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http://www.peptideatlas.org

Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. The raw data, search results, and full builds can be downloaded for other uses. All results of sequence searching are processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner ensuring a high quality database. All peptides are mapped to Ensembl and can be viewed as custom tracks on the Ensembl genome browser. The long term goal of the project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins. The PeptideAtlas provides a method and a framework to accommodate proteome information coming from high-throughput proteomics technologies. The online database administers experimental data in the public domain. You are encouraged to contribute to the database.

Proper citation: PeptideAtlas (RRID:SCR_006783) Copy   

•   Source: SciCrunch Registry

http://www.GeneWeaver.org

Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration.

Proper citation: Gene Weaver (RRID:SCR_003009) Copy   

•   Source: SciCrunch Registry

http://f1000.com/posters

An open access repository of conference posters from across the life sciences and medicine. It provides a permanent, structured environment for the deposition of posters as well as a trustworthy venue for ongoing discussion and development of the information being presented. You can browse posters by Topic or Section or by conference. Please note that most posters on this site present work that is preliminary in nature and has not been peer reviewed. The most interesting posters are selected for evaluation by our expert Faculty and you will receive ideas and feedback. Widen your audience ����?? top performing posters receive 800+ views in a month!

Proper citation: F1000 Posters (RRID:SCR_006503) Copy   

•   Source: SciCrunch Registry

http://sciencecareers.sciencemag.org/

The journal Science is one of the most prestigious and widely cited scientific journals in the world. Founded by Thomas Edison in 1880, Science has been publishing breaking news and seminal research for more than 125 years. Science Careers is the careers component of Science that scientists rely on for career information and job postings. Science Careers offers a wide variety of content designed to assist scientists of all disciplines, backgrounds and experience levels navigate their career path. This includes over 3,000 job listings that are updated daily, thousands of career advice articles written by the Science Careers editorial staff, graduate program information, meetings and event information, funding opportunities on GrantsNet, and a Career Forum where scientists can join a community of experts and peers engaging in real time discussions around career issues. For employers, Science Careers provides multiple platforms for recruiting scientists and extending their employment brand including job postings, banner advertisements, email and newsletters and sponsorships.

Proper citation: Science Careers (RRID:SCR_005156) Copy   

•   Source: SciCrunch Registry

http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi

Database of all of the publicly available, complete prokaryotic genomes. In addition to having all of the organisms on a single website, common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes. CMR offers a wide variety of tools and resources, all of which are available off of our menu bar at the top of each page. Below is an explanation and link for each of these menu options. * Genome Tools: Find organism lists as well as summary information and analyses for selected genomes. * Searches: Search CMR for genes, genomes, sequence regions, and evidence. * Comparative Tools: Compare multiple genomes based on a variety of criteria, including sequence homology and gene attributes. SNP data is also found under this menu. * Lists: Select and download gene, evidence, and genomic element lists. * Downloads: Download gene sequences or attributes for CMR organisms, or go to our FTP site. * Carts: Select genome preferences from our Genome Cart or download your Gene Cart genes. The Omniome is the relational database underlying the CMR and it holds all of the annotation for each of the CMR genomes, including DNA sequences, proteins, RNA genes and many other types of features. Associated with each of these DNA features in the Omniome are the feature coordinates, nucleotide and protein sequences (where appropriate), and the DNA molecule and organism with which the feature is associated. Also available are evidence types associated with annotation such as HMMs, BLAST, InterPro, COG, and Prosite, as well as individual gene attributes. In addition, the database stores identifiers from other centers such as GenBank and SwissProt, as well as manually curated information on each genome or each DNA molecule including website links. Also stored in the Omniome are precomputed homology data, called All vs All searches, used throughout the CMR for comparative analysis.

Proper citation: JCVI CMR (RRID:SCR_005398) Copy   

•   Source: SciCrunch Registry

http://vmd.vbi.vt.edu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Database covering a range of plant pathogenic oomycetes, fungi and bacteria primarily those under study at Virginia Bioinformatics Institute. The data comes from different sources and has genomes of 3 oomycetes pathogens: Phytophthora sojae, Phytophthora ramorum and Hyaloperonospora arabidopsidis. The genome sequences (95 MB for P.sojae and 65 MB for P.ramorum) were annotated with approximately 19,000 and approximately 16,000 gene models, respectively. Two different statistical methods were used to validate these gene models, Fickett''''s and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, putative functions to 17,694 genes in P.sojae and 14,700 genes in P.ramorum could be assigned. An easy-to-use genome browser was created to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are approximately 1600 gene models for P.sojae and approximately 700 models for P.ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs.

Proper citation: VMD (RRID:SCR_004905) Copy   

•   Source: SciCrunch Registry

http://zebrafish.org

Center that supplies access to wild-type, mutant, and transgenic zebrafish lines, EST's/cDNAs, antibodies and fish health services. ZIRC Health Services include diagnostic pathology testing for zebrafish and other small laboratory fish species.

Proper citation: Zebrafish International Resource Center (RRID:SCR_005065) Copy   

•   Source: SciCrunch Registry

http://mendelspod.com/

A collection of content, including podcasts and blogs, to advance life science research, connecting people and ideas in the life sciences. Mendelspod creates a space for probing conversations and deep insight into the topics and trends which shape the industry''s future and therefore our future as a species. The podcasts are engaging, thoughtful thirty minute shows twice a week on highly relevant topics to those working around the life sciences. Their format enables them to go in depth with scientists who are leaders in their field, or CEOs of high growth companies to explore trends and the latest technologies. At Mendelspod, they offer a front row seat to the revolution going on in biology, putting a human face on some complicated, highly technical topics. Here you can tune in to hear Steve Burrill give his ''state of the industry'' overview, or listen to George Church talk about art and science, or find out how the latest developments in NGS are helping in the war on cancer. The blogs cover the latest trends and products, and can be entertaining. Guest bloggers featured and welcomed.

Proper citation: Mendelspod (RRID:SCR_009027) Copy   

•   Source: SciCrunch Registry

http://drugdesigndata.org

Project portal's database of protein-ligand data sets provided by pharmaceutical partners that provide atomic details of drug mechanisms that will be used to improve computer-aided drug-design methods and thus accelerate drug discovery. The project aims to help companies release the high-quality data they have generated, which has incredible value to researchers working to improve methods of computer-aided drug discovery. Everyone stands to benefit from the ability to develop new medications more quickly and inexpensively. What computational chemists globally are trying to do is to make faster, more accurate, more predictive programs to speed up the process. Part of their mission is to engage the community in these challenges to test newly developed predictive algorithms.

Proper citation: Drug Design Data Resource (RRID:SCR_000497) Copy   

•   Source: SciCrunch Registry

http://www.betacell.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented on August 1, 2015. Consortium that aims to facilitate interdisciplinary collaborations to advance the understanding of pancreatic islet development and function, with the goal of developing innovative therapies to correct the loss of beta cell mass in diabetes, including cell reprogramming, regeneration and replacement. They are responsible for collaboratively generating the necessary reagents, mouse strains, antibodies, assays, protocols, technologies and validation assays that are beyond the scope of any single research effort. The scientific goals for the BCBC are to: * Use cues from pancreatic development to directly differentiate pancreatic beta cells and islets from stem / progenitor cells for use in cell-replacement therapies for diabetes, * Determine how to stimulate beta cell regeneration in the adult pancreas as a basis for improving beta cell mass in diabetic patients, * Determine how to reprogram progenitor / adult cells into pancreatic beta-cells both in-vitro and in-vivo as a mean for developing cell-replacement therapies for diabetes, and * Investigate the progression of human type-1 diabetes using patient-derived cells and tissues transplanted in humanized mouse models. Many of the BCBC investigator-initiated projects involve reagent-generating activities that will benefit the larger scientific community. The combination of programs and activities should accelerate the pace of major new discoveries and progress within the field of beta cell biology.

Proper citation: Beta Cell Biology Consortium (RRID:SCR_005136) Copy   

•   Source: SciCrunch Registry

http://ccr.coriell.org/Sections/Collections/NIGMS/?SsId=8

Highly characterized cell lines and high quality DNA for cell and genetic research representing a variety of disease states, chromosomal abnormalities, apparently healthy individuals and many distinct human populations. The NIGMS Repository contains more than 10,600 cell lines, primarily fibroblasts and transformed lymphoblasts, and over 5,500 DNA samples. The NIGMS Repository has a major emphasis on heritable diseases and chromosomally aberrant cell lines. In addition, it contains a large collection dedicated to understanding human variation that includes samples from populations around the world, the CEPH collection, the Polymorphism Discovery Resource, and many apparently healthy controls. Human induced pluripotent stem cell lines, many of which were derived from NIGMS Repository fibroblasts, have recently become available through the NIGMS Repository. Sample donation facilitates all areas of research by making available well-characterized materials to any qualified researcher who might have otherwise been unable to invest the time and resources to collect needed samples independently. Donations to the Repository have created a resource of unparalleled scope. Samples from the collection have been used in more than 5,500 publications and are distributed to scientists in more than 50 countries. This resource is continuously expanding to support new directions in human genetics.

Proper citation: NIGMS Human Genetic Cell Repository (RRID:SCR_004517) Copy   

•   Source: SciCrunch Registry

http://nimh-repository.rti.org/

A program that synthesizes, purifies, and distributes otherwise unavailable essential compounds to stimulate basic and clinical research in psychopharmacology relevant to mental health in areas such as the molecular pharmacology and signaling of CNS receptors, longitudinal studies to evaluate the molecular, biochemical, and behavioral actions of psychoactive compounds, and functional brain imaging in both primates and humans. WHAT IS AVAILABLE: * Ligands for CNS receptors, radiolabeled compounds for autoradiography and neuroimaging, biochemical markers, drug analogs and metabolites, and reference standards * Synthesis (including GMP) of promising compounds for mental health research, including preclinical toxicology and safety studies, especially compounds for PET neuroimaging * A listing of currently available NIMH CSDSP compounds is available online at www.nimh-repository.rti.org. RTI International scientists can provide investigators with technical assistance and additional information about the compounds on request. Data sheets containing purity, storage, and handling information are supplied with all NIMH CSDSP compounds. WHO IS ELIGIBLE: Investigators involved in basic or clinical research relevant to mental health are eligible to submit requests. To learn more about current NIMH research areas, please visit the NIMH website at www.nimh.nih.gov. NIMH CSDSP compounds are free to qualified academic investigators, but payment may be required from nonacademic requestors. Investigators interested in obtaining radiolabeled compounds but uncertain about what type of label or specific activity would work best for them may obtain help by communicating with the technical contacts listed on the website.

Proper citation: NIMH Chemical Synthesis and Drug Supply Program (RRID:SCR_004921) Copy   

•   Source: SciCrunch Registry

http://www.exactantigen.com

Database of hundreds of thousands of products submitted by reagent provider partners, and millions of webpages selected from reagent suppliers. All are organized according to genes, species, and reagent types (antibodies, recombinant proteins, ELISA, siRNA, cDNA clones, biochemicals, and others).

Proper citation: Labome (RRID:SCR_007384) Copy   

•   Source: SciCrunch Registry

https://www.msu.edu/~brains/brains/human/index.html

A labeled three-dimensional atlas of the human brain created from MRI images. In conjunction are presented anatomically labeled stained sections that correspond to the three-dimensional MRI images. The stained sections are from a different brain than the one which was scanned for the MRI images. Also available the major anatomical features of the human hypothalamus, axial sections stained for cell bodies or for nerve fibers, at six rostro-caudal levels of the human brain stem; images and Quicktime movies. The MRI subject was a 22-year-old adult male. Differing techniques used to study the anatomy of the human brain all have their advantages and disadvantages. Magnetic resonance imaging (MRI) allows for the three-dimensional viewing of the brain and structures, precise spatial relationships and some differentiation between types of tissue, however, the image resolution is somewhat limited. Stained sections, on the other hand, offer excellent resolution and the ability to see individual nuclei (cell stain) or fiber tracts (myelin stain), however, there are often spatial distortions inherent in the staining process. The nomenclature used is from Paxinos G, and Watson C. 1998. The Rat Brain in Stereotaxic Coordinates, 4th ed. Academic Press. San Diego, CA. 256 pp

Proper citation: Human Brain Atlas (RRID:SCR_006131) Copy   

•   Source: SciCrunch Registry

http://retractionwatch.wordpress.com/

Retraction Watch is a blog of retractions in the scientific literature. It is maintained by Adam Marcus and Ivan Oransky and has been operating since August 2010.

Proper citation: RetractionWatch.com (RRID:SCR_000654) Copy   

•   Source: SciCrunch Registry

https://bams1.org/connectomes/standard_rat.php, https://bams1.org/connectomes/custom_rat.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. Database of information about brain region circuitry, it collates data from the literature on tract tracing studies and provides tools for analysis and visualization of connectivity between brain regions., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BAMS Connectivity (RRID:SCR_000561) Copy   

•   Source: SciCrunch Registry

http://www.labspaces.net/view_blog.php?ID=15

Blog about technology, molecular biology, and editorial comments on the current state of science on the internet. Brian Krueger PhD, is the owner, creator and coder of LabSpaces by night and a Molecular biologist by day. His posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, his employer, or his educational institution.

Proper citation: H2SO4Hurts (RRID:SCR_000686) Copy   

•   Source: SciCrunch Registry

http://lifespandb.sageweb.org/

Database that collects published lifespan data across multiple species. The entire database is available for download in various formats including XML, YAML and CSV.

Proper citation: Lifespan Observations Database (RRID:SCR_001609) Copy   

•   Source: SciCrunch Registry

http://blogs.plos.org/

PLoS Blogs has been set up to bring a select group of independent science and medicine bloggers together with the editors and staff who run our blogs. Our independent network is made up of writers who love science and medicine, and scientists and physicians that love to write. Here, you'll find an equal mix of blogs from journalists and researchers tackling diverse issues in science and medicine. There are three very distinct types of blogs on the PLoS Blogs network: the official PLoS blog, the PLoS journal blogs (collectively known as The PLoS Blogs), and blogs from the independent network (a.k.a. The PLoS Blogosphere) # The official PLoS blog: This content is produced, edited, and/or maintained by PLoS staff. # The journal blogs: This content is produced, edited, and/or maintained by PLoS journal staff: The current journal blogs are Speaking of Medicine (PLoS Medicine's blog) and everyONE (PLoS ONE's blog). # Our independent network of bloggers (The PLoS Blogosphere): This content is produced, edited, and/or maintained by the authors. * All of the content in The PLoS Blogosphere came from the minds of the authors. PLoS does not screen, edit, or otherwise meddle with content on the these blogs in any way. Our bloggers and our users are held to exactly the same standards, and the community guidelines apply to everyone that uses our site. If a blogger has posted content that you believe violates our site abuse policy, please contact PLoS. * Bloggers monitor their own comment threads: All comments will be reviewed by the author of the blog where you leave your thoughts. Just follow our simple community guidelines and we'll all get along just fine.

Proper citation: PLoS Blogs (RRID:SCR_001371) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-12/search?q=*

A virtual database of several model resources including: CellML Model Repository, ModelDB, Open Source Brain, SimTK, and ModelRun.

Proper citation: Integrated Models (RRID:SCR_001481) Copy   

•   Source: SciCrunch Registry