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http://proteus-biosciences.com/default.aspx

Develops innovative products to advance proteomic research. We specialize in discovering peptides and proteins with novel biological properties, designing and developing enzyme activity assays for diverse screening applications, and producing innovative protein analysis tools for biomarker identification and characterization.

Proper citation: Proteus Biosciences (RRID:SCR_006422) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna

A de novo assembly program targeting populations with high mutation rates.

Proper citation: VICUNA (RRID:SCR_006302) Copy   

•   Source: SciCrunch Registry

http://datastar.mannlib.cornell.edu/

A single library software prototype transitioning to a to an open-source platform ready for adoption and extension at other institutions wishing to provide research data sharing and discovery services. Datastar''''s ability to expose metadata about research datasets in a standard semantic format called Linked Data will be enhanced to support selective interchange of related information with VIVO, an open-source semantic researcher networking tool gaining prominence through adoption at multiple U.S. universities, in the federal government, and internationally.

Proper citation: DataStaR (RRID:SCR_006381) Copy   

•   Source: SciCrunch Registry

https://github.com/ding-lab/msisensor

A C++ software program for automatically detecting somatic and germline variants at microsatellite regions. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples.

Proper citation: MSIsensor (RRID:SCR_006418) Copy   

•   Source: SciCrunch Registry

https://www.ctsacentral.org/editor/index.php?wg=ps625

Data management tool designed to support multicenter research studies including key components needed in a full-featured research data management application. It is web based and builds on mysql, xml, and tomcat components. Key features include: * Support for complex, highly customized case report forms (XML based configuration) * Security and access at the site, user, and form levels * User management * Management of multiple studies from a single instance * CDISC Operational Data Model (ODM) data extraction for input to analysis software * Longitudinal data collection They are working on major revisions to improve performance and add important new features. Version 2 should be available by mid-2013. They are making this version available now so that other centers with multisite study and/or complex form needs can leverage CDART for their needs. CDART will have a higher support requirement than REDCap and is not intended to replace REDCap for single site studies. Files are provided to assist in setting up an instance of CDART.

Proper citation: CDART (RRID:SCR_006378) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/socrates/

Software for detecting genomic rearrangements in tumors that utilizes only split-read data. It features single nucleotide resolution, high sensitivity, and high specificity in simulated data. It takes advantage of parallelism for efficient use of resources.

Proper citation: Socrates (RRID:SCR_006411) Copy   

•   Source: SciCrunch Registry

https://ambystoma.uky.edu/genetic-stock-center/

Maintains breeding colony of Mexican axolotls (Ambystoma mexicanum) that distributes axolotl embryos, larvae, and adults to laboratories and classrooms throughout the United States and abroad. Their mission is to serve biology research programs and educators by providing experimental material and expertise and by encouraging and facilitating the exchange of information and ideas.

Proper citation: Ambystoma Genetic Stock Center (RRID:SCR_006372) Copy   

•   Source: SciCrunch Registry

http://irvinginstitute.columbia.edu/cusp/cgi-bin/ww2ui.cgi/

Web-based, open access scientific networking system providing one-stop shopping for investigators seeking collaborators at Columbia University Medical Center in New York City. Contact information, grants, and publications are integrated to facilitate searches by topic or person.

Proper citation: CUSP (RRID:SCR_006373) Copy   

•   Source: SciCrunch Registry

https://www.unipd.it/

Italian university located in city of Padua, region of Veneto, northern Italy. University of Padua was founded in 1222 by group of students and teachers from Bologna. Padua is the second oldest university in Italy.

Proper citation: University of Padua; Padua; Italy (RRID:SCR_006374) Copy   

•   Source: SciCrunch Registry

http://www.flycircuit.tw/

FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain.

Proper citation: Flycircuit (RRID:SCR_006375) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.oxfordjournals.org/content/early/2014/01/02/bioinformatics.btt759.abstract?sid=e62f3c2b-26dc-428b-ba24-99e92a277d77

Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.

Proper citation: AbsCN-seq (RRID:SCR_006409) Copy   

•   Source: SciCrunch Registry

http://www.ontobee.org/

Web-based linked data server and browser specifically designed for ontology terms, it supports ontology visualization, query, and development. Ontobee provides a web interface for displaying the details and hierarchy of a specific ontology term. Meanwhile, Ontobee provides a RDF source code for the particular web page, which supports remote query of the ontology term and the Semantic Web. Ontobee provides an efficient and publicly available method to promote ontology sharing, interoperability, and data integration.

Proper citation: Ontobee (RRID:SCR_006321) Copy   

•   Source: SciCrunch Registry

http://www.hudsen.org/

Forum for researchers in human developmental biology and related fields to meet and establish links.

Proper citation: HUDSEN (RRID:SCR_006324) Copy   

•   Source: SciCrunch Registry

http://biotea.idiginfo.org/

Access to semantically processed full-text of the open-access subset of PubMed Central. The RDF model and resulting dataset make extensive reuse of existing ontologies and semantic enrichment services. The entire enriched data set is available for download or via REST services. A SPARQL query interface to 10,000 enriched articles is available. The entire collection of RDF documents is available for download as a collection of ZIP files. Each document consists of three RDF files serialized as XML.

Proper citation: Biotea (RRID:SCR_006285) Copy   

•   Source: SciCrunch Registry

http://folk.uio.no/einarro/Projects/KFM-index/

Provides a compact storage of de Bruijn subgraphs representing the k-subwords of a set of strings.

Proper citation: kFM-index (RRID:SCR_006435) Copy   

•   Source: SciCrunch Registry

http://www.whoi.edu/

The world''s largest private, nonprofit ocean research, engineering and education organization.

Proper citation: Woods Hole Oceanographic Institution; Massachusetts; USA (RRID:SCR_006315) Copy   

•   Source: SciCrunch Registry

http://w3.cns.org/university/nsimages/index2.asp

Data set of almost 2,000 neurosurgical images using a variety of search options.

Proper citation: Congress of Neurological Surgeons Online Image Database (RRID:SCR_006310) Copy   

•   Source: SciCrunch Registry

http://biocreative.sourceforge.net/

Community-wide effort (Challenge) for evaluating text mining and information extraction systems applied to the biological domain. It is focused on the comparison of methods and the community assessment of scientific progress, rather than on the purely competitive aspects. There is a considerable difficulty in constructing suitable gold standard data for training and testing new information extraction systems which handle life science literature. Thus the data sets derived from the BioCreAtIvE challenge - because they have been examined by biological database curators and domain experts - serve as useful resources for the development of new applications as well as helping to improve existing ones. Two main issues are addressed at BioCreAtIvE, both concerned with the extraction of biologically relevant and useful information from the literature. The first one is concerned with the detection of biologically significant entities (names) such as gene and protein names and their association to existing database entries. The second one is concerned with the detection of entity-fact associations (e.g. protein - functional term associations ).

Proper citation: BioCreative (RRID:SCR_006311) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/functionalconnectivitytoolbox/

MATLAB toolbox for performing functional connectivity analyses includes many of the most commonly-used approaches researchers have utilized to date for the identification of condition-dependent functional interactions between fMRI time-series obtained from two or more brain regions. The approaches are either bivariate or multivariate methods defined in time or frequency domains that emphasize distinct features of relationships among the time-series.

Proper citation: Functional Connectivity Toolbox (RRID:SCR_006394) Copy   

•   Source: SciCrunch Registry

http://antibodyregistry.org/

Public registry of antibodies with unique identifiers for commercial and non-commercial antibody reagents to give researchers a way to universally identify antibodies used in publications. The registry contains antibody product information organized according to genes, species, reagent types (antibodies, recombinant proteins, ELISA, siRNA, cDNA clones). Data is provided in many formats so that authors of biological papers, text mining tools and funding agencies can quickly and accurately identify the antibody reagents they and their colleagues used. The Antibody Registry allows any user to submit a new antibody or set of antibodies to the registry via a web form, or via a spreadsheet upload.

Proper citation: Antibody Registry (RRID:SCR_006397) Copy   

•   Source: SciCrunch Registry