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http://www.nature.com/protocolexchange/
Open Repository for the deposition and sharing of protocols for scientific research. These protocols are posted directly on the Protocol Exchange by their authors and hence have not been further styled, peer reviewed or copy edited. Rather they are made freely available to the scientific community for use and comment. The Protocol Exchange strives to facilitate rapid and unencumbered distribution of protocols for scientific research. They welcome Protocols from any branch of science however we focus particularly on Protocols being used to answer outstanding biological and biomedical science research questions, which includes methods grounded in physics and chemistry with a practical application to the study of biological problems. The content of Protocol Exchange is currently classified under the following broad subject categories: Biochemistry; Cell biology; Cell culture; Chemical modification; Computational biology; Developmental biology; Epigenomics; Genetic analysis; Genetic modification, Genomics; Imaging; Immunological techniques; Isolation, Purification and Separation; Lipidomics; Metabolomics; Microbiology; Model organisms; Nanotechnology; Neuroscience; Nucleic acid based molecular biology; Pharmacology; Plant biology; Protein analysis; Proteomics; Spectroscopy; Structural biology; Synthetic chemistry; Tissue culture; Toxicology; and Virology. If your protocol does not fall into any of these categories please contact us at protocol.exchange (at) nature.com before uploading.
Proper citation: Protocol Exchange (RRID:SCR_006393) Copy
http://hereditaryhearingloss.org/
Overview of the genetics of hereditary hearing impairment for researchers and clinicians. The site lists data and references for all known gene localizations and identifications for nonsyndromic hearing impairment, and several for syndromic hearing loss. For syndromic hearing impairment, only a few of the most frequent forms are covered. An atlas of cochlea with genes listed can be accessed from this site.
Proper citation: Hereditary Hearing Loss Homepage (RRID:SCR_006469) Copy
http://webdav.tuebingen.mpg.de/u/karsten/Forschung/research.html?page=research&topic=SV-M&html=text
Software for accurate indel prediction using paired-end short reads.
Proper citation: SV-M (RRID:SCR_006461) Copy
Global online employment solution for people seeking jobs and the employers who need great people. They''ve been doing this for over ten years, and have expanded from their roots as a job board to a global provider of a full array of job seeking, career management, recruitment and talent management products and services.
Proper citation: Monster (RRID:SCR_006463) Copy
http://lincs.hms.harvard.edu/db/
Database that contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents and experimental and data analysis protocols. Experimental reagents include small molecule perturbagens, cells, antibodies, and proteins.
Proper citation: HMS LINCS Database (RRID:SCR_006454) Copy
A bibliographic database that provides a highly concentrated source of reports of randomized controlled trials. Records contain the list of authors, the title of the article, the source, volume, issue, page numbers, and, in many cases, a summary of the article (abstract). They do not contain the full text of the article. Cochrane Groups maintain and update Specialized Registers, which are collections of controlled trials relevant to the groups. CENTRAL is comprised of these Specialized Registers, relevant records retrieved from MEDLINE and EMBASE, and records retrieved through handsearching (planned manual searching of a journal or conference proceedings to identify all reports of randomized controlled trials and controlled clinical trials). The Cochrane Collaboration contracts a technology company, Metaxis, to merge the records from the sources outlined above and provide a data feed to the publisher. New and changed data are delivered to the publisher on a monthly basis.
Proper citation: Cochrane Central Register of Controlled Trials (RRID:SCR_006576) Copy
Fund the best research to eradicate diseases and support the warfighter to benefit the American Public. They promote innovative research, recognizing untapped opportunities, creating partnerships, and guarding the public trust. Research Program topics include: * Amyotrophic Lateral Sclerosis * Autism * Bone Marrow Failure * Breast Cancer * Defense Medical Research and Development Program * Duchenne Muscular Dystrophy * Gulf War Illness * Lung Cancer * Multiple Sclerosis * Neurofibromatosis * Ovarian Cancer * Peer Reviewed Cancer * Peer Reviewed Medical * Peer Reviewed Orthopaedic * Prostate Cancer * Psychological Health / Traumatic Brain Injury * Spinal Cord Injury * Tuberous Sclerosis Complex
Proper citation: Congressionally Directed Medical Research Program (RRID:SCR_006456) Copy
http://bioinformatics.ubc.ca/ermineJ/
Data analysis software for gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are doing something interesting in the data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ. Major features include: * Implementation of multiple methods for gene set analysis: ** Over-representation analysis ** A resampling-based method that uses gene scores ** A rank-based method that uses gene scores ** A resampling-based method that uses correlation between gene expression profiles (a type of cluster-enrichment analysis). * Gene sets receive statistical scores (p-values), and multiple test correction is supported. * Support of the Gene Ontology terminology; users can choose which aspects to analyze. * User files use simple text formats. * Users can modify gene sets or create new ones. * The results can be visualized within the software. * It is simple to compare multiple analyses of the same data set with different settings. * User-definable hyperlinks are provided to external sites to allow more efficient browsing of the results. * For programmers, there is a command line interface as well as a simple application programming interface that can be used to plug ermineJ functionality into your own code Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Proper citation: ErmineJ (RRID:SCR_006450) Copy
For over 40 years, NIST has provided well-documented numeric data to scientists and engineers for use in technical problem-solving, research, and development. These recommended values are based on data which have been extracted from the world''s literature, assessed for reliability, and then evaluated to select the preferred values. These data activities are conducted by scientists at NIST. NIST Data Gateway-provides easy access to many (currently over 80) of the NIST scientific and technical databases. These databases cover a broad range of substances and properties from many different scientific disciplines. The Gateway includes links to free online NIST data systems as well as to information on NIST PC databases available for purchase.
Proper citation: NIST Standard Reference Data (RRID:SCR_006452) Copy
http://www.palamedestoolbox.org/
Matlab routines for analyzing psychophysical data * sychometric function fitting * Multi-condition model fitting * Adaptive procedures * Signal detection measures * Maximum likelihood difference scaling * Model comparisons
Proper citation: Palamedes Toolbox (RRID:SCR_006521) Copy
http://colt.ccbr.utoronto.ca/cancer/
The COLT-Cancer database is a collection of shRNA dropout signatures profiles, covering ~16000 human genes, and derived from more than 70 Pancreatic, Ovarian and Breast human cancer cell-lines using the microarray detection platform developed in the COLT (CCBR-OICR Lentiviral Technology) facility at the Moffat Lab. All shRNA dropout profiles are freely available through download or queries via this website.
Proper citation: COLT-Cancer (RRID:SCR_006485) Copy
https://code.google.com/p/saap-rrbs/
Streamlined Analysis and Annotation Pipeline for reduced representation bisulfite sequencing.
Proper citation: SAAP-RRBS (RRID:SCR_006516) Copy
Public archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource.
Proper citation: European Nucleotide Archive (ENA) (RRID:SCR_006515) Copy
The BATB is open to individuals who are involved or interested in Tissue Banking, research, clinical or donor-related activities. Corporate membership is available for organizations that supply technology/services to tissue banks (or have an interest in the use of human tissue for research, bio-engineering or other medical purposes). The Association is instituted for the advancement of tissue banking: * to contribute to the preparation and maintenance of professional standards for the practice of tissue banking in the United Kingdom * to facilitate the interchange of information between members * to provide opportunities for the discussion of all aspects of tissue banking practice * to encourage relevant research and development: to provide informed comment to external agencies * to foster education and training in tissue banking: to maintain national and international links with relevant bodies * to make knowledge in the field of tissue banking available to any person for the general good of the community
Proper citation: British Association for Tissue Banking (RRID:SCR_006477) Copy
CurePSP+ is an organization dedicated to increasing awareness of progressive supranuclear palsy, corticobasal degeneration, and related disorders, advancing research toward a cure, educating health professionals, and providing support, education and hope for persons with PSP, CBD and their families. PSP provides a number of resources, including a research grants/funding program, support for patients and families, educational materials, and PSP-related events. Patient and family support services include an online magazine, a resources guide, an educational center that provides The Guide for Persons with PSP, videos, support group meetings, and outreach and education brochures and conferences. In addition, CurePSP offers ART2CURE, a program of CurePSP (The Society for Progressive Supranuclear Palsy) that helps to generate essential revenue for research, advocacy, outreach, education and operating through the promotion and sale of artwork provided by various artists throughout the country. CurePSP is located in Hunt Valley, Maryland. :NIF thanks the : :Parkinson''s Disease Foundation : : :for their referral of this resource to us.
Proper citation: Cure PSP: Society for Progressive Supranuclear Palsy (RRID:SCR_006478) Copy
Pictorial database of an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of their interactions. Extensive use is made of the freely available RasMol molecular graphics program to view the molecules and their interactions in 3D. Entries are accessed either by their 4-character PDB code, or by one of the two search boxes provided on the PDBsum home page: text search or sequence search. The information given on each PDBsum entry is spread across several pages, as listed below and accessible from the tabs at the top of the page. Only the relevant tabs will be present on any given page. * Top page - summary information including thumbnail image of structure, molecules in structure, enzyme reaction diagram (where relevant), GO functional assignments, and selected figures from key reference * Protein - wiring diagram, topology diagram(s) by CATH domain, and residue conservation (where available) * DNA/RNA - DNA/RNA sequence and NUCPLOT showing interactions made with protein * Ligands - description of bound molecule and LIGPLOT showing interactions made with protein * Prot-prot - schematic diagrams of any protein-protein interfaces and the residue-residue interactions made across them * Clefts - listing of top ten clefts in the surface of the protein, listed by volume with any bound ligands shown * Links - links to external databases Additionally, it accepts users'''' own PDB format files and generates a private set of analyses for each uploaded structure.
Proper citation: PDBsum (RRID:SCR_006511) Copy
http://projects.tcag.ca/autism/
The Autism Chromosome Rearrangement Database is a collection of hand curated breakpoints and other genomic features, including phenotypes, organized by chromosome, related to autism, taken from publicly available literature: databases and unpublished data. The database welcomes submission of data and comments regarding the database from the research community. The database is continuously updated with information from in-house experimental data as well as data from published research studies.
Proper citation: Autism Chromosome Rearrangement Database: A database of structural variants in autism spectrum disorder (RRID:SCR_006474) Copy
http://code.google.com/p/google-refine/
Software tool that stores definitions of views of data, along with the ontology concepts they represent. This is a part of the Neuroscience Information Framework (NIF) code stack.
Proper citation: ConceptMapper (RRID:SCR_006548) Copy
http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
A set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina''''s Solexa, Roche''''s 454 and Applied Biosystems'''' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format.
Proper citation: ART (RRID:SCR_006538) Copy
Private research university with four campuses in New York City.
Proper citation: Yeshiva University; New York; USA (RRID:SCR_006534) Copy
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