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http://www.isi.edu/projects/bioscholar/overview

Knowledge management and engineering system software for experimental biomedical scientists permitting a single scientific worker (at the level of a graduate student or postdoctoral worker) to design, construct and manage a shared knowledge repository for a research group derived on a local store of PDF files. Usability is especially emphasized within a laboratory so that this software could provide support to experimental scientists attempting to construct a personalized representation of their own knowledge on a medium scale. The BioScholar system uses a graphical interface to create experimental designs based on the experimental variables in the system. The design is then analyzed to construct a tabular input form based on the data flow. They call this methodology "Knowledge Engineering from Experimental Design" or "KEfED". The approach is domain-independent but domain-specific modules reasoning can be constructed to generate interpretations from the observational data represented in the KEfED model. The application is available for download as platform-specific installers including Linux, Unix, Mac OS, and Windows. The installer will install an application that will run the BioScholar server. This server uses Jetty as its integrated web server.

Proper citation: Bioscholar (RRID:SCR_001380) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/DiD

Software application for removing patient-identifying information from medical image files. Removing this information is often necessary for enabling investigators to share image files in a HIPAA compliant manner.

Proper citation: LONI De-identification Debablet (RRID:SCR_009593) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/cibc/software/231-biomesh3d.html

A free, easy to use program for generating quality meshes for use in biological simulations. It is currently integrated with SCIRun and uses the SCIRun system to visualize the intermediate results. The BioMesh3D program uses a particle system to distribute nodes on the separating surfaces that separate the different materials and then uses the TetGen software package to generate a full tetrahedral mesh.

Proper citation: BioMesh3D (RRID:SCR_009534) Copy   

•   Source: SciCrunch Registry

http://researchiq.bmi.osumc.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented March 14, 2016. Research Integrative Query (ResearchIQ) tool, a semantically anchored resource discovery platform that facilitates semantic discovery of local and publicly available data through a single web portal designed for researchers in the biomedical informatics domain within The Ohio State University.

Proper citation: ResearchIQ (RRID:SCR_014304) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/X2K/

Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures.

Proper citation: eXpression2Kinases (RRID:SCR_016307) Copy   

•   Source: SciCrunch Registry

http://www.birncommunity.org/collaborators/function-birn/

The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source.

Proper citation: Function BIRN (RRID:SCR_007291) Copy   

•   Source: SciCrunch Registry

http://www.proteometools.org/index.php?id=home

Project for building molecular and digital tools from human proteome to facilitate biomedical research, drug discovery, personalized medicine and life science research.

Proper citation: ProteomeTools (RRID:SCR_018535) Copy   

•   Source: SciCrunch Registry

http://www.i2b2cictr.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A two year Clinical and Translational Science Award (CTSA) supplement that set up a SHRINE (Shared Health Research Informatics NEtwork) network to create an information exchange environment that successfully shared 4.2M deidentified patient records. The network successfully linked i2b2 sites at UW, UCSF, UC Davis and Harvard Catalyst. Recombinant Data Corporation was actively involved in this implementation. This is a collaborative information exchange pilot project to adapt and extend data discovery tools and processes to enhance research design and retrospective data study capabilities for clinical translational investigators. The novel approach of this project will be to incrementally build a common technical, semantic and appropriately secure and governed distributed system in close partnership with active researchers at three large and geographically distributed academic medical centers. This collaboration will extend the Informatics for Integrating Biology and the Bedside (i2b2) software architecture developed by the Harvard based National Center for Biomedical Computing (NCBC) to support multi-institution data query capabilities. The anticipated outcome of this two-year project is to make high-level anonymized descriptive characteristics of population-level data discoverable for research design, hypothesis generation and retrospective data studies.

Proper citation: i2b2 Cross-Institutional Clinical Translational Research project (RRID:SCR_003367) Copy   

•   Source: SciCrunch Registry

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

A filter which allows the Laplace-Beltrami operator to determine surface harmonics in terms of PointData at each vertex. It determines the requested N most significant harmonics of a surface.

Proper citation: Laplace Beltrami Filter on QuadEdge Meshes (RRID:SCR_014133) Copy   

•   Source: SciCrunch Registry

http://www.geneatlas.org/gene/main.jsp

This website allows visitors to search for genes of interest based on their spatial expression patterns in the Postnatal Day 7 mouse brain. Geneatlas provides two searching tools: A graphical interface for customized spatial queries; A textual interface for querying annotated structures. Geneatlas is the product of a collaboration between researchers at Baylor College of Medicine, Rice University, and University of Houston.

Proper citation: Gene Atlas (RRID:SCR_008089) Copy   

•   Source: SciCrunch Registry

http://brainmap.wisc.edu/monkey.html

NO LONGER AVAILABLE. Documented on September 17, 2019. A set of multi-subject atlas templates to facilitate functional and structural imaging studies of the rhesus macaque. These atlases enable alignment of individual scans to improve localization and statistical power of the results, and allow comparison of results between studies and institutions. This population-average MRI-based atlas collection can be used with common brain mapping packages such as SPM or FSL.

Proper citation: Rhesus Macaque Atlases for Functional and Structural Imaging Studies (RRID:SCR_008650) Copy   

•   Source: SciCrunch Registry

http://mouseatlas.caltech.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 on October, 01, 2019.
3D digital atlas of normal mouse development constructed from magnetic resonance image data. The download is a zipped file containing the six atlases Theiler Stages (ts) 13, 21,23, 24, 25 and 26 and MRI data for an unlabeled ts19 embryo. To view the atlases, download and install MBAT from: http://mbat.loni.ucla.edu Specimens were prepared in aqueous, isotonic solutions to avoid tissue shrinkage. Limited specimen handling minimized physical perturbation of the embryos to ensure accurate geometric representations of developing mouse anatomy. Currently, the atlas contains orthogonal sections through MRI volumes, three stages of embryos that have annotated anatomy, photographs of several stages of development, lineage trees for annotated embryos and a gallery of images and movies derived from the annotations. Anatomical annotations can be viewed by selecting a transverse section and selecting a pixel on the displayed slice.

Proper citation: 3D MRI Atlas of Mouse Development (RRID:SCR_008090) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/validate29/

Atlas was created from MRI scans of squirrel monkey brains. The atlas is currently comprised of multiple anatomical templates, diffusion MRI templates, and ex vivo templates. In addition, the templates are combined with histologically defined cortical labels, and diffusion tractography defined white matter labels.

Proper citation: VALiDATe29 Squirrel Monkey Brain Atlas (RRID:SCR_015542) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/Eagle/

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

Proper citation: Eagle (RRID:SCR_015991) Copy   

•   Source: SciCrunch Registry

http://www.yerkes.emory.edu/

Center for advancing scientific understanding and improving the health and well-being of humans and nonhuman primates. The Center conducts research in microbiology and immunology, neurologic diseases, neuropharmacology, behavioral, cognitive and developmental neuroscience, and psychiatric disorders.

Proper citation: Yerkes National Primate Research Center (RRID:SCR_001914) Copy   

•   Source: SciCrunch Registry

https://github.com/hms-dbmi/spp

R analysis and processing package for Illumina platform Chip-Seq data.

Proper citation: SPP (RRID:SCR_001790) Copy   

•   Source: SciCrunch Registry

http://bio3d.colorado.edu/imod

A free, cross-platform set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD 4.1.8 Is Now Available for Linux, Windows, and Mac OS X

Proper citation: IMOD (RRID:SCR_003297) Copy   

•   Source: SciCrunch Registry

https://www.cgl.ucsf.edu/chimera/

Software tool for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials.

Proper citation: UCSF Chimera (RRID:SCR_004097) Copy   

•   Source: SciCrunch Registry

http://bix.ucsd.edu/projects/singlecell/

Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria.

Proper citation: Velvet-SC (RRID:SCR_004377) Copy   

•   Source: SciCrunch Registry

http://vivoweb.org/

Open source semantic web application that enables the discovery of research and scholarship across disciplines at a particular institution and across institutions by creating a semantic cloud of information that can be searched and browsed. Participants include institutions with local installations of VIVO or those with research discovery and profiling applications that can provide semantic web-compliant data. The information accessible through the national network''''s search and browse capability will therefore reside and be controlled locally within institutional VIVOs or other semantic web applications. The VIVO ontology provides a set of types (classes) and relationships (properties) to represent researchers and the full context of their experience, outputs, interests, accomplishments, and associated institutions. https://wiki.duraspace.org/display/VIVO/VIVO-ISF+Ontology VIVO is populated with detailed profiles of faculty and researchers including information such as publications, teaching, service, and professional affiliations. It also supports browsing and a search function which returns faceted results for rapid retrieval of desired information. The rich semantically structured data in VIVO support and facilitate research discovery. Examples of applications that consume these rich data include: visualizations, enhanced multi-site search through VIVO Search, and applications such as VIVO Searchlight, a browser bookmarklet which uses text content of any webpage to search for relevant VIVO profiles, and the Inter-Institutional Collaboration Explorer, an application which allows visualization of collaborative institutional partners, among others. Institutions are free to participate in the national network by installing and using the application. The application provides linked data via RDF data making users a part of the semantic web! or any other application that provides linked data can be used. Users can also get involved with developing applications that provide enhanced search, new collaboration capabilities, grouping, finding and mapping scientists and their work.

Proper citation: VIVO (RRID:SCR_005246) Copy   

•   Source: SciCrunch Registry