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http://www.jax.org/imr/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 08, 2012. The function of the IMR is to select, import, cryopreserve, maintain, and distribute these important strains of mice to the research community. To improve their value for research, the IMR also undertakes genetic development of stocks, such as transferring mutant genes or transgenes to defined genetic backgrounds and combining transgenes and/or targeted mutations to create new mouse models for research. The function of the IMR is to: * select biomedically important stocks of transgenic, chemically induced, and targeted mutant mice * import these stocks into the Jackson Laboratory by rederivation procedures that rid them of any pathogens they might carry * cryopreserve embryos from these stocks to protect them against accidental loss and genetic contamination * backcross the mutation onto an inbred strain, if necessary * distribute them to the scientific community More than 1000 mutant stocks have been accepted by the IMR from 1992 through December 2006. Current holdings include models for research on cancer; breast cancer; immunological and inflammatory diseases; neurological diseases; behavioral, cardiovascular and heart diseases; developmental, metabolic and other diseases; reporter (e.g., GFP) and recombinase (e.g., cre/loxP) strains. About eight strains a month are being added to the IMR holdings. Research is being conducted on improved methods for assisted reproduction and speed congenic production. Most of the targeted mutants arrive on a mixed 129xC57BL/6 genetic background, and as many of these as possible are backcrossed onto an inbred strain (usually C57BL/6J). In addition, new mouse models are being created by intercrossing carriers of specific transgenes and/or targeted mutations. Simple sequence length polymorphism DNA markers are being used to characterize and evaluate differences between inbred strains, substrains, and embryonic stem cell lines.

Proper citation: Induced Mutant Resource (RRID:SCR_008366) Copy   

•   Source: SciCrunch Registry

http://www.osc.riken.jp/english/

Omics Science Center is aiming to develop a comprehensive system called Life Science Accelerator(LSA) for the advancement of omics research. The LSA is a comprehensive system consists of biological resources, human resources, technologies, know-how, and essential administrative ability. Ultimate goal of LSA is to support and accelerate the advancement in life science research. Omics is the comprehensive study of molecules in living organisms. The complete sequencing of genomes (the complete set of genes in an organism) has enabled rapid developments in the collection and analysis of various types of comprehensive molecular data such as transcriptomes (the complete set of gene expression data) and proteomes (the complete set of intracellular proteins). Fundamental omics research aims to link these omics data to molecular networks and pathways in order to advance the understanding of biological phenomena as systems at the molecular level.

Proper citation: RIKEN Omics Science Center (RRID:SCR_008241) Copy   

•   Source: SciCrunch Registry

http://www.repairgenes.org/index.shtml

The aim of the repairGenes site is to be a source of information about DNA repair genes and a useful resource for research on DNA repair. At the moment, the site contains information about a number of DNA repair genes from a set of selected species. The information is organized by organism and by biological process term as defined by the Gene Ontology (GO) project. The coverage of DNA repair genes is not complete, but hopefully it satisfies to demonstrate the concept and generate ideas for future versions of the system. At present, the raw data about DNA repair genes is extracted from the SWISS-PROT database, and categorized using the GO system. SWISS-PROT entries are being annotated by the Gene Ontology Annotation project at EBI. GOA is an ongoing project which will become more complete with time. As more data is released, this will be fed into repairGenes to keep it up-to-date. In future versions, the user will be able to search freely among organisms and categories of repair genes, enabling easy comparisons between species. For a taste of this, please have a look at the overview of repair genes from five major organisms. The amount of information in the system will be increased and the quality will be improved in the future. So will the features of the system.

Proper citation: repairGenes (RRID:SCR_008240) Copy   

•   Source: SciCrunch Registry

http://www.reciprocalnet.org/

Database of crystallographic information. Its membership includes crystallographic service facilities (that analyze crystals submitted by research chemists) located at major universities. These labs analyze anywhere from a few dozen to several hundred molecular structures each year and post the data online for the public to access. A distributed database engine takes care of shuttling this data across the Internet so that every structure can be located by the search engine. There may be a delay of a year or more between the time a structure is first analyzed and the time it finally becomes available for the public to see. This is due to intellectual property issues - the intervening time allows the chemists who first discovered the structure to publish it in a trade journal.

Proper citation: Reciprocal Net (RRID:SCR_008238) Copy   

•   Source: SciCrunch Registry

http://www.sp2000.org/

Species 2000 is a federation of database organizations working closely with users, taxonomists and sponsoring agencies. The goal of the Species 2000 project is to create a validated checklist of all the world''s species (plants, animals, fungi and microbes). This is being achieved by bringing together an array of global species databases covering each of the major groups of organisms. Each database covers all known species in the group, using a consistent taxonomic system. The participating databases are widely distributed throughout the world and currently number 52. The existing global species databases presently account for some 60% of the total known species, so substantial investment in new databases will be needed for full coverage of all taxa to be achieved.

Proper citation: Species 2000 (RRID:SCR_008231) Copy   

•   Source: SciCrunch Registry

http://www.liden.cc/Visionary/

It is a dictionary for terminology used in the study of human and animal vision. It includes terms from the areas of biological and machine vision, visual psychophysics, visual neuroscience and other related fields. Sponsors: Visionary is sponsored by Educational Software for Autism.

Proper citation: Visionary: A Dictionary for the Study of Vision (RRID:SCR_008307) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/simtkcore

SimTK Core is one of the two packages that together constitute SimTK, the biosimulation toolkit from the Simbios Center. The other major component of SimTK is OpenMM which is packaged separately. This SimTK Core project collects together all the binaries needed for the various SimTK Core subprojects. These include Simbody, Molmodel, Simmath (including Ipopt), Simmatrix, CPodes, SimTKcommon, and Lapack. See the individual projects for descriptions. SimTK brings together in a robust, convenient, open source form the collection of highly-specialized technologies necessary to building successful physics-based simulations of biological structures. These include: strict adherence to an important set of abstractions and guiding principles, robust, high-performance numerical methods, support for developing and sharing physics-based models, and careful software engineering. Accessible High Performance Computing We believe that a primary concern of simulation scientists is performance, that is, speed of computation. We seek to build valid, approximate models using classical physics in order to achieve reasonable run times for our computational studies, so that we can hope to learn something interesting before retirement. In the choice of SimTK technologies, we are focused on achieving the best possible performance on hardware that most researchers actually have. In today''s practice, that means commodity multiprocessors and small clusters. The difference in performance between the best methods and the do-it-yourself techniques most people use can be astoundingeasily an order of magnitude or more. The growing set of SimTK Core libraries seeks to provide the best implementation of the best-known methods for widely used computations such as: Linear algebra, numerical integration and Monte Carlo sampling, multibody (internal coordinate) dynamics, molecular force field evaluation, nonlinear root finding and optimization. All SimTK Core software is in the form of C++ APIs, is thread-safe, and quietly exploits multiple CPUs when they are present. The resulting pre-built binaries are available for download and immediate use. Audience: Biosimulation application programmers interested in including robust, high-performance physics-based simulation in their domain-specific applications.

Proper citation: SimTKCore (RRID:SCR_008268) Copy   

•   Source: SciCrunch Registry

http://www.vetmed.vt.edu/research/amrv.asp

An institutional training program to train veterinarians in conducting research. The program trains veterinarians in acquiring the skills of a researcher as they undergo a specific M.S. or Ph.D program. The program urges graduates to take part in research concerning animal models of infectious diseases, immunology, and nutrition, among other health topics.

Proper citation: Post-DVM Training Program on Animal Model Research for Veterinarians (RRID:SCR_008303) Copy   

•   Source: SciCrunch Registry

http://www.cabiatl.com/mricro/

MRIcro allows Windows and Linux computers view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyze MRI, fMRI and PET images). MRIcro allows efficient viewing and exporting of brain images. In addition, it allows neuropsychologists to identify regions of interest (ROIs, e.g. lesions). MRIcro can create Analyze format headers for exporting brain images to other platforms. Some features of MRIcro are: - Converts medical images to SPM friendly Analyze format. - View Analyze format images (big or little endian). - Create Analyze format headers (big or little endian). - Create 3D regions of interest (with computed volume & intensity). - Overlap multiple regions of interest. - Rotate images to match SPM template images. - Export images to BMP, JPEG, PNG or TIF format. - Yoked images: linked viewing of multiple images (e.g. view same coordinates of PET and MRI scans). Users familiar with other Windows programs will find that this software is fairly straightforward to use. Resting the mouse cursor over a button will cause a text hint to appear over the button. However, a tutorial with a step by step guide of how to use MRIcro with SPM is available.

Proper citation: MRIcro Software (RRID:SCR_008264) Copy   

•   Source: SciCrunch Registry

http://www.amber.org.au/

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. AMBeR's aim is to bring together Australia's unique resources for genetic epidemiology and genomics with high level expertise in bioinformatics and statistical science, conduct advanced methodological research, develop new research capacity and competitiveness in cutting-edge techniques, bring them to bear on important medical research problems, train young Australians in bioinformatics and advanced biostatistics, and transfer this expertise to the medical research community.

Proper citation: Australian Medical Bioinformatics Resource (RRID:SCR_008385) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/isim_interface

A simple Java graphical user interface for running the program ISIM. ISIM is a package that simulates the thermodynamic ensemble of ions around a macromolecule using a grand canonical Monte Carlo scheme and simple hard sphere ion models. It is meant to provide an alternative mechanism to mean field approaches to allow the calculation of ion distributions around a highly charged molecule using a simple model that takes into account ion-ion correlations and steric interactions. The original source was created in the McCammon group at UCSD but is no longer available. The version of ISIM used is available in the ISIM project on simtk.org.

Proper citation: Ion Simulator Interface (RRID:SCR_008267) Copy   

•   Source: SciCrunch Registry

http://www.nia.nih.gov/research/dab/interventions-testing-program-itp

NIA''s ITP is a multi-institutional study investigating treatments with the potential to exte nd lifespan and delay disease and dysfunction in mice. Priority consideration will be given to the treatments that are easily obtainable, reasonably priced, and can be delivered in the diet (preferred) or water. Interventions that require labor intensive forms of administration, such as daily injections or gavage, are not feasible within the design of the ITP. Treatments currently under study include: - Pharmaceuticals - Nutraceuticals - Foods - Diets - Dietary supplements - Plant extracts - Hormones - Peptides - Amino acids - Chelators - Redox agents - Other agents or mixtures of agents Although the mice involved in this study will be housed at the University of Michigan, the Jackson Laboratories, and the University of Texas Health Sciences Center at San Antonio, the project is designed to involve collaborations with investigators at any university, institute, or other organization that has ideas about pharmacological interventions that might decelerate aging and wishes to test these in a lifespan study of mice. Sponsors: This program is supported by the National Institute of Aging.

Proper citation: Interventions Testing Program (RRID:SCR_008266) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-16/search?q=%2A&l=&facet[]=Database:ResearchCrossroads

THIS RESOURCE IS NO LONGER IN SERVICE, documented on Feb. 05, 2014, however, NIF holds the Research Crossroads data and makes it available through Integrated Grants. World of publicly funded research aggregated into a database providing funding, publication, clinical trial and grant data from government and private research agencies. Advanced reporting and analysis tools are then used to connect research to researchers, organizations and topic areas to uncover non-obvious associations. Use ResearchCrossroads for: Researchers * Make your research visible to funding organizations and collaborators. * Connect with peers to stay up to date on their research progress * Update your investigator profile, biography and publications so funding organizations can find you * Discover available funding from private foundations and government funding organizations * Annotate your previous research grants with outcomes * Create a research diary and participate in discussions with your peers Foundations Participating in ResearchCrossroads is free if you share your research data. Send us a spreadsheet with your grant and investigator information. * Create a community for your researchers to learn from each other * Locate potential investigators and collaborators * Post available funding and be matched with investigator profiles * Access to analytical reporting of funding and research statistics * Update your personalized organization profile page * Display your logo in search results * Link to your ResearchCrossroads grants and investigator profiles from your own website Corporations, Academia & Governments Contact us about subscriptions to funding trend analytics and marketing opportunities. * In-depth reporting of 15 years of funding data from government and private institutions * Subscriptions available to advanced analysis & reporting tools * Display your corporate logo in search results * Update your organization profile page * Highly targeted marketing & advertising by research areas, keywords and categories of investigator * Register for notifications of the newest grants in your area of interest

Proper citation: ResearchCrossroads (RRID:SCR_008261) Copy   

•   Source: SciCrunch Registry

http://www.cdc.gov/nccdphp/ace/

A clinical study linking childhood maltreatment and later-life health and well-being. As a collaboration between the Centers for Disease Control and Prevention and Kaiser Permanente''s Health Appraisal Clinic in San Diego, Health Maintenance Organization (HMO) members undergoing a comprehensive physical examination provided detailed information about their childhood experience of abuse, neglect, and family dysfunction. Over 17,000 members chose to participate. To date, over 50 scientific articles have been published and over 100 conference and workshop presentations have been made. Future Directions: The ACE study is now in its 10th year and the prospective phase is currently underway. In this ongoing stage of the study, data are being gathered from various sources including outpatient medical records, pharmacy utilization records, and hospital discharge records to track the subsequent health outcomes and health care use of ACE Study participants. In addition, an examination of National Death Index records will be conducted to establish the relationship between ACE and mortality among the ACE Study population. The ACE Study findings suggest that these experiences are major risk factors for the leading causes of illness and death as well as poor quality of life in the United States. Progress in preventing and recovering from the nation''s worst health and social problems is likely to benefit from the understanding that many of these problems arise as a consequence of adverse childhood experiences. :Sponsors: This resource is supported by the Centers for Disease Control and Prevention and the Kaiser Permanente''s Health Appraisal Clinic in San Diego.

Proper citation: Adverse Childhood Experiences Study (RRID:SCR_008382) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/RJaCGH/index.html

Software for Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models.

Proper citation: RJaCGH (RRID:SCR_008381) Copy   

•   Source: SciCrunch Registry

http://www.cerc.utexas.edu/OnlineCall/

A fast basecalling scheme for Illumina''s Next Generation sequencing machines, specifically designed for GAII.

Proper citation: OnlineCall (RRID:SCR_008263) Copy   

•   Source: SciCrunch Registry

http://diademchallenge.org/data_sets.html

A software development competition, the DIADEM Challenge,to benefit the scientific community by encouraging the development of better software for automating three-dimensional reconstructions of neuronal arbors. The intent of the Sponsors is to ensure that the best software submitted for the competition is made available to the scientific community within a reasonable time and on reasonable terms. No purchase is necessary to enter or win. The competition will have two rounds. As of April 10, 2009, individuals and teams may register to participate in the competition and may download sets of image stacks (Data Sets) of non-human animal brains along with three-dimensional reconstructions for some of these Data Sets for training purposes. Submissions of software, including executable programs, supporting documentation, and reconstruction files for the Data Sets, must be uploaded to the competition website no later than April 9, 2010. In order to be eligible to win the competition, the individuals and at least one member of any teams whose submissions are selected for the Final Round (Finalists) must participate in the Final Round and scientific conference. Personal participation in the Final Round and scientific conference is important for two main reasons: first, because the Finalists software will be tested at the Final Round against additional Data Sets so that the judges can select a winner or winners, and second, because the larger scientific conference, of which the Final Round will be a part, is intended to foster extensive scientific interaction among neuroscientists and computational scientists, including plenary and poster sessions to discuss challenges, solutions, and future directions. There are 5 datasets, all of which have to be reconstructed for the qualifier phase. Once you have registered your group, dataset download information will be sent to you via E-mail. The 5 datasets are: - Cerebellar Climbing Fibers - Hippocampal CA3 Interneuron - Neocortical Layer 6 Axons - Neuromuscular Projection Fibers - Olfactory Projection Fibers Sponsors: The sponsors of this competition are: Allen Institute for Brain Science, Seattle, Washington; Howard Hughes Medical Institute (HHMI), Chevy Chase, Maryland; and Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia.

Proper citation: DIADEM Challenge: DIgital reconstruction of Axonal and DEndritic Morphology (DIADEM) Software Development Competition (RRID:SCR_008262) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.kmutt.ac.th/list-of-courses-2/

This program is an international Bioinformatics course at KMUTT designed for students who desire focused training in the elements of computer science, biology and biochemistry needed for a successful career in this exciting new discipline. Students in this program will receive comprehensive training in genomics, algorithms for sequence analysis, database design and management, software engineering and programming (including web-based development). Each student will apply their skills to a practical project, where they will design and implement a solution to a real-world problem under the guidance of an experienced mentor in industry or academia. In order to receive a Masters degree, students must demonstrate mastery of the core subject matter (expected to maintain a minimum grade of B in all core courses) and reach a minimum TOEFL test score of 500 (paper) or 173 (computer) or equivalent prior to or on completion of the course. In 24 monhs students gain the knowledge and skills necessary to enter a career with industry or a career in research as a bioinformatics or biocomputing specialist. The program offers fifteen scholarships each year include tuition and fees plus an additional to cover living expenses for 24 months. :Keywords: Bioinformatics, Computer Science, Biology, Biochemistry, Genomics, Algorithms, Sequence, Analysis, Database, Design, Management, Software, Engineering, Programing, Industry, Academia, Master''s, :

Proper citation: Bioinformatic: Programs and Courses (RRID:SCR_008379) Copy   

•   Source: SciCrunch Registry

http://bioinfo.cipf.es/isacghtrac

Software to analyze CNV that will now normalize arrays CGH and it will visually integrate different genome annotations.

Proper citation: IsaCGH (RRID:SCR_008375) Copy   

•   Source: SciCrunch Registry

http://flj.hinv.jp/

A human full-length cDNA sequence analysis database focused on mRNA varieties caused by variations of transcription start site (TSS) and splicing. Also available is ATGpr, a program for identifying the translational initiation codons in cDNA sequences. Data are derived from several full-length cDNA studies in Japan. Human gene number was estimated to be 20-25 thousand. However, the number of human mRNA varieties was predicted to be about 100 thousand. The varieties are thought to be caused by variations of TSS and splicing. In their previous human cDNA project, about 30 thousand of FLJ human full-length sequenced cDNAs were deposited to DDBJ/GenBank/EMBL, and they obtained about 1.4 million of 5''-end sequences (5''-EST) of FLJ full-length cDNAs from about 100 kinds of cDNA libraries consist of human tissues and cells constructed by oligo-capping method. The majority of the insert cDNA sizes were over 2 kb and the full-length rate of 5''-end was 90. And our FLJ cDNAs were covered about 80 of human genes. About 22 thousand of finished grades of full-length sequenced cDNAs were obtained in this project. The sequence analysis databases is focused on mRNA variations using human genome and cDNA sequences, FLJ full-length sequenced cDNAs, 5-ESTs of FLJ full-length cDNAs and other cDNA sequences described below. After those sequences were mapped onto the human genome sequences, clustering of the cDNA sequences were done based on the mapping results.

Proper citation: FLJ Human cDNA Database (RRID:SCR_008253) Copy   

•   Source: SciCrunch Registry