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http://bmbpcu36.leeds.ac.uk/RE1db_mkII/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A database containing all genomic human and mouse binding sites of the Repressor Element 1 Silencing Transcription factor (REST), identified by PSSM. The RE1 silencing transcription factor (REST; also known as the neuron-restrictive silencer factor), is a nine zinc-finger transcription factor, related to the Gli-Kruppel family. REST binds to a conserved 21-nucleotide element, known as repressor element 1 (RE1; also known as the neuron-restrictive silencer element). REST was proposed to be a ''master'' silencer of neuron specific gene expression in non-neuronal tissues and undifferentiated neuroepithelium (precursor of neuronal cells), preventing the default expression of the neuronal phenotype during embryogenesis. It has been shown to function independently of orientation and distance from a gene promoter. REST has an important role during embryonic development, as homozygous gene knockout mice (Rest-/-) die by embryonic day 11.5. The constitutive expression of REST has also been shown to disrupt neuronal gene expression and cause axon path finding errors in chicken embryos (Paquette et al. 2000). RE1 sequences that are known to bind REST have also been found near to non-neuronal genes, including keratin and cytochrome P450 genes.

Proper citation: Neuron-Restrictive Silencer Factor (RRID:SCR_008546) Copy   

•   Source: SciCrunch Registry

http://discovermagazine.com/

Popular science magazine which includes news and blogs on topics including Health & Medicine, Mind & Brain, Technology, Space, Human origins, Living World, Environment, and Physics & Math. NIF Indexes include: The Brain: DISCOVER blogger, columnist, and contributing editor Carl Zimmer''s monthly column will make your brain happy. Discover Interview: The magazine''s signature in-depth discussion with the leading lights of the world of science Vital Signs: A medical mystery, as written by the doctor involved.

Proper citation: Discover Magazine (RRID:SCR_008787) Copy   

•   Source: SciCrunch Registry

http://alizadehlab.stanford.edu/

This is an open-source Mouse Exonic Evidence-Based Oligonucleotide Chip (MEEBOChip), and are in the process of building the human counterpart, HEEBOChip. The set of 70mers for MEEBOChip is already available from Illumina, Inc., with synthesis of HEEBOChip 70mers in progress. Both arrays are based on a novel selection of exonic long-oligonucleotides (70-mers) from a genomic annotation of the corresponding complete genome sequences, using a transcriptome-based annotation of exon structure for each genomic locus. Using a combination of existing and custom-tailored tools and datasets (including millions of mRNA and EST sequences), we built and performed a systematic examination of transcript-supported exon structure for each genomic locus at the base-pair level (i.e., exonic evidence). This strategy allowed them to select both constitutive and in many cases alternative exons for nearly every gene in the corresponding genome (e.g., protocadherin locus), allowing an unprecedented exploration of human and mouse biology. Furthermore, they used experimentally derived data to hone the selection of these 70mers, helping maximize their performance under typical fluorescent labeling and hybridization conditions. Specifically, they applied and refined the ArrayOligoSelector algorithm from Joe DeRisis laboratory to select 70mers, considering not only their uniqueness (i.e., hybridization specificity) within the content of the entire genome, but also to overcome the known biases of labeling and hybridization methods (e.g., 3-biased reverse transcription and in vitro transcription reactions).

Proper citation: Alizadehlab: MeeboChip and HeeboChip Open Source Project (RRID:SCR_008384) Copy   

•   Source: SciCrunch Registry

http://HIVBrainSeqDB.org

The HIV Brain Sequence Database (HIVBrainSeqDB) is a public database of HIV envelope sequences, directly sequenced from brain and other tissues from the same patients. For inclusion in the database, sequences must: (i) be deposited in Genbank; (ii) include some portion of the HIV env region; (iii) be clonal, amplified directly from tissue; and (iv) be sampled from the brain, or sampled from a patient for which the database already contains brain sequence. Sequences are annotated with clinical data including viral load, CD4 count, antiretroviral status, neurocognitive impairment, and neuropathological diagnosis, all curated from the original publication. Tissue source is coded using an anatomical ontology, the Foundational Model of Anatomy, to capture the maximum level of detail available, while maintaining ontological relationships between tissues and their subparts. 44 tissue types are represented within the database, grouped into 4 categories: (i) brain, brainstem, and spinal cord; (ii) meninges, choroid plexus, and CSF; (iii) blood and lymphoid; and (iv) other (bone marrow, colon, lung, liver, etc). Currently, the database contains 2517 envelope sequences from 90 patients, obtained from 22 published studies. 1272 sequences are from brain; the remaining 1245 are from blood, lymph node, spleen, bone marrow, colon, lung and other non-brain tissues. The database interface utilizes a faceted interface, allowing real-time combination of multiple search parameters to assemble a meta-dataset, which can be downloaded for further analysis. This online resource will greatly facilitate analysis of the genetic aspects of HIV macrophage tropism, HIV compartmentalization and evolution within the brain and other tissue reservoirs, and the relationship of these findings to HIV-associated neurological disorders and other clinical consequences of HIV infection.

Proper citation: HIV Brain Sequence Database (RRID:SCR_008819) Copy   

•   Source: SciCrunch Registry

http://www.demogr.mpg.de/databases/ktdb/

A database that includes data on death counts and population counts classified by sex, age, year of birth, and calendar year for more than 30 countries. This database was established for estimating the death rates at the highest ages (above age 80). The core set of data in the database was assembled, tested for quality, and converted into cohort mortality histories by V��in�� Kannisto, the former United Nations advisor on demographic and social statistics. Comparable materials on England and Wales, was made available by A. Roger Thatcher, the former Director of the Office of Population Censuses and Surveys and Registrar-General of England and Wales (Kannisto, 1994). The Kannisto-Thatcher database was computerized under the supervision of James W. Vaupel at the Aging Research Unit of the Centre for Health and Social Policy at Odense University Medical School in 1993. Currently, the database is maintained by the Max Planck Institute for Demographic Research, Germany.

Proper citation: Kannisto-Thatcher Database on Old Age Mortality (RRID:SCR_008936) Copy   

•   Source: SciCrunch Registry

http://omicsomics.blogspot.fr/

A computational biologist''s personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery.

Proper citation: OMICS! OMICS! (RRID:SCR_008533) Copy   

•   Source: SciCrunch Registry

http://www.bioscience.org/atlases/fert/embrper.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. During the embryogenesis of human embryo, the development of each organ may be impaired during specific time periods. As illustrated, such impairment leads to congenital anomalies. After such critical periods, the environmental factors cause either minor congenital anomalies or lead to functional abnormalities. True beginning of gestation starts with the fertilization of the ovum which normally occurs one to several days after ovulation. By convention, however, due the fact that the day of the last menstrual period is easily defined, gestation starts on such day. During the first two weeks of pregnancy the embryo does not exist and endometrium is undergoing its normal menstrual and then proliferative phases. Stage one of the development starts with the fertilization of the ovum and stage 2 is initiated by the cleavage of the fertilized ovum. It is during the 4th and 5th stages of development that blastocyst starts its implantation process. By the end of the second week after fertilization, the stage 6 is initiated. During this stage, the primary chorionic villi and embryonic disc are formed.

Proper citation: Human Embryogenesis at a glance (RRID:SCR_008499) Copy   

•   Source: SciCrunch Registry

http://www.oie.int/fileadmin/Home/eng/Health_standards/aahc/2010/en_sommaire.htm

For the purposes of the Aquatic Code, spring viraemia of carp (SVC) means infection with the viral species SVC virus (SVCV) tentatively placed in the genus Vesiculovirus of the family Rhabdoviridae.
Methods for surveillance and diagnosis are provided in the Aquatic Manual.
The recommendations in this Chapter apply to: common carp (Cyprinus carpio carpio) and koi carp (Cyprinus carpio koi), crucian carp (Carassius carassius), sheatfish (also known as European catfish or wels) (Silurus glanis), silver carp (Hypophthalmichthys molitrix), bighead carp (Aristichthys nobilis), grass carp (white amur) (Ctenopharyngodon idellus), goldfish (Carassius auratus), orfe (Leuciscus idus), and tench (Tinca tinca). These recommendations also apply to any other susceptible species referred to in the Aquatic Manual when traded internationally.
1) Periodicals
*Scientific and Technical Review (available on the Online Bookshop and Website);
*Bulletin (available on the Online Bookshop and Website);
*Disease Information (available on the WAHID interface);
*World Animal Health (available on the Online Bookshop and on the WAHID interface);
Health standards
*Terrestrial Animal Health Code (available on the Online Bookshop and Website);
*Aquatic Animal Health Code (available on the Online Bookshop and Website);
*OIE Quality Standard and Guidelines for Veterinary Laboratories: Infectious Diseases (available on the Online Bookshop);
*Manual of Diagnostic Tests and Vaccines for Terrestrial Animals (available on the Online Bookshop and Website);
*Manual of Diagnostic Tests for Aquatic Animals (available on the Online Bookshop in English only (2009 version) and also on the Website).

Proper citation: Aquatic Animal Health Code - 2008 (RRID:SCR_008413) Copy   

•   Source: SciCrunch Registry

http://www.embase.com

You can begin your search immediately using the Quick form on the home page or you can access the other specialized search forms in Embase. You can choose any section from the options on the top menu bar: Search, Emtree, Journals, Authors, or Help. You can start to search without logging in but if you would like to set up an email alert or save a search, then you may Login or Register from the upper-right part of the screen. Note: if you are outside your institution IP range, you will first be directed to the info site before accessing the Embase Home page. For more information on remote access, please see Login section. Search Forms Search is at the core of Embase and all search forms are designed to allow you to look for biomedical and pharmaceutical clinical and research information easily and quickly, whether you are a new or experienced searcher. The Embase search engine allows Boolean searching with wildcard and truncation features, as well as many predefined search limits. Search is divided into five options: Quick, Advanced, Drug, Disease and Article. Quick lets you perform easy yet powerful searches without having to learn a complex search language. It is perfect if you are starting your research and looking for an overview of the literature or good terms to include in your search strategy. Autocomplete will help you to search using the bext terminology. Advanced incorporates options from Emtree term mapping including explosion searching for maximum precision in subject searching (see Emtree) and Drug and Disease provide access to specialized features useful to search these topics, such as ''Adverse Drug Reaction''''Drug Combination''. Generally speaking, drug searches are best carried out in the Drug form, diseases in the Disease form and non-drug and disease searches in the Advanced form. Article allows you to pinpoint individual articles. Embase is owned and operated by Elsevier B.V., Radarweg 29, 1043 NX Amsterdam, The Netherlands, Reg. No. 33156677, BTW No. 002967455B65 (Elsevier).

Proper citation: Embase Biomedical Answers (RRID:SCR_008498) Copy   

•   Source: SciCrunch Registry

http://www.emsdiasum.com

A complete online Product Catalog of chemicals, supplies, accessories, and equipment for Electron and Light Microscopy, Histology, Cell Biology, Neuroscience, and all biological related research fields. At the site, you can find technical tips and recommended articles of interest, technical and product data sheets, Material Safety Data Sheets, and many revolutionary new products and exclusive items. A complete product catalog of the entire Diatome collection of Diamond knives, tools, and accessories for Electron and Light microscopy for Biological and Materials Science at room and cryo temperatures. Available on-line as well is information on our services, programs, specials, and policies. The complete handling and use technical manual as well as troubleshooting can also be found at our site. The Summers Optical on-line catalog including a complete line of optical cements and adhesives, decementing agents, hardness testers, ultrasonic baths and UV lights as well as technical and transmission data and problem solving can be found at this site. As well as, our unique bonding manual including troubleshooting and charts for how to choose a cement for specific applications and a complete set of MSDS on all of our products can be seen here. EMS Contract Packaging is a total service contract manufacturer, packager, and formulator with over 40 years experience in drug and cosmetic formulating and packaging. Negafile furniture quality wood filing systems and storage cases for grids, negatives, film and microscope glass slides. And a full line of shipping and packaging solutions for all your traditional or digital media.

Proper citation: Emsdiasum (RRID:SCR_008497) Copy   

•   Source: SciCrunch Registry

http://rd.plos.org/pbio.0050257

Resources for macromolecular X-ray crystallography from the Richardson Laboratory, including kinemages (a scientific illustration presented as an interactive computer display), databases, software, training materials and images

Proper citation: 3D Macromolecular Analysis and Kinemage Home Page (RRID:SCR_008569) Copy   

•   Source: SciCrunch Registry

http://www.molecularbrain.org/

MolecularBrain is an attempt to collect, collates, analyze and present the microarray derived gene expression data from various brain regions side by side. Transcription Profile of any gene in Mouse (online) and Human Brain (not yet) can be accessed as a histogram along with links to access various aspects of that gene. The expression levels were calculated from microarray data deposited at GEO (Gene expression omnibus). The molecular brain database could be searched using the built in search tool with the terms Entrez GeneID, gene symbol, synonym or description. Gene information along with their expression values can be also accessed from the alphabetical list of gene symbols on the footer. The protocol and GEO sample information is available.

Proper citation: Molecular Brain: Transcription Profiles of Mouse and Human Brains (RRID:SCR_008689) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.picr.man.ac.uk/adapt/Welcome.adapt

Library of many-to-many relationships between Affymetrix probesets transcripts and genes, by directly mapping every probe against publicly available mRNAs/cDNA sequences from RefSeq and Ensembl. You can search the database by AffymetrixProbeset ID, Transcript Accession, Gene Symbol or Gene Accession. Currently, the ADAPT database holds information on 23 Array Types containing 255771 unique Probesets, that themselves map onto 252788 entries in both RefSeq and Ensembl. ADAPT is clusterable, cross platform, runs on any Java Virtual machine after version 1.4, and utilises the following software: :- Apache Tomcat :- Apache Struts :- JBoss Application Server :- Postgresql Sponsors: ADAPT has been written with funding by Cancer Research UK. Keywords: Database, Gene, Transcript, Mapping, Probe, mRNA, cDNA, Sequence, Association, Array, Probeset,

Proper citation: ADAPT: A Database of Affymetrix Probesets and Transcripts (RRID:SCR_008688) Copy   

•   Source: SciCrunch Registry

http://www.BioMedSearch.com

BioMedSearch is a biomedical search engine that contains NIH/PubMed documents, plus a large collection of theses, dissertations, and other publications not found anywhere else for free, making it the most comprehensive free search on the web. :Besides free-form search, users can search based on Author, Journal Title, Publication Date, the Language in which the article was published (many non-English articles have English language abstracts), MeSH (Medical Subject Headings) and more. : The goal of BioMedSearch.com is to provide free access to a massive collection of authoritative documents relating to the biomedical field. Our mission is to make these important works available to the community in a way that is fast and easy, while still offering the advanced features demanded by power users such as portfolios, collaboration features, bibliographical citation export, alerts, and more. Whether you are doctor, scientist, or someone interested in researching a medical topic out of personal interest, BioMedSearch aggregates a vast number of authoritative documents in one place to make finding medical information easy, fast and free.

Proper citation: Biomedical Search: Medical Research and Health Resources (RRID:SCR_008683) Copy   

•   Source: SciCrunch Registry

http://bioinf.xmu.edu.cn:8080/software/CYTOSVM/cytosvm.php

Cytokines are a diverse group of cell intercellular messengers responsible for signaling variety of cell functions, such as immunity, hematopoiesis, chemotactic activities, cell maturation, proliferation, growth and differentiation through their interactions with respective receptors on cell membranes. Currently, a number of cytokines have been identified and classified

Proper citation: CytoSVM statistics (RRID:SCR_008442) Copy   

•   Source: SciCrunch Registry

http://rsat.ulb.ac.be/rsat/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Retrieve-ensembl-seq is included in the software suite regulatory sequence analysis tools (RSAT), allowing instant submission of retrieved sequences to further analysis tools. AVAILABILITY: retrieve-ensembl-seq is integrated in the RSAT suite: http://rsat.ulb.ac.be/rsat. Web site: http://rsat.ulb.ac.be/rsat/retrieve-ensembl-seq_form.cgi. Web services: http://rsat.ulb.ac.be/rsat/web_services/RSATWS.wsdl. Stand-alone distribution: freely available under an academic licence to download from the RSAT web site. The complete manual, a convenient tutorial and demos are available from the RSAT website. Additional help can be found on the RSAT public forum.

Proper citation: Regulatory Sequence Analysis Tools (RRID:SCR_008560) Copy   

•   Source: SciCrunch Registry

http://www.anxietyinsights.info/

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016.

Proper citation: Anxiety Insights (RRID:SCR_008717) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/group/exonarray/cgi-bin/plot_selector.pl

Transcriptome database of acutely isolated purified astrocytes, neurons, and oligodendrocytes. Provides improved cell-type-specific markers for better understanding of neural development, function, and disease.

Proper citation: Exon Array Browser (RRID:SCR_008712) Copy   

•   Source: SciCrunch Registry

http://www.functionalneurogenesis.com/blog/

A blog focusing on the function of adult neurogenesis in the dentate gyrus of the hippocampus, including discussion of scientific research papers, methods and protocols, and other trends or observations about the field.

Proper citation: Functional Neurogenesis (RRID:SCR_008830) Copy   

•   Source: SciCrunch Registry

http://cushing.med.yale.edu/gsdl/cgi-bin/library

The images in this collection are derived from high resolution scans of glass 3.25 X 4 inch lantern slides that were part of a large collection of slides covering his years at the Rockefeller University and Yale University School of Medicine. These selected images were scanned by James D. Jamieson, M.D., Ph.D., a student of Palade. The images also include some of the earliest electron micrographs taken by collaborators of George Palade both at the Rockefeller University (1945 - 1973) and at Yale (1973 - 1990). They include micrographs taken by Professor Marilyn Farquhar, Ph.D., whose studies elucidated the function of the glomerular basement membrane in renal filtration. There are 5 ways to find information in this collection: search for particular words that appear in the text by clicking the Search button; browse documents by Title by clicking the Titles button; browse documents by Subject by clicking the Subjects button; browse documents by Creator by clicking the Creators button, and browse documents by References by clicking the References button. Sponsors: This collection is the result of a collaboration between James D. Jamieson, M.D., Ph.D., Professor, Dept. of Cell Biology, and Arthur R. Belanger, OBE, Systems Manager, Harvey Cushing/John Hay Whitney Medical Library, both at the Yale University School of Medicine.

Proper citation: George E. Palade EM Slide Collection. (RRID:SCR_008675) Copy   

•   Source: SciCrunch Registry