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http://taylorlab.ucsf.edu/software_data.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documentedt on January 10, 2023. Software that implements babel routines for identifying unusual ribosome protected fragment counts given mRNA counts, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Babel (RRID:SCR_004307) Copy   

•   Source: SciCrunch Registry

http://www.egappreviews.org/

Initiative to develop a systematic, evidence-based process for evaluating genetic tests and other applications of genomic technology that are rapidly moving from research to use in clinical practice. A key objective of this process is to provide objective, timely, and credible information that is clearly linked to the scientific evidence on specific applications of genetic and genomic tests. The primary focus of EGAPP activities is an independent, nonfederal expert panel, the EGAPP Working Group. Other components of the EGAPP initiative include a federal interagency, the CDC staff and consultants, and an EGAPP initiative evaluation team.

Proper citation: EGAPP (RRID:SCR_004189) Copy   

•   Source: SciCrunch Registry

http://www.drugdev.com/

Organization founded to meet a growing, urgent need for streamlining clinical trials that brings together an online network of clinical trial sites, the leading investigator identification and start-up platform, the industry''s best trial optimization system, and the leading grants payment capabilities to transform the way drug developers find, engage and pay doctors to run clinical trials. Specialties include: Site Identification, Protocol Feasibility, Building Investigator Communities, Site Startup, Investigator Payments, Contracts and Essential Documents, Investigator Budget Development

Proper citation: DrugDev (RRID:SCR_004064) Copy   

•   Source: SciCrunch Registry

https://brainspan.org/

Atlas of developing human brain for studying transcriptional mechanisms involved in human brain development. One of the BrainSpan datasets, Exon microarray summarized to genes, is presented. It is a downloadable archive of files containing normalized RNA-Seq expression values for analysis.

Proper citation: BrainSpan (RRID:SCR_004219) Copy   

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http://bioinfo.au.tsinghua.edu.cn/software/TAGS/

Software tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations. The installation file is for Windows., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TAGS (RRID:SCR_004294) Copy   

•   Source: SciCrunch Registry

http://www.aidshivresearch.com/

AIDS and HIV Research is a disease-related portal that includes Articles, News, Jobs, Free Journals, Links, Forum, Structures, Labs & Rankings. * AIDS and HIV research links are profiled and rated. You can rate each website and view the websites in a number of categories including portals, blogs, databases, software and several other categories. Below you will find the top 10 rated AIDS and HIV research links. * Recent AIDS and HIV research literature is highlighted. We have taken the entire set of AIDS and HIV research articles and arranged them according to their previous or expected citation rate. This allows you to quickly identify the most important articles in the field. * Recent AIDS and HIV research news and press releases are highlighted. We scour over 20,000 news sources to bring you the latest AIDS and HIV research news. * AIDS and HIV research laboratories are featured. We have actually profiled nearly 99% of all AIDS and HIV research laboratories. We have also ranked all labs based upon the citation rating of the papers of the principal investigator. Laboratories may alter information on each lab page including picture, publications, affiliation, and biography. You will find the top 20 AIDS and HIV research laboratories.

Proper citation: AIDS and HIV Research (RRID:SCR_004243) Copy   

•   Source: SciCrunch Registry

http://kwanlab.bio.cuhk.edu.hk/BSRD/

A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets.

Proper citation: BSRD (RRID:SCR_004249) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/NHSQI2009

Ontology to organise a 2009 set of over 200 NHS quality indicators from different sources. Relationships between indicators, a basic set of inclusion / exclusion criteria, clinical pathway, clinical code and purpose (per 1992 Institute of Medicine, originally intended to categorise clinical guidelines) are identifies and made searchable.

Proper citation: NHS Quality Indicators (RRID:SCR_004005) Copy   

•   Source: SciCrunch Registry

http://openconnectomeproject.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go.

Proper citation: Open Connectome Project (RRID:SCR_004232) Copy   

•   Source: SciCrunch Registry

http://www.cure.med.ucla.edu/

Center whose interests and activities encompass several facets of gastrointestinal regulatory physiology and cell biology. It provides an infrastructure to support basic, translational and clinical research and to facilitate interdisciplinary research and training activities in digestive diseases.

Proper citation: CURE - Digestive Diseases Research Center (RRID:SCR_004238) Copy   

•   Source: SciCrunch Registry

http://www.cancerdiagnosis.nci.nih.gov/

National program to improve the diagnosis and assessment of cancer by moving scientific knowledge into clinical practice by coordinating and funding resources and research for the development of innovative in vitro diagnostics, novel diagnostic technologies and appropriate human specimens. The Cancer Diagnosis Program is divided into four branches: Biorepository and Biospecimen Research Branch (BBRB), Diagnostic Biomarkers and Technology Branch (DBTB), Diagnostics Evaluation Branch (DEB), and the Pathology Investigation and Resources Branch (PIRB).

Proper citation: CDP (RRID:SCR_004236) Copy   

•   Source: SciCrunch Registry

http://www.euadr-project.org/

Consortium that created the capability to detect Adverse Drug Response (ADR) signals by creating the infrastructure for large-scale monitoring of drug safety using electronic health records (EHR). The platform leverages EHR''''s comprising demographics, drug use and clinical data of over 30 million patients from several European countries. Special attention was given to patient groups that are not routinely involved in clinical trials, for ethical or practical reasons (e.g. pregnant women, elderly people, people using many drugs simultaneously, and children). This project also studies and compares a number of different techniques that all aim to detect unexpected or disproportional rates of events. The algorithms that they studied originate not only from the field of (pharmaco)epidemiology, but also from fields such as bio-terrorism, machine learning, and classical signal detection. EU-ADR specific objectives are: To detect events, To relate these events to drugs, To develop hypothesis that explain adverse events, To detect adverse events earlier, and To avoid false positives. The web-based platform is available at https://bioinformatics.ua.pt/euadr/ EU-ADR has contributed to the ability to conduct better drug safety studies based on the re-use of healthcare data. By facilitating the early detection of adverse drug reactions, but also providing key information on populations at risk, potential drug interactions, potential underlying mechanisms and intervening pathways in adverse events, etc., the project will allow for improved and more complete information to be available for drug and healthcare delivery, leading to increased patient safety and its associated cost savings. The EU-ADR system can be considered as a complementary tool to already existing pharamcovigilance systems. Should the system be widespread in the long term, it has the potential to contribute to the development of future electronic health record systems, insofar as the expected benefits of these IT tools are only fully attainable when EHRs develop themselves in consistency, richness and formats that allow them to be subject of such tools. In anticipation, EU-ADR has been designed to be modular and scalable, so that different EHR databases (other than those participating in the Consortium) can be progressively enlisted in the future, adopt the software for data extraction and therefore become susceptible of exploitation by the system, for maximum global effect.

Proper citation: EU-ADR (RRID:SCR_004028) Copy   

•   Source: SciCrunch Registry

http://www.medpedia.com/

Medpedia is an open platform connecting people and information to advance medicine. This wiki is the collaborative encyclopedia and resource for information about health, medicine and the body. Only physicians and Ph.D.s are allowed to edit the Articles on Medpedia after they create an account and are approved as an Editor. Non-Editors can create an account and then suggest changes that must be approved by an Editor before going live on the site. To suggest changes, click the link Suggest Changes at the top of Article Pages. Intended Uses and Benefits: * Reference source for both medical professionals and the lay-public covering information about health, medicine and the body * Forum for individuals and groups to be recognized for their areas of expertise * Clearinghouse of bio-medical journal articles, data, research, and educational materials * Forum for debating emerging issues * Platform for advancing medical knowledge Medpedia Portals - Adult Primary Care, Allergy and Immunology, Anatomy, Cardiology, Emergency Medicine, Endocrinology, Epidemiology, Gastroenterology and Hepatology, General Medicine, Infectious Diseases, Internal Medicine, Neurology & Neurobiology, Nutrition, OB/GYN and Reproductive Health, Oncology, Orthopedics, Pathology, Pediatrics, Pharmacology, Psychiatry, Public Health, Pulmonology, Rheumatology, Women''s Health In association with Harvard Medical School, Stanford School of Medicine, Berkeley School of Public Health, University of Michigan Medical School and other leading global health organizations, Medpedia will be a commons for the gathering of the information and people critical to health care.

Proper citation: Medpedia (RRID:SCR_004269) Copy   

•   Source: SciCrunch Registry

http://danstem.ku.dk/

Center consisting of 9 research groups who all address basic questions in stem cell and developmental biology with the overall aim of developing new stem cell-based therapeutic approaches for diabetes and cancer. DanStem comprises two sections: * The Novo Nordisk Foundation Section for Basic Stem Cell Biology (BasicStem) * The Section for Strategic Translational Stem Cell Research and Therapy (TransStem) DanStem was established as a result of a series of international recruitments coupled with internationally recognized research groups focused on insulin producing beta cells and cancer research already located at the University of Copenhagen. They all have well-established, international collaborations and actively participate in several international scientific consortia. DanStem is also active in training undergraduates, PhD students and postdocs.

Proper citation: DanStem (RRID:SCR_004021) Copy   

•   Source: SciCrunch Registry

http://www.mcewencentre.com/

Center aiming to be a catalyst for regenerative medicine by facilitating collaboration, supporting research, and promoting awareness of the field. The center includes 15 scientists at five Toronto hospitals, as well as the University of Toronto, currently working to accelerate the development of more effective treatments for conditions such as heart disease, diabetes, respiratory disease and spinal cord injury. They collaborate with many other research institutions throughout North America, Europe and the Asia / Pacific region. The research is powered by a team of recent doctoral graduates recruited from around the world that are selected through a competitive process. They are a critical tool for supporting the work of McEwen Centre, allowing them to find medical breakthroughs faster.

Proper citation: McEwen Centre for Regenerative Medicine (RRID:SCR_004020) Copy   

•   Source: SciCrunch Registry

https://sfari.org/

Launched in 2005, the Simons Foundation Autism Research Initiative (SFARI) is a research campaign within the Simons Foundation''s overall suite of programs. SFARI''s mission is to improve the diagnosis and treatment of autism spectrum disorders by funding, catalyzing and driving innovative research of the greatest quality and relevance. Although SFARI''s priority is to benefit individuals challenged by these disorders, its efforts are certain to yield insights into the neural mechanisms of fundamental human capabilities, thereby promoting the broader mission of the Simons Foundation to advance the frontiers of research in the basic sciences and mathematics. Autism spectrum disorders are a set of complex developmental disorders characterized by persistent deficits in social communication and interaction, as well as restricted behaviors, interests or activities. The Centers for Disease Control and Prevention estimates that roughly 1 in 110 children in the U.S. have autism, with many more boys affected than girls. These disorders cost the U.S. economy an estimated $35 billion dollars each year in direct care costs and lost productivity, and extract an incalculable human toll.

Proper citation: SFARI - Simons Foundation Autism Research Initiative (RRID:SCR_004261) Copy   

•   Source: SciCrunch Registry

http://webvision.med.utah.edu/

Online textbook that has evolved into an interactive, dynamic blog that covers all things related to the bioscience of the visual system. It summarizes recent advances in knowledge and understanding of the visual system through dedicated chapters and evolving discussion to serve as a clearing house for all things related to retina and vision science.

Proper citation: Webvision - The Organization of the Retina and Visual System (RRID:SCR_004254) Copy   

•   Source: SciCrunch Registry

http://www.cclg.org.uk/index.php

THIS RESORUCE IS NO LONGER IN SERVICE. Documented on April 27,2023. CCLG is an association of healthcare professionals involved in the treatment and care of children and younger teenagers with cancer, and underpins all the activity in pediatric oncology in the British Isles. CCLG is committed to research and development in the treatment of cancer in this age group, the ultimate goal of which is to maximize cure while minimizing the early and late side effects of treatment. Provision of information for patients and families is a core activity. The Children''s Cancer and Leukaemia Group was formed in 2006 as a result of the merger of the UK Children''s Cancer Study Group and the UK Childhood Leukaemia Working Party, both of which had been in existence since the 1970s.

Proper citation: CCLG (RRID:SCR_004137) Copy   

•   Source: SciCrunch Registry

http://www.penta-id.org/

A Level 1 network for pediatric infectious disease in Europe recognized by the European networks of paediatric research at the European Medicines Agency (EnprEMA) whose activities vary from clinical trials, to cohort studies and training. It is currently developing a portfolio of clinical trials in antimicrobials in children, including antibiotics, antivirals and antifungals.

Proper citation: PENTA-ID (RRID:SCR_004092) Copy   

•   Source: SciCrunch Registry

https://zenodo.org/

Repository for all research outputs from across all fields of science in any file format as well as both positive and negative results. They assign all publicly available uploads a Digital Object Identifier (DOI) to make the upload easily and uniquely citeable. They further support harvesting of all content via the OAI-PMH protocol. They promote peer-reviewed openly accessible research, and curate uploads. ZENODO allows users to create their own collection and accept or reject all uploads to it. They allow for uploading under a multitude of different licenses and access levels.

Proper citation: ZENODO (RRID:SCR_004129) Copy   

•   Source: SciCrunch Registry