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http://www.rms.org.uk/

It is at the forefront of new ideas and developments in microscopy and imaging. The RMS is the only truly international microscopical society, drawing distinguished members from all over the world. It also serves the needs of its company members who represent all the major manufacturers and suppliers of microscopes, equipment and services. In addition to this, the Society is pursuing an initiative to encourage young microscope users who may go on to influence microscopy in years to come. The Society is dedicated to advancing science, developing careers and supporting wider understanding of science and microscopy through its Science and Society activities. In support of the above, it publishes The Journal of Microscopy and microscopy handbooks, as well as helping young scientists through bursaries. The Society is incorporated by Royal Charter. Its governing documents are its Charter and By-laws. The most recent AGM minutes, Trustees Report and Accounts are available below - 2007 AGM draft minutes Full 2007 Trustees Report and Accounts - as submitted to the Charity Commission The RMS is a member of: - the Foundation for Science and Technology - the Biosciences Federation - the International Federation of Societies for Microscopy - the European Microscopy Society training opportunities; jobs.

Proper citation: RMS (RRID:SCR_007415) Copy   

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http://pharmacy.ouhsc.edu/prospective/admission_grad/

Department of Graduate Pharmaceutical Sciences offers programs leading to the Master of Science (M.S.) and Doctor of Philosophy (Ph.D.) degrees. These programs are designed to prepare scientists, educators, and practitioners for careers in pharmaceutical education, research, industry, and related areas of pharmacy practice. The graduate programs do not prepare students for practice as a registered pharmacist, so applicants who are interested in a pharmacy career should apply to the Doctor of Pharmacy (Pharm.D.) program. However, students who have already completed one year in the Pharm.D. program may apply to the dual degree, Pharm.D./M.S. program and study concurrently for a graduate degree.

Proper citation: University of Oklahoma Health Sciences Center College of Pharmacy (RRID:SCR_007524) Copy   

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http://www.hmdb.ca

Curated collection of human metabolite and human metabolism data which contains records for endogenous metabolites, with each metabolite entry containing detailed chemical, physical, biochemical, concentration, and disease information. This is further supplemented with thousands of NMR and MS spectra collected on purified reference metabolites.

Proper citation: HMDB (RRID:SCR_007712) Copy   

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http://mousediversity.alleninstitute.org/

A database, and associated atlas, that characterizes gene expression across genetic backgrounds and sex, expanding beyond the adult male C57BL/6J reference brain comprising the Allen Mouse Brain Atlas to include seven strains of male mice and female C57BL/6J mice. Gene expression was detected using colorimetric RNA in situ hybridization (ISH) that provides cellular level anatomic resolution. ISH data are searchable and organized by gene, strain, or sex.

Proper citation: Allen Institute Mouse Diversity Study (RRID:SCR_008009) Copy   

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http://www.oncomine.org

Oncomine Research Platform is a partially-commercial suite of products for online cancer gene expression analysis dedicated to the academic and non-profit research community. Oncomine combines a rapidly growing compendium of 20,000+ cancer transcriptome profiles with a sophisticated analysis engine and a powerful web application for data-mining and visualization. Oncomine facilitates rapid and reliable biomarker and therapeutic target discovery, validation and prioritization. Oncomine was developed by physicians, scientists, and software engineers at the University of Michigan and is now fully supported for the academic and non-profit research community by Compendia Bioscience.

Proper citation: Oncomine Research Platform (RRID:SCR_007834) Copy   

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http://genolist.pasteur.fr/SubtiList/

Subtilist is a database dedicated to the analysis of the genome of Bacillus subtilis. It provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments. It also allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.). The purpose of the website is to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria. The data contained in SubtiList originated mainly from the worldwide collaborative B. subtilis genome sequencing project, supplemented with information from the B. subtilis entries present in the EMBL/GenBank/DDBJ databanks, as well as observations either published in international journals or communicated directly to us by individual researchers.

Proper citation: SubtiList (RRID:SCR_007950) Copy   

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http://www.bioimage.ucsb.edu/BioView3D

bioView3D is an open source and cross-platform application intended for biologists to visualize 3D stack (laser scanning confocal, etc.) imagery. It runs on Windows, MacOS X and Linux. Features include: - Cross-platform with binaries for Windows, Mac, Linux - Reads many bio image and video formats - Reads meta-data from BioRad PIC, TIFF, Metamorph STK (uncompressed and LZW compressed), Fluoview TIFF, Carl Zeiss LSM 5, PSIA TIFF, Nanoscope II/III - Has two modes of rendering: textures and voxels - On-the-fly 3D visualization (mapping/enhancement) of multi-channel data - Export of fly-over video to several popular formats: QuickTime, WMV, AVI, Flash, MPEG1/2/4 - Visualization of graphical annotations: XML GObjects Sponsors: This work is supported in part by an NSF infrastructure award No. EIA-0080134 and IIS-0808772.

Proper citation: Center for Bio-Image Informatics: bioView3D (RRID:SCR_008005) Copy   

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http://www.selventa.com/technology/bel-framework

A markup language and a set of technologies for capturing, storing and operationalizing structured biological knowledge. It also makes the knowledge available to other applications, such as the GTP, as a navigable network of biological facts. The BEL Framework assembles biological facts recorded using BEL syntax. BEL is a use-neutral format for unambiguously capturing biological entities and their inter-relationships and associating them with external vocabularies and ontologies. To facilitate context-based analysis, BEL syntax captures causal (e.g., AKT1 phosphorylates SKP2 at serine 72) and correlative relationships (e.g., increased LRG1 levels in serum are correlated with ovarian cancer) along with the experimental context in which the relationships were observed (e.g., AKT1 phosphorylates SKP2 at serine 72 in HeLa cells) and citations in which the peer reviewed knowledge has been reported (Pubmed ID 19270695 illustrates AKT1 phosphorylation of SKP2 and Pubmed ID 20831812 discusses the correlation between LRG1 and ovarian cancer). The BEL Framework provides an environment for managing and operationalizing biological facts stored in the BEL format (BEL document) and consists of the following components: * A user-friendly, web-based, knowledge-capture and knowledge-management application * A compiler that can assemble composite knowledge networks from multiple sources containing BEL statements from the BEL document store * A portable storage format for compiled BEL statements * Application Programming Interfaces (APIs) to allow applications such as the GTP to access and use the knowledge The BEL Framework is unique in that it is designed to deal with the fundamental contradictions and ambiguities associated with assimilating scientific findings from disparate biological experiments and quality issues associated with manual and algorithm-driven collation methods. Following eight years of development and proprietary use, BEL has proven to be an intuitive and effective language for scientists, supporting the creation of a large knowledgebase used in the interpretation of ''omics data sets via causal relationship-based analytics. BEL and supporting tools are now being made publicly available to the research community through the introduction of the BEL Web Portal. The BEL Web Portal provides public access to BEL language specifications, documentation, knowledge representation examples, and BEL software tools.

Proper citation: Biological Expression Language Framework (RRID:SCR_008004) Copy   

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http://senselab.med.yale.edu/ordb/

Database of vertebrate olfactory receptors genes and proteins. It supports sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family. The database also incorporates a broad range of chemosensory genes and proteins, including the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfaction receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), and fungal pheromone receptors (FPRs). ORDB currently houses chemosensory receptors for more than 50 organisms. ORDB contains public and private sections which provide tools for investigators to analyze the functions of these very large gene families of G protein-coupled receptors. It also provides links to a local cluster of databases of related information in SenseLab, and to other relevant databases worldwide. The database aims to house all of the known olfactory receptor and chemoreceptor sequences in both nucleotide and amino acid form and serves four main purposes: * It is a repository of olfactory receptor sequences. * It provides tools for sequence analysis. * It supports similarity searches (screens) which reduces duplicate work. * It provides links to other types of receptor information, e.g. 3D models. The database is accessible to two classes of users: * General public www users have full access to all the public sequences, models and resources in the database. * Source laboratories are the laboratories that clone olfactory receptors and submit sequences in the private or public database. They can search any sequence they deposited to the database against any private or public sequence in the database. This user level is suited for laboratories that are actively cloning olfactory receptors.

Proper citation: Olfactory Receptor DataBase (RRID:SCR_007830) Copy   

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http://www.imperial.ac.uk/AP/faces/pages/read/Home.jsp?person=l.coin&_adf.ctrl-state=pekvgdj4t_3&_afrRedirect=4092914325174000

Software for identifying haplogroups from low coverage sequence data.

Proper citation: YHap (RRID:SCR_007951) Copy   

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http://www.genomesize.com

Comprehensive catalogue of animal genome size data. Haploid DNA contents (C-values, in picograms) are available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources. Data may be submitted directly to the database or reprints and notifications of new papers may be sent to database curation staff.

Proper citation: Animal Genome Size Database (RRID:SCR_007551) Copy   

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http://gene3d.biochem.ucl.ac.uk/Gene3D/

A large database of CATH protein domain assignments for ENSEMBL genomes and Uniprot sequences. Gene3D is a resource of form studying proteins and the component domains. Gene3D takes CATH domains from Protein Databank (PDB) structures and assigns them to the millions of protein sequences with no PDB structures using Hidden Markov models. Assigning a CATH superfamily to a region of a protein sequence gives information on the gross 3D structure of that region of the protein. CATH superfamilies have a limited set of functions and so the domain assignment provides some functional insights. Furthermore most proteins have several different domains in a specific order, so looking for proteins with a similar domain organization provides further functional insights. Strict confidence cut-offs are used to ensure the reliability of the domain assignments. Gene3D imports functional information from sources such as UNIPROT, and KEGG. They also import experimental datasets on request to help researchers integrate there data with the corpus of the literature. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Gene3D (RRID:SCR_007672) Copy   

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http://genomics.senescence.info/

Collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses. A major resource in HAGR is GenAge, which includes a curated database of genes related to human aging and a database of ageing- and longevity-associated genes in model organisms. Another major database in HAGR is AnAge. Featuring over 4,000 species, AnAge provides a compilation of data on aging, longevity, and life history that is ideal for the comparative biology of aging. GenDR is a database of genes associated with dietary restriction based on genetic manipulation experiments and gene expression profiling. Other projects include evolutionary studies, genome sequencing, cancer genomics, and gene expression analyses. The latter allowed them to identify a set of genes commonly altered during mammalian aging which represents a conserved molecular signature of aging. Software, namely in the form of scripts for Perl and SPSS, is made available for users to perform a variety of bioinformatic analyses potentially relevant for studying aging. The Perl toolkit, entitled the Ageing Research Computational Tools (ARCT), provides modules for parsing files, data-mining, searching and downloading data from the Internet, etc. Also available is an SPSS script that can be used to determine the demographic rate of aging for a given population. An extensive list of links regarding computational biology, genomics, gerontology, and comparative biology is also available.

Proper citation: Human Ageing Genomic Resources (RRID:SCR_007700) Copy   

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https://neuroscience.wustl.edu/

The Neuroscience PhD Program at Washington University in St. Louis aims to train the next generation of leaders in neurobiology. The main objectives of the program are to: Provide students with the skills necessary to conduct research including the planning and implementation of a unique research project in the field of neuroscience. Teach students the fundamental concepts within neuroscience and how to apply those concepts in the critical analysis of scientific research. Promote the professional development of students in the areas of scientific writing and oral presentation. Promote interdisciplinary science by encouraging cooperation and collaboration among students in different programs and departments.

Proper citation: Washington University in St. Louis Neuroscience (RRID:SCR_007544) Copy   

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http://flybrain.neurobio.arizona.edu/

An interactive database of the Drosophila melanogaster nervous system. It is used by the drosophila neuroscience community and by other researchers studying arthropod brain structure. Flybrain contains neuroanatomical peer reviewed descriptions of the central and peripheral nervous system of Drosophila melanogaster. It also contains an introductory hypertext tour guide to the basic structure of the nervous system, as well as more specific information concerning different anatomical structures, developmental stages, and visualization techniques for the Drosophila nervous system. Additionally, The site contains schematic representations, a 3D project, immunocytology stains, a library of golgi impregnations, and enhancer-trap images.

Proper citation: MIRROR: FlyBrain, An Online Atlas and Database of the Drosophila Nervous System (RRID:SCR_007661) Copy   

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https://code.google.com/p/ampliconnoise/

A collection of programs for the removal of noise from 454 sequenced PCR amplicons. This project also includes the Perseus algorithm for chimera removal.

Proper citation: AmpliconNoise (RRID:SCR_007814) Copy   

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http://cbio.mskcc.org/CancerGenes/Select.action

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2015. The CancerGenes resource simplifies the process of gene selection and prioritization in large collaborative projects. CancerGenes combines gene lists annotated by experts with information from key public databases. Gene lists in the CancerGenes resource are from various sources and have been mapped to UCSC canonical gene IDs. Each gene is annotated with gene name(s), functional description, organism, chromosome number, location, Entrez Gene ID, GO terms, InterPro descriptions, gene structure, protein length, transcript count, and experimentally determined transcript control regions, as well as links to Entrez Gene, COSMIC, and iHOP gene pages and the UCSC and Ensembl genome browsers. The user-friendly interface provides for searching, sorting and intersection of gene lists. Users may view tabulated results through a web browser or may dynamically download them as a spreadsheet table.

Proper citation: CancerGenes (RRID:SCR_007577) Copy   

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http://www.dnaform.jp/products/cage_e.html

Expression profiling and promoter identification software tool for transcriptional network analysis and transcriptome characterization. DeepCAGE, the combination of next-generation sequencing with next generation expression profiling provides unsurpassed solutions for expression profiling and genome annotation. CAGE will be the experimental approach at need to link gene expression and control regions in the genome. With the availability of next-generation sequencing methods, DNAFORM now offers DeepCAGE services. DeepCAGE libraries are prepared for direct analysis by an Illumina/Solexa Sequencer. One sequencing run using one channel on an Illumina/Solexa Sequencer can yield in over 4,000,000 reads per sample. CAGE is based on our full-length cDNA library technology, where an adaptor is ligated to the 5''''-end of full-length cDNAs, which introduces a recognition site for a Class IIs restriction endonuclease adjacent to the 5''''-end of the cDNA. The Class IIs restriction endonuclease, here MmeI, allows for the cloning of short tags as derived from the 5''''-end of transcripts into concatemers for high-throughput sequencing. CAGE tags are further characterized by mapping to genomic sequences, which enables the identification of transcriptional start sites. As such CAGE can contribute to projects in Gene Discovery, Gene Expression, and Promoter Identification. After the genome sequencing projects have provided us with the genetic blueprints for many organisms, new questions have to be answered on how to correlate the observed genotypes with related phenotypes, and how to understand the regulation of genetic information in time and space. The dynamics of living systems and the functional behavior of cells in multicellular organisms has thus become the subject of the emerging field of system biology. Integration of experimental approaches and computer aided theories on a system level will be the fundamental principle to drive systems biology in order to understand the principles behind complex regulatory networks, which will be an ambitious goal requiring new approaches in life sciences. For ordering and additional information, please contact us under contact_at_dnaform.jp

Proper citation: CAGE (RRID:SCR_007574) Copy   

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http://archpsyc.ama-assn.org/

The Archives of General Psychiatry strives to publish original, state-of-the-art studies and commentaries of general interest to clinicians, scholars, and research scientists in psychiatry, mental health, behavioral science, and allied fields. The Archives seeks to inform and to educate its readers as well as to stimulate debate and further exploration into the nature, causes, treatment, and public health importance of mental illness. Archives of General Psychiatry is an international peer-reviewed journal published 12 times a year. The online version is published on the first Monday of the month. There is a Middle Eastern edition of Archives of Neurology/Psychiatry published quarterly. The editor is interested in publishing high-impact articles that cover the field broadly, from genetic mechanisms to psychotherapeutic intervention trials. The acceptance rate is 17%. The average time from submission to first decision is 32 days; from acceptance to publication, 5.4 months. Its 2008 impact factor is 14.27 (the impact factor is a measure of citation rate per article, and is calculated by dividing 1 year''s worth of citations to a journal''s articles published in the previous 2 years by the number of major articles (eg, research papers, reviews) published by that journal in those 2 years).

Proper citation: Archives of General Psychiatry (RRID:SCR_008016) Copy   

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http://web1.sph.emory.edu/users/hwu30/polyaPeak.html

An R package for ranking ChIP-seq peaks with shape information.

Proper citation: polyaPeak (RRID:SCR_007687) Copy   

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