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http://icebox.lbl.gov:8080/ApolloWebDemo/jbrowse/

WebApollo is an extensible web-based sequence annotation editor for community annotation. No software download is required and the annotations are saved to a centralized database with real-time annotation updating. (The edit server mediates annotation changes made by multiple users.) The Web based client uses JBrowse, is fast and highly interactive. WebApollo accesses many types of genomic data including access to public data from UCSC, Ensembl, and GMOD Chado databases. Source code (BSD License) * Client source code: https://github.com/berkeleybop/jbrowse * Annotation editing engine: http://code.google.com/p/apollo-web * Data model and I/O layer: http://code.google.com/p/gbol * Trellis server code: http://code.google.com/p/genomancer

Proper citation: WebApollo: A Web-Based Sequence Annotation Editor for Community Annotation (RRID:SCR_005321) Copy   

•   Source: SciCrunch Registry

http://www.virtualflybrain.org

An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain.

Proper citation: Virtual Fly Brain (RRID:SCR_004229) Copy   

•   Source: SciCrunch Registry

http://www.portugene.com/SPInDel/SPInDel_webworkbench.html

A multifunctional workbench for species identification using insertion/deletion variants. The SPInDel workbench provides a step-by-step environment for the alignment of target sequences, selection of informative hypervariable regions, design of PCR primers and the statistical validation of the species-identification process. It includes a large dataset comprising nearly 1,800 numeric profiles for the identification of eukaryotic, prokaryotic and viral species.

Proper citation: SPInDel (RRID:SCR_004509) Copy   

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http://www.roslin.ed.ac.uk/about-roslin/

The world''s largest collection of tick cell lines, enabling scientists to carry out advanced research. This biobank is establishing a collection of all the continuous cell lines derived from ixodid and argasid ticks of medical and veterinary importance available worldwide now and in future. Ticks are blood feeding arthropods which transmit many human and animal diseases. Research into prevention and cure of these diseases, which are caused by viruses, bacteria and protozoa, is greatly assisted by the use of cell culture systems which enable study of both how tick cells function, and how and why ticks transmit these disease-causing pathogens. Cell lines will always be shipped to recipient laboratories as growing cultures, since we cannot guarantee successful resuscitation of frozen stabilates. Tick cells in culture can tolerate the range of temperatures experienced during transit by air for up to a week. Training: We will provide training in tick cell line care and maintenance. This is an essential component of successful transfer of tick cells to, and their establishment in, laboratories with little or no previous experience of tick cell culture. Recipient scientists (preferably the person who will actually look after the cells) can visit the biobank for between 2 days and 2 weeks, depending on their level of previous experience, to be trained in the specific approach and methods for tick cell cultivation. Establishment of new cell lines: In response to requests and on receipt of suitable starting material (engorged female or moulting nymphal ticks), we will attempt to establish new cell lines from tick species or strains which are not already represented in the collection. Deposition of new tick cell lines: We invite researchers anywhere in the world who have established new tick cell lines to deposit samples for safekeeping free of charge and, if requested, for distribution alongside the existing biobank portfolio.

Proper citation: Roslin Wellcome Trust Tick Cell Biobank (RRID:SCR_004228) Copy   

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http://www.nitrc.org/projects/asltbx

Tool box for arterial spin labeled perfusion MRI data processing. It is based on SPM and Matlab. More detailed documentation can be found in asl_perf_subtract.m, the main function for calculating CBF value. It supports 3D or 4D Analyze or Nifiti format and PASL, CASL, and PCASL data. It contains the code for calculating CBF and a set of SPM batch scripts for preprocessing and statistical analysis.

Proper citation: ASL data processing tool box (RRID:SCR_005997) Copy   

•   Source: SciCrunch Registry

http://www.jgi.doe.gov/

Institute to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. Supported by the DOE Office of Science, the DOE JGI unites the expertise at Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory, and the HudsonAlpha Institute for Biotechnology. The facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.

Proper citation: DOE Joint Genome Institute (RRID:SCR_003045) Copy   

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http://www.stanford.edu/group/nolan/retroviral_systems/phx.html

A second-generation retrovirus producer lines for the generation of helper free ecotropic and amphotropic retroviruses. The lines are based on the 293T cell line (a human embryonic kidney line transformed with adenovirus E1a and carrying a temperature sensitive T antigen co-selected with neomycin). The unique feature of this cell line is that it is highly transfectable with either calcium phosphate mediated transfection or lipid-based transfection protocols-- up to 50% or higher of cells can be transiently transfected. The lines were created by placing into 293T cells constructs capable of producing gag-pol, and envelope protein for ecotropic and amphotropic viruses. The lines offered advantages over previous stable systems in that virus can be produced in just a few days. Academic and non-profit laboratories may obtain the Phoenix cells from either Allele Biotechnology or the National Gene Vector Bank. The vectors may be obtained from Addgene. They are no longer distributing these reagents from the lab.

Proper citation: Phoenix (RRID:SCR_003163) Copy   

•   Source: SciCrunch Registry

http://www.neurodevnet.ca/

NeuroDevNet, a Canadian Network of Centres of Excellence (NCE), is dedicated to helping children overcome neurodevelopmental disorders. Network investigators seek to understand the causes of neurological deficits, and to transfer this knowledge to health care professionals, policy makers, and communities of interest. NeuroDevNet works with its partners in academia, the community, not-for-profit sector, industry, and government, and across traditional disciplinary boundaries and sectors, to ensure generated knowledge is translated into tangible diagnostic, preventative, therapeutic, social, economic, and health benefits for all. NeuroDevNet supports transformative research, provides training to build a new generation of Canadian researchers, strengthens communities with the right tools and information, and translates research findings into early diagnostic, preventative, and therapeutic strategies for children with neurological disorders to live healthier lives. Currently, the network''s research focuses on autism spectrum disorder, cerebral palsy, and fetal alcohol spectrum disorder. These demonstration projects are supported by NeuroDevNet''s central infrastructure and cores, including Neuroethics, Neuroinformatics, and Knowledge Translation.

Proper citation: NeuroDevNet (RRID:SCR_004925) Copy   

•   Source: SciCrunch Registry

http://www.jainlab.org/downloads.html

Automatic software program for microarray image quantification.

Proper citation: UCSF Spot (RRID:SCR_002985) Copy   

•   Source: SciCrunch Registry

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

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

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

•   Source: SciCrunch Registry

http://g2d2.ogic.ca

The Institute for Advanced Biosciences, Keio University, is an academic research institute pioneering the new life science field of Systems Biology, using both experimental and computational biology. There are several groups working in collaboration, focusing mainly on genome biology and engineering, genome design and synthetic biology, metabolic engineering, proteomics, metabolomics, RNA biology, bioinformatics and computational biology. Using cutting-edge technologies, intracellular components can be analyzed comprehensively to construct computer simulation models that can find numerous applications in fields such as biomedical, environmental, and agricultural science. Experimental and computational facilities are located in Tsuruoka, Yamagata prefecture, in northern Japan while the SFC campus, in the Tokyo area, hosts the bioinformatics laboratory and most undergraduate curricular activities. IAB has successfully attracted very significant funding for multiple research projects from major funding organizations including the New Energy and Industrial Technology Development Organization (NEDO) (2002-2006), for bioprocesses and cell modeling, the Ministry of Education, Culture, Sports, Science and Technology (MEXT) and its COE network, for biosimulation and systems biology (2003-2008), the Japan Science and Technology Agency (CREST, 2004-2009) for simulation and systems biology, the Ministry of Health, for cancer biology (2005), as well as from Yamagata prefecture and Tsuruoka city, 2001-2006 and 2006-2011). Over the past few years, IAB scientists have accumulated several awards including the 1st prize during the 5th Japan Biotechnology Business Competition (2005), the Minister of State for Science and Technology Policy award in recognition for industry-academia-government collaboration performance (2004), the IBM Shared University Research Award (2003), and the Nihon Kogyo Shimbunsha Award (2003) during the 17th Leading-edge Technology for Originality and Creativity. Sponsor. This study was supported by a grant from the Global COE Program entitled, Human Metabolomic Systems Biology and by a Grant-in-Aid for Scientific Research on Priority Areas Systems Genomes and on Lifesurveyor from the Ministry of Education, Culture, Sports, Science and Technology of Japan as well as research funds from the Yamagata prefectural government and the City of Tsuruoka.

Proper citation: Institute for Advanced Biosciences (RRID:SCR_008526) Copy   

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http://galton.uchicago.edu/~junzhang/LAPSTRUCT.html

Software application to describe population structure using biomarker data ( typically SNPs, CNVs etc.) available in a population sample. The main features different from PCA are: (1) geometrically motivated and graphic model based; (2)robustness of outliers. (entry from Genetic Analysis Software)

Proper citation: LAPSTRUCT (RRID:SCR_007550) Copy   

•   Source: SciCrunch Registry

http://www.floridaaquaculture.com

This web site is your introduction to the world of Florida Aquaculture. It represents a compilation of information about a division in the Florida Department of Agriculture and Consumer Services-the Division of Aquaculture. The Division plays a key role in the regulation of aquaculture facilities and shellfish processing plants, is responsible for opening/closing of shellfish harvesting waters to protect human health, ensures the continued productivity of oyster reefs through a restoration program and issues leases of submerged state lands for aquaculture. The creation of this division is unprecedented for a state agriculture department. Florida''s Division of Aquaculture is one-of-a-kind and serves a unique industry like no other in the United States. Please browse this site and learn more about Florida Aquaculture. I welcome your comments on the topics contained in this web site.

Proper citation: Division of Aquaculture (RRID:SCR_008484) Copy   

•   Source: SciCrunch Registry

http://senselab.med.yale.edu

The SenseLab Project is a long-term effort to build integrated, multidisciplinary models of neurons and neural systems. It was founded in 1993 as part of the original Human Brain Project, which began the development of neuroinformatics tools in support of neuroscience research. It is now part of the Neuroscience Information Framework (NIF) and the International Neuroinformatics Coordinating Facility (INCF). The SenseLab project involves novel informatics approaches to constructing databases and database tools for collecting and analyzing neuroscience information, using the olfactory system as a model, with extension to other brain systems. SenseLab contains seven related databases that support experimental and theoretical research on the membrane properties: CellPropDB, NeuronDB, ModelDB, ORDB, OdorDB, OdorMapDB, BrainPharmA pilot Web portal that successfully integrates multidisciplinary neurocience data.

Proper citation: SenseLab (RRID:SCR_007276) Copy   

•   Source: SciCrunch Registry

http://www.dtu.ox.ac.uk

It was founded in 1985 by Professor Rury Holman, specialises in performing diabetes-related national and multinational mega trials in partnership with the NHS, NIH, MRC, BHF, DUK, academic institutions and industry. The DTU also undertakes major modelling and statistical programmes to utilise fully the data available from its many studies, with a particular emphasis on modelling diabetes and cardiovascular disease processes. Current studies include 4-T, ACE, TECOS and UKPDS~Post Study Monitoring. Sponsor. Funded by the UK National Institute for Health Research

Proper citation: DTU (RRID:SCR_008481) Copy   

•   Source: SciCrunch Registry

http://brainsia.github.io/BRAINSTools/

Medical image processing software suite for brain analysis.

Proper citation: BRAINSTools (RRID:SCR_006618) Copy   

•   Source: SciCrunch Registry

http://www.exactantigen.com

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

Proper citation: Labome (RRID:SCR_007384) Copy   

•   Source: SciCrunch Registry

http://informedmedicaldecisions.org/

Mission The Foundation for Informed Medical Decision Making is a non-profit organization dedicated to assuring that people understand their choices and have the information they need to make sound decisions affecting their health and well being. To accomplish our mission: We promote understanding and adoption of informed medical decision-making. We organize and frame medical evidence in an unbiased manner to help people evaluate their options, particularly in instances where differences in individual preferences and perspectives are likely to affect personal choice. We sponsor research to expand knowledge of how to improve decision quality in health care. Medical Evidence The science of medical care is advancing at a rate that makes the delivery of quality patient-focused care an enormous challenge. New information about disease biology and genetics, rapid development of new tests and treatments, and the shift in disease from largely acute to largely chronic are all important contributing factors. Patient Perspective Medical research on practice variation indicates that patient perspectives are often less important in treatment decisions than factors having little to do with patients or their illnesses, such as geography, economics or supplier-induced demands. The Foundation brings the patient perspective into focus by interviewing real patients who can talk about the choices they made and why. Without the perspective of the patient, we cannot achieve a quality medical decision. Informed Medical Decisions The Foundation believes that it is the convergence of the two concepts: medical evidence and patient perspectives that create a truly informed decision in medical care. Funding The Foundation has worked in a unique partnership with Health Dialog since 1997. Health Dialog delivers patient support services to employers and health plans that are committed to providing excellence to their members or employees. As of July 2006, Health Dialog served seventeen million people through its contracts with healthcare insurers and corporations. Access to the Foundation''s decision support materials is a key benefit that Health Dialog''s clients receive. Health Dialog produces the Foundation''s new programs and distributes decision support materials and services to patients. A portion of Health Dialog''s revenue goes to the Foundation in the form of royalties to support the development of new decision support materials and research on how best to support patient decisions. The Foundation does not accept funding from any source that has a financial interest in any particular approach to medical testing or treatment. Foundation employees and clinical content experts do not accept support from companies that commercially market any kind of treatment or device that might be relevant to a program.

Proper citation: Foundation for Informed Medical Decision Making (RRID:SCR_008509) Copy   

•   Source: SciCrunch Registry

http://www.biorad.com

Commercial instrument and chemical vendor. Developer and manufacturer of specialized technological products for life science research and clinical diagnostics markets.

Proper citation: Bio-Rad Laboratories (RRID:SCR_008426) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/sdp-svm/

A statistical framework for genomic data fusion is a computational framework for integrating and drawing inferences from a collection of genome-wide measurements. Each dataset is represented via a kernel function, which defines generalized similarity relationships between pairs of entities, such as genes or proteins. The kernel representation is both flexible and efficient, and can be applied to many different types of data. Furthermore, kernel functions derived from different types of data can be combined in a straightforward fashion. Recent advances in the theory of kernel methods have provided efficient algorithms to perform such combinations in a way that minimizes a statistical loss function. These methods exploit semidefinite programming techniques to reduce the problem of finding optimizing kernel combinations to a convex optimization problem. Computational experiments performed using yeast genome-wide datasets, including amino acid sequences, hydropathy profiles, gene expression data and known protein-protein interactions, demonstrate the utility of this approach. A statistical learning algorithm trained from all of these data to recognize particular classes of proteins--membrane proteins and ribosomal proteins--performs significantly better than the same algorithm trained on any single type of data. Matlab code to center a kernel matrix and Matlab code for normalization are available.

Proper citation: A statistical framework for genomic data fusion (RRID:SCR_007219) Copy   

•   Source: SciCrunch Registry