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http://www.mssm.edu/research/programs/manhattan-hiv-brain-bank/

Biorepository of tissues and fluids relevant for the neurologic, neuropsychologic, psychiatric and neuropathologic manifestations of HIV infection, linked to medical records and an on-going clinical trial for research use by the scientific community. The MHBB conducts a longitudinal, observational study that follows a group of HIV-infected individuals who have agreed to be fluid and organ donors for the purposes of AIDS research. They are currently the largest, multidisciplinary neuroAIDS cohort in New York City, the epicenter of the US HIV epidemic. Research participants undergo regular neurologic, neuropsychologic, and psychiatric evaluations, and provide body fluid samples that are linked to clinical information. Upon their demise, study participants become organ donors. This program has supplied clinical information, tissue, and fluid samples to over 70 qualified AIDS researchers across America, Europe and Australia. In fulfilling its resource mission, the MHBB functions as part of the National NeuroAIDS Tissue Consortium (NNTC). MHBB provides a means by which people living with HIV can be engaged in the struggle to improve our knowledge about HIV infection and the damage it causes to the body.

Proper citation: Manhattan HIV Brain Bank (RRID:SCR_010520) Copy   

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http://homer.ucsd.edu/

Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.

Proper citation: HOMER (RRID:SCR_010881) Copy   

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http://ciliate.org/index.php/home/welcome

TGD Wiki is a user-updatable database of information about the Tetrahymena thermophila genome sequence determined at The Institute for Genomic Research (TIGR). TGD Wiki provides information on the genome, genes, and proteins of Tetrahymena collected from the scientific literature, research community and many other resources. In order to keep the information in our database as current as possible, we will soon be inviting the members of the Tetrahymena community to add and update these annotations to reflect published research. TGD Wiki currently offers the following features: * Free, unrestricted read access to all available data * Sequence and annotation data for 24,725 genes (TIGR v.2008) * GBrowse genome browser with links to and from each gene page (TIGR v.2006) * BLAST searching of the TIGR gene models and genome sequence (TIGR v.2006) Tetrahymena Genome Database (TGD) Wiki began in 2004 at Stanford University using the schema and programs of its parent project, Saccharomyces Genome Database. TGD Wiki is now a collaboration between Bradley University, Stanford University, and Cornell University. As we begin TGD Wiki at its new home at Bradley University, the TGD Wiki database contains the following data from TGD: * Gene Names and Aliases * Gene Descriptions * Gene Ontology (GO) Annotations * Homologs (similar genes in selected organisms) * Protein Domains * Associated Literature * Paragraphs (longer, free-text descriptions of gene function, structure, and significance) * Coding and Protein Sequences We have updated the following fields to match the newest gene model sequences (TIGR v.2008): Coding and Protein Sequences, Protein Domains and Gene Descriptions. We will also be recalculating the GO Annotations (IEA evidence code) and Homologs as part of our effort to keep the annotations in TGD Wiki as current as possible. We will be relying on members of the Tetrahymena community to maintain high-quality, updated annotations in the remainder of the fields using our annotation interface. Also setting up new database superdb - for unpublished data Look at Ciliate.org for news on this and other new databases

Proper citation: TGD (RRID:SCR_012803) Copy   

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http://www.rcsb.org/#Category-welcome

Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.

Proper citation: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) Copy   

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http://helixweb.nih.gov/dnaworks

DNAWorks automates the design of oligonucleotides for gene synthesis by PCR-based methods. The availability of sequences of entire genomes has dramatically increased the number of protein targets, many of which will need to be overexpressed in cells other than the original source of DNA. Gene synthesis often provides a fast and economically efficient approach. The synthetic gene can be optimized for expression and constructed for easy mutational manipulation without regard to the parent genome. DNAWorks accesses a computer program that automates the design of oligonucleotides for gene synthesis. The website provides forms for simple input information, i.e. amino acid sequence of the target protein and melting temperature (needed for the gene assembly) of synthetic oligonucleotides. The program outputs a series of oligonucleotide sequences with codons optimized for expression in an organism of choice. Those oligonucleotides are characterized by highly homogeneous melting temperatures and a minimized tendency for hairpin formation. The approach presented here simplifies the production of proteins from a wide variety of organisms for genomics-based studies.

Proper citation: DNAWorks at Helix Systems (RRID:SCR_008470) Copy   

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http://www.med.upenn.edu/cndr/biosamples-brainbank.html

A brain and tissue bank that contains human brain samples from patients with Alzheimer's disease (AD), Parkinson's disease (PD) and other related neurodegenerative dementias and movement disorders. This brain bank serves as a resource for scientists and researchers, providing access to tissue samples for further research. While priority is given to University of Pennsylvania researchers, this bank will provide requests to researchers not associated with the University of Pennsylvania. This tissue bank accepts donations from those seeing a University of Pennsylvania physician or collaborator.

Proper citation: University of Pennslyvania Brain Bank (RRID:SCR_008820) Copy   

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http://www.neuroanatomy.ca/

The WEB ATLAS contains photographs of dissected brains showing important structures. The diagrams folder contains drawings showing functionally important parts of the brain as well as drawings of dissections adapted from C.G. Smith. We are particularly pleased to make Nan Cheney''s medical illustrations of the brain and the head available. The STROKE MODEL portion of the website has syndromes associated with strokes of different vessels of the brain as well as extensive diagrams and tables about the vessels of the brain. The 3D RECONSTRUCTIONS featured on this website were made from MRI scans through the brain - where indicated the source material was from the NIH Visible Human Project. The website will also contain material important for the neuroanatomy labs for med students at UBC. Weekly quizzes will help you keep up with studying the material, the podcasts will help you review material presented in the labs, and the weekly wikis will help you share information with your peers.

Proper citation: Neuroanatomy at UBC (RRID:SCR_008744) Copy   

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https://portal.dbmi.hms.harvard.edu/projects/GRDR/

Data repository of de-identified patient data, aggregated in a standardized manner, to enable analyses across many rare diseases and to facilitate various research projects, clinical studies, and clinical trials. The aim is to facilitate drug and therapeutics development, and to improve the quality of life for the many millions of people who are suffering from rare diseases. The goal of GRDR is to enable analyses of data across many rare diseases and to facilitate clinical trials and other studies. During the two-year pilot program, a web-based template will be developed to allow any patient organization to establish a rare disease patient registry. At the conclusion of the program, guidance will be available to patient groups to establish a registry and to contribute de-identified patient data to the GRDR repository. A Request for Information (RFI) was released on February 10, 2012 requesting information from patient groups about their interest in participating in a GRDR pilot project. ORDR selected 30 patient organizations to participate in this pilot program to test the different functionalities of the GRDR. Fifteen (15) organizations with established registries and 15 organizations that do not have patient registry. The 15 patient groups, each without a registry, were selected to assist in testing the implementation of the ORDR Common Data Elements (CDEs) in the newly developed registry infrastructure. These organizations will participate in the development and promotion of a new patient registry for their rare disease. The GRDR program will fund the development and hosting of the registry during the pilot program. Thereafter, the patient registry is expected to be self-sustaining.The 15 established patient registries were selected to integrate their de-identified data into the GRDR to evaluate the data mapping and data import/export processes. The GRDR team will assist these organizations in mapping their existing registry data to the CDEs. Participating registries must have a means to export their de-identified registry data into a specified data format that will facilitate loading the data into the GRDR repository on a regular basis. The GRDR will also develop the capability to link patients'''' data and medical information to donated biospecimens by using a Voluntary Global Unique Patient Identifier (GUID). The identifier will enable the creation of an interface between the patient registries that are linked to biorepositories and the Rare Disease Human Biospecimens/Biorepositories (RD-HUB) http://biospecimens.ordr.info.nih.gov/.

Proper citation: GRDR (RRID:SCR_008978) Copy   

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http://www.vetmed.vt.edu/research/amrv.asp

An institutional training program to train veterinarians in conducting research. The program trains veterinarians in acquiring the skills of a researcher as they undergo a specific M.S. or Ph.D program. The program urges graduates to take part in research concerning animal models of infectious diseases, immunology, and nutrition, among other health topics.

Proper citation: Post-DVM Training Program on Animal Model Research for Veterinarians (RRID:SCR_008303) Copy   

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http://salilab.org/modeller/modeller.html

Software tool as Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Used for homology or comparative modeling of protein three dimensional structures. User provides alignment of sequence to be modeled with known related structures and MODELLER automatically calculates model containing all non hydrogen atoms.

Proper citation: MODELLER (RRID:SCR_008395) Copy   

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http://ndct.nimh.nih.gov

A database which houses human subjects clinical trial data. NDCT currently contains data on 13,409 subjects and has access to data on 100,500 subjects from the NIMH Data Archive. Users can also sign up for news updates and watch video tutorials.

Proper citation: National Database for Clinical Trials related to Mental Illness (RRID:SCR_013795) Copy   

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http://www.ncbi.nlm.nih.gov/pmc/about/pubreader/

A web application which serves as an alternate way to read scientific literature in PubMed Central and Bookshelf. PubReader features an easy-to-read multi-column display, a figure strip for access to figures, and a search function. It is designed especially to support reading on tablets and other smaller devices but is available for reading on laptops and desktops.

Proper citation: PubReader (RRID:SCR_013814) Copy   

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http://www.sci.utah.edu/cibc-research/highlights/24-research-highlights/cibc-highlights/221-scirun-biopse.html

A simulation software package which hosts a collection of algorithms used to run bioelectric field simulations inside of SCIRun. The software provided in the package may be used for geometric modeling, simulation, and visualization for solving bioelectric field problems.

Proper citation: BioPSE (RRID:SCR_014044) Copy   

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http://www.nitrc.org/projects/gscca_2013/

Group Sparse Canonical Correlation Analysis is a method designed to study the mutual relationship between two different types of data.

Proper citation: Group Sparse Canonical Correlation Analysis (RRID:SCR_014977) Copy   

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http://cerebrovascularportal.org

Portal enables browsing, searching, and analysis of human genetic information linked to cerebrovascular disease and related traits, while protecting the integrity and confidentiality of the underlying data.

Proper citation: Cerebrovascular Disease Knowledge Portal (RRID:SCR_015628) Copy   

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http://med.stanford.edu/narcolepsy.html

The Stanford Center for Narcolepsy was established in the 1980s as part of the Department of Psychiatry and Behavioral Sciences. Today, it is the world leader in narcolepsy research with more than 100 articles on narcolepsy to its name. The Stanford Center for Narcolepsy was the first to report that narcolepsy-cataplexy is caused by hypocretin (orexin) abnormalities in both animal models and humans. Under the direction of Drs. Emmanuel Mignot and Seiji Nishino, the Stanford Center for Narcolepsy today treats several hundred patients with the disorder each year, many of whom participate in various research protocols. Other research protocols are conducted in animal models of narcolespy. We are always looking for volunteers in our narcolepsy research studies. We are presently recruiting narcoleptic patients for genetic studies, drug clinical trials, hypocretin measurement studies in the CSF and functional MRI studies. Monetary gifts to the Center for Narcolepsy are welcome. If you wish to make the ultimate gift, please consider participating in our Brain Donation Program. To advance our understanding of the cause, course, and treatment of narcolepsy, in 2001 Stanford University started a program to obtain human brain tissue for use in narcolepsy research. Donated brains provide an invaluable resource and we have already used previously donated brains to demonstrate that narcolepsy is caused by a lack of a very specific type of cell in the brain, the hypocretin (orexin) neuron. While the brain donations do not directly help the donor, they provide an invaluable resource and a gift to others. The real answers as to what causes or occurrs in the brain when one has narcolepsy will only be definitively understood through the study of brain tissue. Through these precious donations, narcolepsy may eventually be prevented or reversible. We currently are seeking brains from people with narcolepsy (with cataplexy and without), idiopathic hypersomnia and controls or people without a diagnosed sleep disorder of excessive sleepiness. Control brains are quite important to research, as findings must always be compared to tissue of a non-affected person. Friends and loved ones of people who suffer with narcoleps may wish to donate to our program to help fill this very important need. Refer to the Movies tab for movies of Narcolepsy / Cataplexy.

Proper citation: Stanford Center for Narcolepsy (RRID:SCR_007021) Copy   

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https://mctfr.psych.umn.edu/

Composed of many projects, including the Minnesota Twin Family Study (MTFS) and The Sibling Interaction and Behavior Study (SIBS), this research center seeks to identify genetic and environmental influences on development and psychological traits. Both projects are longitudinal research studies including twins, siblings, and parents. Over 9800 individuals have contributed to these exciting projects! By studying twins and siblings and their families, we can estimate how genes and environment interact to influence character, strengths, vulnerabilities and values. Participants in the MTFS include families with same-sex identical or fraternal twins who were born in Minnesota. The SIBS study is comprised of adoptive and biological siblings and their parents. Most participants partake in day-long visits to the MCTFR, and due to the longitudinal nature of our projects, they return every 3-4 years for follow-up visits.

Proper citation: Minnesota Center for Twin and Family Research (RRID:SCR_006948) Copy   

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http://www.alliancegenome.org/

Organization that aims to develop and maintain sustainable genome information resources to promote understanding of the genetic and genomic basis of human biology, health, and disease. The Alliance is composed of FlyBase, Mouse Genome Database (MGD), the Gene Ontology Consortium (GOC), Saccharomyces Genome Database (SGD), Rat Genome Database (RGD), WormBase, and the Zebrafish Information Network (ZFIN).

Proper citation: Alliance of Genome Resources (RRID:SCR_015850) Copy   

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https://github.com/KravitzLab/fed/wiki

Flexible open-source device for measuring feeding behavior. FED measures food intake in mice. It is battery powered and designed to be used in rodent colony caging.Home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers alternative to commercial feeders, with convenience of use in tradition colony rack caging.

Proper citation: Feeding Experimentation Device project (RRID:SCR_015942) Copy   

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http://www.genetherapyreview.com/gene-therapy-research

The National Gene Vector Laboratories (NGVL) was established as a cooperative national effort to produce and distribute vectors for human gene transfer studies.

Proper citation: National Gene Vector Laboratories (RRID:SCR_015944) Copy   

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