordinating Center (DCC), and phenotype data for all subjects with DNA samples are available. The resulting DNA samples have already been utilized by the Consortium to complete various association studies, including genome-wide association studies using dense genotyping arrays. Researchers can obtain DNA samples and phenotype, genotype, and pedigree data through the Data Repository. GWAS data must be requested through dbGAP. The IBDGC is involved with independent genetic research studies and actively works with members of the IBD and genetic communities on collaborative projects. They are also members of the International IBD Genetics Consortium. Phenotype Tools: The Consortium Phenotype Committee, led by Dr. Hillary Steinhart designed and validated paper forms to collect extensive phenotype data on Crohn's Disease and ulcerative colitis. Consortium phenotype tools are available for use by non-Consortium members.
Proper citation: NIDDK Inflammatory Bowel Disease Genetics Consortium (RRID:SCR_001461) Copy
Portal as data resource, map repository, and GIS service provider for federally-funded scientists conducting research in the Arctic and Antarctic. The PGC holds an extensive collection of satellite imagery and aerial photography at varying resolutions.
Proper citation: Polar Geospatial Center (RRID:SCR_000402) Copy
http://www.uef.fi/en/-neurotieteet
Portal of neuroscience and neurology resources pertaining to the University of Eastern Finland.
Proper citation: UKU Neuroscience and Neurology Links (RRID:SCR_001733) Copy
Consortium represents all publicly available gene trap cell lines, which are available on non-collaborative basis for nominal handling fees. Researchers can search and browse IGTC database for cell lines of interest using accession numbers or IDs, keywords, sequence data, tissue expression profiles and biological pathways, can find trapped genes of interest on IGTC website, and order cell lines for generation of mutant mice through blastocyst injection. Consortium members include: BayGenomics (USA), Centre for Modelling Human Disease (Toronto, Canada), Embryonic Stem Cell Database (University of Manitoba, Canada), Exchangeable Gene Trap Clones (Kumamoto University, Japan), German Gene Trap Consortium provider (Germany), Sanger Institute Gene Trap Resource (Cambridge, UK), Soriano Lab Gene Trap Resource (Mount Sinai School of Medicine, New York, USA), Texas Institute for Genomic Medicine - TIGM (USA), TIGEM-IRBM Gene Trap (Naples, Italy).
Proper citation: International Gene Trap Consortium (RRID:SCR_002305) Copy
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