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http://aidb.crbs.ucsd.edu

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 October 4, 2017.

A sub-project of the Cell Centered Database (http://ccdb.ucsd.edu) providing a public repository for animal imaging data sets from MRI and related techniques. The public AIDB website provides the ability for browsing, visualizing and downloading the animal subjected MRI data. The AIDB is a pilot project to serve the current need for public imaging repositories for animal imaging data. The Cell Centered Database (CCDB) is a web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy. The AIDB data model is modified from the basic model of the CCDB where microscopic images are combined to make 2D, 3D and 4D reconstructions. The CCDB has made available over 40 segmented datasets from high resolution magnetic resonance imaging of inbred mouse strains through the prototype AIDB. These data were acquired as part of the Mouse BIRN project by Drs. G. Allan Johnson and Robert Williams. More information about these data can be found in Badea et al. (2009) (Genetic dissection of the mouse CNS using magnetic resonance microscopy - Pubmed: 19542887)

Proper citation: Animal Imaging Database (RRID:SCR_008002) Copy   

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http://swift.cmbi.kun.nl/swift/FUNPEP/gergo/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. As a part of the FUNPEP project, we made a small collection of peptides, which are known to form these amyloid plaques (Known amyloidogenic peptides). Sequences, including respective animal analogues, were extracted from SWISSPROT, and aligned. These sequences and some words about the peptides can be found under the links in the table below. Some molecular modelling was also perfomed, to show some possible structures of amyloids. The peptides on these pages were not chosen because of some kind of sequence similarity, what is more, they hardly have any. Their common, and very starnge property is the ability to form amyloid plaques (or fibrils). The exact structure and the formation of these supermolacular structures are still subject of research, but there are lots of promising results.

Proper citation: FUNPEP (RRID:SCR_007667) 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://molpharm.wisc.edu/

Modern molecular biology, protein biochemistry, immunology, cell biology, genetics, electrophysiology, and morphology are well represented in the Program in Molecular and Cellular Pharmacology. Students will be instructed thoroughly in these fields as well as in the unique principles of Pharmacology. One major objective of the Program is to teach the students a fundamental understanding of the molecular basis of signal transducing systems and their regulation. The Program brings together an outstanding group of dedicated trainers with a focus on cellular signal transduction. Graduates of the Program will be well prepared for a career in basic biomedical sciences. The Program provides a unique training experience for young scientists who want to elucidate basic principles of cellular signal pathways. Detailed knowledge of these pathways is the most important prerequisite for the discovery of new drugs and the treatment of diseases.

Proper citation: University of Wisconsin Madison WI. Molecular and Cellular Pharmacology (RRID:SCR_007542) 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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https://hsc.unm.edu/medicine/departments/neurosciences/

This interdisciplinary Neuroscience Program is one division of the Biomedical Sciences Graduate Program at the University of New Mexico. Participating faculty are affiliated with the Department of Neurosciences. Students complete a core curriculum in biomedical sciences and then an individualized program of courses and research in neuroscience. Students may choose among neuroscience research laboratories in the Neurosciences Department or at the Los Alamos National Laboratories. Neuroscience graduate students are part of an active neuroscience group that sponsors weekly seminars and journal clubs.

Proper citation: University of New Mexico Department of Neurosciences (RRID:SCR_007972) Copy   

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http://www.cephb.fr/

The Centre d''Etude du Polymorphisme Humain (CEPH) is a research laboratory, the main activities of which are the setting up, storage, processing and distribution of DNA collections for the identification of genetic factors conferring susceptibility to complex disorders. These collections are established in partnership and full collaboration with external French or international research groups. The Foundation currently hosts the CEPH reference panel, the HGDP panel (Human genome Diversity Cell Line Panel) and several collections amounting mid-2008 to more than 250 000 samples. The goal of CEPH is to understand complex multifactorial disorders necessitates the establishment of structures facilitating access to large and integrated collection of individuals, characterized by a large number of variables emanating from different technologies and platforms. To achieve this goal, CEPH facilitates the setting up of integrated analyses combining clinical, genetic and environmental data, for the identification of susceptibility factors to complex multifactorial disorders Additionally, CEHP allows the reception, storage, processing and distribution of biological sample collections. At the same time, it promotes and participates in the design and setting up of genetic studies: - in partnership and full collaboration with external research groups - giving access to a large number of variables - in a sufficient number of subjects - allowing large scale integrated analyses

Proper citation: Centre dEtude du Polymorphisme Humain (RRID:SCR_008026) Copy   

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http://www.bio.dist.unige.it/

The Bio-Lab is a Bioengineering and Bioimages laboratory and it''s part of DIST (Department of Computer Science, Control Systems and Telecommunications- University of Genoa). The main research activities of the Bioengineering Laboratory are related with the acquisition, processing and rendering of bioimages with the aim of exploring the links between structure and functionality of biological systems (images of cells in optical confocal microscopy) and for diagnostic and therapeutical processes (images of the human body in Magnetic Resonance, Computerized X-ray Tomography, ultrasounds and other modalities). The main research activities of the laboratory are related to: - Bioimages: medical/biological image analysis and visualization methods are investigated, with a deep attention to the applications development for the driven therapy. - Bioinformatics: in this field, advanced technologies and knowledge related to production and treatment of gene expression microarray distributed data have been implemented. - Tissue Engineering: this research activity is addressed to the development and testing of biomaterials, coupled with adult stem cells for the in vivo bone formation. - Neuroinformatics: the interaction between results of functional neuroimaging and brain computational models has been studied. Among the equipment of the Bioengineering Laboratory there are of particular interest: 2D-3D cell culture bioreactor systems and a virtual reality platform for the interaction person-bioimages, medical data and 3D models. The Bio-Lab also manages a GRID node belonging to the international GILDA network, which is built by 6 server, for a total amount of 12 CPU, 7 GB RAM and 500 GB Disk Space. Additionally, the confocal laser is a very essential tool in this lab; it is a scanning optical microscope with a hardware/software framework virtual reality-like for the interaction person-bioimages, with stereovision, and equipment for head tracking and pointing. The Bio-Lab collaborates with several research institutes and centers, such as the National Institute of Nuclear Physics, the National Research Council, and the Advanced Biotechnology Center (visit Research area or Project area in the web site). Promising collaborations are also on going with different technological companies in the national scenario. The laboratory has also been involved in several international and national projects funded by the European Commission and MUR. Specifically, it is involved in several projects funded by the European Commission projects related to the area of Health Care Telematics, with special reference to emergency telemedicine.

Proper citation: biolab - Bioengineering and Bioimages Laboratory (RRID:SCR_008029) 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.dnaftb.org/dnaftb/

An animated primer on the basics of DNA, genes, and heredity organized around three key concepts: Classical Genetics, Molecules of Genetics, and Genetic Organization and Control. The science behind each concept is explained by: animation, image gallery, video interviews, problem, biographies, and links.

Proper citation: DNA From The Beginning: AN Animated Primer on the Basics of DNA, Genes, and Heredity (RRID:SCR_008028) 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://www.fisio.cinvestav.mx/

The National Polytechnic Institute''s (Instituto Politecnico Nacional) department of Physiology, Biophysics, and Neurosciences (Departamento de Fisiologa, Biofsica y Neurociencias) is an institutional topical portal and offers a Masters and doctorate program. The web sites content is in Spanish. In forty years of life, this Department has maintained constant activity and has a well sustained scientific prestige within the national and international levels; in addition, the departments of the Center for Research and Advanced Studies (Centro de Investigacin y de Estudios Avanzados (CINVESTAV)) has had more recognition and support of external agencies. The achievements realized during this time yields the following results: 245 graduate students (140 Masters and doctorate 108), 272 directed theses, 190 research articles published in national journals and 831 in international journals with strict arbitration, 75 chapters in books published abroad, 210 chapters in national books, five complete books published outside the country, fourteen national books, and thousands of citations at the international level to the research work done by its members. Today, its teaching plant is composed of 31 teachers and there are 38 students enrolled in the doctorate program and 11 in the Masters program. The rigorous selection of students has allowed for the production of scientists concerned about the quality of their research. In the Department an atmosphere of cordiality exists and collective performance of the delivery of the work. Lines of inquiry Medication access and drugs across the epithelia and endothelium Accession, proliferation, differentiation and cancer Biophysics of Ionic Channels Endocrinology Sensorimotor integration in the spinal cord Environment and cellular injury Developmental neurobiology Neuropharmacology Nervous system pathologies Gene therapy

Proper citation: National Polytechnic Institute; Department of Physiology, Biophysics, and Neurosciences (RRID:SCR_008024) Copy   

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http://ivl.calit2.net/wiki/

This resource is a Wiki page providing information about the Immersive Visualization Laboratory of Cal-IT2 at the UCSD. Sponsors: This resource is supported by Cal-IT2.

Proper citation: Cal-IT2: Immersive Visualization Laboratory (RRID:SCR_008021) 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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http://ap.psychiatryonline.org/

A publisher of original scholarly work focused on psychiatric education and professional development in academic psychiatry. The journal features work that furthers knowledge in psychiatric education and stimulates improvements in academic psychiatry. Articles address teaching, research, and administration, as well as clinical, organizational, and economic issues relevant to the academic missions of departments of psychiatry. Overview articles present empirical research and critical analysis of important topics in academic psychiatry. Other features include a new ideas section, commentaries, and letters to the editor. Academic Psychiatry also publishes the best papers from meeting workshops, provides a forum for debates, and often presents theme issues that focus on a single area of psychiatric education.

Proper citation: Academic Psychiatry: Psychiatry Online (RRID:SCR_008014) Copy   

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http://claire.bardel.free.fr/software.html

Software package to perform phylogeny based association and localization analysis.Used for association detection and localization of susceptibility sites using haplotype phylogenetic trees. Performs these two phylogeny-based analysis: tests association between candidate gene and disease; pinpoints markers (SNPs) that are putative disease susceptibility loci.

Proper citation: ALTree (RRID:SCR_007562) Copy   

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http://organelledb.lsi.umich.edu/

Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light.

Proper citation: Organelle DB (RRID:SCR_007837) Copy   

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