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https://github.com/qqpigass/FREEPII

Software application encompassing autonomous feature extraction and feature representation enhancement for PPIs and protein complexes inference. FREEPII establishes feature maps that are consistent with model training, and emphasizes learning the feature representation of proteins rather than the feature representation of PPI, reducing the computational complexity from N^2 to N (N: number of proteins). FREEPII uses protein sequences to expand the information available for calculating data similarity between proteins. Furthermore, it introduces network-level information into the final feature representation to rescale the strength of interactions present in CF-MS data.

Proper citation: Feature Representation Enhancement End-to-end Protein Interaction Inference (RRID:SCR_026316) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/

Sage Bionetworks, Mount Sinai School of Medicine (MSSM), University of Pennsylvania (Penn), the National Institute of Mental Health (NIMH), and Takeda Pharmaceuticals Company Limited (TAKEDA) have launched a Public-Private Pre-Competitive Consortium, the CommonMind Consortium, to generate and analyze large-scale genomic data from human subjects with neuropsychiatric disease and to make this data and the associated analytical results broadly available to the public. This collaboration brings together disease area expertise, large scale and well curated brain sample collections, and data management and analysis expertise from the respective institutions. As many as 450 million people worldwide are believed to be living with a mental or behavioral disorder: schizophrenia and bipolar disorder are two of the top six leading causes of years lived with disability according to the World Health Organization. The burden on the individual as well as on society is significant with estimates for the health care costs for these individuals as high as four percent GNP. This highlights a grave need for new therapies to alleviate this suffering. Researchers from MSSM including Dr. Pamela Sklar, Dr. Joseph Buxbaum and Dr. Eric Schadt will join with Dr. Raquel Gur and Dr. Chang-Gyu Hahn from Penn to combine their extensive brain bank collections for the generation of whole genome scale RNA and DNA sequence data. Dr.Pamela Sklar, Professor of Psychiatry and Neuroscience at MSSM commented this is an exciting opportunity for us to use the newest genomic methods to really expand our understanding of the molecular underpinnings of neuropsychiatric disease, while Dr Raquel Gur, Professor of Psychiatry from Penn observed this will be a great complement to some of the large-scale genetic analyses that have been carried out to date because it will give a more complete mechanistic picture. The CommonMind Consortium is committed to generating an open resource for the community and invites others with common goals to contact us at info (at) CommonMind.org.

Proper citation: CommonMind Consortium (RRID:SCR_000139) Copy   

•   Source: SciCrunch Registry

http://www.omicia.com/products/opal-research

Software which integrates a comprehensive, automated genome annotation engine with the VAAST and Phevor disease gene prioritization tools to rank gene variants on the severity of their impact on protein function and likelihood to cause disease. Each variant in a gene is analyzed for its impact on protein function, conservation and frequency. Each gene is ranked rather than filtered in order to ensure critical targets are not prematurely removed.

Proper citation: Opal Research (RRID:SCR_000405) Copy   

•   Source: SciCrunch Registry

http://archives.niddk.nih.gov/patient/mpsa/mpsa.aspx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Cross-disciplinary, multi-institutional network with wide range of experts to analyze serum and tissue samples collected in the Medical Therapy of Prostatic Symptoms (MTOPS) trial. Consortium aims to discover and validate biomarkers for the detection, risk assessment, and disease progression assessment of benign prostatic hyperplasia (BPH).

Proper citation: MTOPS Prostate Samples Analysis Consortium (RRID:SCR_000041) Copy   

•   Source: SciCrunch Registry

http://homedialyzorsunited.org/

A non-profit patient organization dedicated to educate, support and advocate for home dialysis. Their main focus is advocating and supporting those on home hemodialysis and peritoneal dialysis modalities. Membership is free and inclusive of dialyzors, care partners, nurses, nephrologists, renal professionals and others.

Proper citation: Home Dialyzors United (RRID:SCR_000275) Copy   

•   Source: SciCrunch Registry

http://www.bu.edu/alzresearch/about/cores/neuro.html

The Neuropathology Core leads neuropathological analyses of brains donated by research registry participants of the Boston University Alzheimer's Disease Center. The Core works with the Clinical Core to carry out the Brain Tissue Donation Program, which provides brain tissue for analyses that will help to understand the underlying pathology of AD. The Core also works closely with the Data Management and Statistics Core to maintain a comprehensive computerized database of information resulting from neuropathological analyses. The Boston University Brain Bank of the Neuropathology Core documents neuropathological findings of Center research registry participants, but also of brain donors from important related BUSM studies such as the Framingham Heart Study and the Centenarian Study.

Proper citation: Boston University Alzheimer's Disease Center Neuropathology Core Facility (RRID:SCR_000513) Copy   

•   Source: SciCrunch Registry

http://www.africacentre.ac.za/Biobank/tabid/460/Default.aspx

THIS RESOURCE IS NO LONGER IN SERVICE, documented November 30, 2015. Extensive collection of biological specimens of various kinds that are mostly collected from the population around the Africa Centre in northern KwaZulu-Natal, but there are also specimens collected from populations in and around Durban and elsewhere in KwaZulu-Natal. The results of tests carried out on these specimens are generally stored in the main databases of the various studies involved, and are linkable back to the demographic and other data collected from the individuals concerned. The Biobank is curated by staff of the Africa Centre's Virology Laboratory in Durban, where all the specimens are currently stored, mostly in -80C freezers. A particular strength of its holdings are the dried blood spot (DBS), specimens five drops of blood on a filter-paper card, obtained via a finger-prick - of which there are now nearly 115,000. The following is a list of its holdings (May 2011): * 67,700 DBS specimens collected since late 2002 primarily for HIV prevalence estimation of the population covered by the Africa Centre Demographic Surveillance population. All have at least been tested for HIV, and just over 21% give a Positive result. Specimens are collected annually, so for some individuals we might have a sequence of 8-10 specimens covering 2002-2011. * 36,601 DBS specimens collected by the Vertical Transmission Study (VTS) between Sep 2001 and Dec 2006. This study focussed on mother-child pairs and investigated the vertical transmission of HIV from mother to child. DBS specimens were collected from both the mothers (at initial screening, and then from their children at Birth, 6, 10, 14, 18, 22 weeks, and 7, 8, 9, 12, 15, 18, 21 and 24 months. * 6,585 DBS specimens collected as part of the KZN IMPACT study of PMTCT effectiveness in six districts of kwaZulu-Natal. The specimens were collected during 2004-2006 from infants aged 4-8 weeks when mothers brought them to clinics for immunisation. These DBS specimens are stored at room temperature, not in freezers. * 3,524 DBS specimens collected as part of the Kesho Bora study from Sep 2007 . They were collected from mothers at enrollment, and from the infants at delivery, 2 weeks, and at 4, 5, 7, 8 and 15 months. * 50,068 Plasma specimens * 28,775 breastmilk specimens * 11,277 breastmilk products (Pellets and lactoserum). These have all been extracted from the BM specimens in prev. item? * 11,188 RNA and DNA products extracted from DBS and plasma specimens from all our major studies. * 5,735 Serum specimens * 3,505 cell pellets * 1,778 whole blood specimens * 1,284 Peripheral Blood Mononuclear Cells from the Kesho Bora study mothers (665) and their children (619) * 179 skin tissue specimens from the KST study (Kaposi's Sarcoma) * 176 foreskins

Proper citation: Africa Centre Biobank (RRID:SCR_000638) Copy   

•   Source: SciCrunch Registry

http://www.thebrainproject.org/

The Mission of the Sarah Jane Brain Project is to create a model system of care for children and young adults suffering from all Pediatric Acquired Brain Injuries in order to advance our knowledge of the brain fifty years over the next five years! As a father of a child suffering from a Pediatric Acquired Brain Injury (PABI), I have spent countless hours searching the internet and speaking with Sarah Jane's development team (doctors, therapists and other professionals) trying to improve the development of my daughter. What I found was that while there are a countless number of wonderful and informative prevention sites for Shaken Baby Syndrome and advocacy sites for brain injuries, there is no one centralized resource for research and rehabilitation for PABI. Furthermore, many of the issues families and children face are the same whether the brain injury was caused by a car crash, a sports-related concussion, an assault or by a tumor. No one person or organization has all the answers to the questions that parents of children suffering from PABI face. Yet through my own experience, I learned that the coordination and dissemination of Sarah Jane's medical and therapy records and data in an orderly manner greatly helps her development team better help her. These wonderful individuals are constantly looking for additional ways to improve Sarah Jane's progress by speaking with their colleagues, reading literature on brain injury, and collaborating with other parents. But they all admit there is a considerable amount that still needs to be learned about the human brain, particularly the developing brain. The field of neuroscience today is similar to the computer science field of the 1950s and 1960s: you have a diverse group of very smart people working independently of one another throughout the United States and the world, yet few know what the others are doing behind closed doors. Fast- forward 50 years and many of the breakthroughs in the computer industry have been made utilizing the principles of open source a research method that promotes free and open access to the design and production of goods and knowledge. Its use was made well-known through the creation of the Linux computer operating system, in which professionals share knowledge to make corrections and fix problems. Open source is commonly used by millions of people today through the Wikipedia online free encyclopedia, a collection of public entries on established subjects that allows anyone to make additions or corrections. The National Institute of Mental Health launched The Human Brain Project in 1993 to develop and support the new science of neuro-informatics. From this initiative, it became obvious what needed to be done. That's why we created the Sarah Jane Brain Virtual Center of Excellence an ecosystem for professionals and families dealing with PABI around the world and a vehicle to help implement the PABI Plan by establishing a model system for PABI.

Proper citation: Sarah Jane Brain Project (RRID:SCR_000620) Copy   

•   Source: SciCrunch Registry

http://php.med.unsw.edu.au/embryology/index.php?title=Main_Page

A wiki / educational resource for learning concepts in embryological development with sections including medicine, science, movies - audio, human embryo, systems, abnormal and animals. Pages on developmental topics can be added by experts in that specific research area and the content subject to easy review and update. Students can also contribute and several undergraduate courses use content on this site. Editing of pages will be restricted to registered users and all changes are logged.

Proper citation: UNSW Embryology (RRID:SCR_000655) Copy   

•   Source: SciCrunch Registry

http://www.geuvadis.org/web/geuvadis/home

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. A European Medical Sequencing Consortium committed to gaining insights into the human genome and its role in health and medicine by sharing data, experience and expertise in high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GEUVADIS (RRID:SCR_000684) Copy   

•   Source: SciCrunch Registry

http://www.genet.sickkids.on.ca/cftr/

Collection of mutations in CFTR gene for international cystic fibrosis genetics research community. Provides up to date information about individual mutations in CFTR gene. All known CFTR mutations and sequence variants have been converted to standard nomenclature recommended by Human Genome Variation Society. On line process for submission of new mutations has been added.While they continue to ensure quality of data, they urge international community to give them feedback and suggestions. Clinical information in this database relates only to details of discovery of specific mutations. As part of 2010 upgrade, CFTR1 joined new project called CFTR2 - Clinical and Functional TRanslation of CFTR. Links to CFTR2 for many mutations in CFTR1 will provide up-to-date summaries of genotype-phenotype information from patient registries around the world.

Proper citation: Cystic Fibrosis Mutation Database (RRID:SCR_000685) Copy   

•   Source: SciCrunch Registry

http://isc.temple.edu/neuroanatomy/lab/atlas/S5/

Sectional atlas featuring sections of the spinal cord and brain for a neuroanatomy course offered by Temple University. Labels may be turned on and off.

Proper citation: Sectional Atlas of Human Brain and Spinal Cord (RRID:SCR_000799) Copy   

•   Source: SciCrunch Registry

http://vesalius.northwestern.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 10,2026. English translation of Andreas Vesalius' Renaissance anatomical atlas On the Fabric of the Human Body (1543, 1555) and an explanation of the work in progress at Northwestern University to translate and annotate this historic work (by Daniel Garrison and Malcolm Hast). This detailed account of human anatomy transformed its subject and forever changed medical education in the West. Its woodcut illustrations became the basis of medical art and illustrations for generations to come, and continue to influence the way we look at the human body. * Book One -- The things that sustain and support the entire body, and what braces and attaches them all. (the bones and the ligaments that interconnect them) * Book Two -- All the ligaments and muscles, instruments of voluntary and deliberate motion * Book Three -- The series of veins and arteries throughout the body * Book Four -- The nerves * Book Five -- The organs of nutrition and generation * Book Six -- The heart and organs serving the heart (Chiefly the heart and lungs) * Book Seven -- The brain and organs of sense Note: Only introduction, images, and essays appear to be available.

Proper citation: De Humani Corporis Fabrica (RRID:SCR_000699) Copy   

•   Source: SciCrunch Registry

http://hospitals.jefferson.edu/diseases-and-conditions/alzheimers-disease/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. If you or someone you love has been diagnosed with dementia caused by Alzheimer's disease, you'll be in good hands at Jefferson. Our neurologists and psychiatrists are dedicated to: Compassionate care for individuals with Alzheimer's disease; Supporting families; Advancing care through research into the epidemiology and treatment of neurodegenerative diseases. We interact with patients very early in the disease progression, when impairment is typically mild; deliver state-of-the-art care; provide information; build care-giving skills; and help caregivers connect with community support and plan for the future.

Proper citation: Jefferson Hospital for Neuroscience Alzheimers Disease and Dementia Center (RRID:SCR_000579) Copy   

•   Source: SciCrunch Registry

http://wannovar.usc.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web interface to the ANNOVAR software, a tool to annotate functional consequences of genetic variation from high-throughput sequencing data, to help biologists without bioinformatics skills to easily submit a list of mutations (even whole-genome variants calls) to the web server, select the desired annotation categories, and receive functional annotation back by emails. Given a list of single nucleotide variants (SNVs) and insertions / deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a variants reduction protocol to identify a subset of potentially deleterious variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: wANNOVAR (RRID:SCR_000565) Copy   

•   Source: SciCrunch Registry

http://www.ebire.org/hcnlab/software/vamca.html

A stand-alone, open source human cortical meta-analysis and visualization toolbox for MatLab. It projects stereotaxic coordinates to a mean cortical surface by using an anatomical database of 60 young adults to provide multiple mappings of normalized cortical surfaces into MNI space. VAMCA performs the following analyses: # Multi-Fiducial Projection Mapping: Map stereotaxic 3D coordinates to the normalized cortical location for each of 60 database subjects. # Computing Centroid Locations for groups of foci both on a mean cortical surface and in MNI space. # Comparing Two Groups of Foci for differences in location (surface or 3D) of their group centroids and computing the groups' overlap extent using permutation tests. # Detecting Significant Densities of Foci or Density Differences of Two Groups within anatomical ROIs on a mean cortical surface by using Monte Carlo analyses. Coordinate weights allow fixed or random effects type analyses.

Proper citation: VAMCA (RRID:SCR_007028) Copy   

•   Source: SciCrunch Registry

http://www.nybb.hs.columbia.edu/

A brain bank which collects postmortem human brains to meet the needs of neuroscientists investigating specific psychiatric and neurological disorders. NYBB disburses tissue samples to investigating clinicians or scientists whose research has been approved by their Institutional Review Board. The tasks of the NYBB include: collection and processing of human postmortem brain samples for research; neuropathological evaluation and diagnosis; storage and computerized inventory of brain samples; and distribution of brain samples to investigating clinicians and scientists. Brains from individuals without neurological or psychiatric disorders are used as normal controls.

Proper citation: New York Brain Bank at Columbia University (RRID:SCR_007142) Copy   

•   Source: SciCrunch Registry

http://pathology.duke.edu/files/neuroanat/nawr_index.html

Comprehensive neuroanatomy resource created for course PTA 201 Practical Neuroanatomy, including animated images and hyperlinked descriptions with the following major categories: Blood supply, motor systems, cranial nerves, neurohistology, functional organization, sensory systems, and major coverings.

Proper citation: Duke University NeuroAnatomy Web Resources (RRID:SCR_007145) Copy   

•   Source: SciCrunch Registry

http://humancyc.org/

The HumanCyc database describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of Homo sapiens at the genomic level. A computational pathway analysis of the human genome assigned human enzymes to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary step toward quantitative modeling of metabolism. HumanCyc contains the complete genome sequence of Homo sapiens, as presented in Build 31. Data on the human genome from Ensembl, LocusLink and GenBank were carefully merged to create a minimally redundant human gene set to serve as an input to SRI''s PathoLogic software, which generated the database and predicted Homo sapiens metabolic pathways from functional information contained in the genome''s annotation. SRI did not re-annotate the genome, but worked with the gene function assignments in Ensembl, LocusLink, and GenBank. The resulting pathway/genome database (PGDB) includes information on 28,783 genes, their products and the metabolic reactions and pathways they catalyze. Also included are many links to other databases and publications. The Pathway Tools software/database bundle includes HumanCyc and the Pathway Tools software suite and is available under license. This form of HumanCyc is faster and more powerful than the Web version.

Proper citation: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism (RRID:SCR_007050) Copy   

•   Source: SciCrunch Registry

http://www.researchals.org/

A research forum portal for ALS-related resources targeted specifically towards academic and industry-based researchers. The aim of the ALS Forum is to identify existing research resources and build new tools to help veteran researchers accelerate their work and to help those new to the ALS field quickly get up to speed. It currently consists of content developed through a partnership with the Alzforum and filtered for its relevance to ALS, as well as links to ALS review articles, and a dynamic listing of current drug development efforts relevant to ALS.

Proper citation: ALS Forum (RRID:SCR_007160) Copy   

•   Source: SciCrunch Registry