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http://cytoscape.org

Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Proper citation: Cytoscape (RRID:SCR_003032) 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://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

http://www.pharmabase.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2015. Open content cheminformatics database linking physiology with pharmacology, it targets the action and use of pharmacological compounds in modifying protein function, while revealing molecular relationships and linking out to related databases and sites. Pharmabase has been developed as a research tool, a resource for students, and an ongoing interactive forum on the use of pharmacological compounds in cellular research. It has several navigational routes, including a graphics browser (shows graphics of cell types and pathways) and membrane transport, which also illustrates the diversity of mechanisms that are covered. Users have access to detailed compound records with interactive features, and a form to send comments to the editor. Investigators are encouraged to alert the editors to mistakes, omissions or new compound information available from their reading and research.

Proper citation: Pharmabase - an open content cheminformatics resource linking physiology with pharmacology (RRID:SCR_002462) Copy   

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

Workflow environment bringing together heterogenous, online biological image resources, a user's image data and biological atlases in a concise, unified and intuitive workspace. The MBAT viewer displays multiple images on a single virtual canvas allowing easy side-by-side comparisons and image compositing. MBAT is written in Java so it is platform independent and is highly extensible through it's plugin architecture. MBAT integrates three distinct workspaces for online search, image alignment (registration) and image display: * Search Workspace: able to submit a query to multiple databases simultaneously and online literature searches. * Registration Workspace: performs 2D landmark based registration. * Viewer Workspace: displays & composites images and image volumes using high performance graphics hardware. * Atlas Viewer: allows navigation and interrogation of volumetric atlases. * Hierarchy Editor: create logical groupings of atlas labels.

Proper citation: Mouse BIRN Atlasing Toolkit (RRID:SCR_002814) Copy   

•   Source: SciCrunch Registry

http://www.umc.edu/Administration/Centers_and_Institutes/Center_for_Psychiatric_Neuroscience/Core_Research_Resources.aspx

Core facility that provides access to psychiatrically characterized post-mortem brain specimens, state-of-the-art equipment, cutting-edge technologies and the technical advice of highly trained faculty members who serve as Core Directors. The sophisticated imaging systems and biotechnologically advanced molecular core resources are provided on a shared-use basis to CPN and UMMC researchers. The CPN Research Resources Cores include the Human Brain Collection Core, Animal Core, Imaging Core, Molecular Biology Core, and Information Technologies Core.

Proper citation: UMMC Center for Psychiatric Neuroscience Labs and Facilities (RRID:SCR_002688) Copy   

•   Source: SciCrunch Registry

http://www.wanprc.org/

Center that aims to provide an environment to support biomedical research directed towards human health issues and nonhuman primate health and biology. To meet this mission, the WaNPRC supports biomedical research activities, professional research staff, specifically bred and maintained nonhuman primate colonies, and dedicated facilities and equipment required for nonhuman primate research protocols.

Proper citation: Washington National Primate Research Center (RRID:SCR_002761) Copy   

•   Source: SciCrunch Registry

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

A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes. The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer. A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is especially important when viewing cryotome, histological or stained data-sets which may reach 1GB (109 bytes) in size. The user could overlay several pre-registered volumes, change intensity colors and ranges and the inter-volume opacities to visually inspect similarities and differences between the different subjects/modalities. Several image-processing aids provide histogram plotting, image-smoothing, etc. Specific Features: * Region description DataBase * Moleculo-genetic database * Brain anatomical data viewer * BrainMapper tool * Surface (LightWave objects/scenes) and Volume rendering tools * Interactive Contour Drawing tool Implementation Issues: * Applet vs. Application - the software is available as both an applet and a standalone application. The former could be used to browse data from within the LONI database, however, it imposes restrictions on file-size, Internet connection and network-bandwidth and client/server file access. The later requires a local install and configuration of the LONI_Viz software * Extendable object-oriented code (Java), computer architecture independent * Complete online software documentation is available at http://www.loni.ucla.edu/LONI_Viz and a Java-Class documentation is available at http://www.loni.ucla.edu/~dinov/LONI_Vis.dir/doc/LONI_Viz_Java_Docs.html

Proper citation: LONI Visualization Tool (RRID:SCR_000765) Copy   

•   Source: SciCrunch Registry

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

A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely.

Proper citation: LONI Pipeline Processing Environment (RRID:SCR_001161) Copy   

•   Source: SciCrunch Registry

http://www.itk.org

Open source, cross platform library that provides developers with extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on proven, spatially oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

Proper citation: Insight Segmentation and Registration Toolkit (RRID:SCR_001149) Copy   

•   Source: SciCrunch Registry

https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view

Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences.

Proper citation: Skyline (RRID:SCR_014080) 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.primate.wisc.edu/

Research center aimed towards increasing understanding of basic primate biology and improving human health and quality of life. Its goals include helping discover treatments, preventative measures and cures for human disease; gathering knowledge of primate biology and ecosystems; providing resources to scientists world wide; and collecting and disseminating research to the larger scientific community and public.

Proper citation: Wisconsin National Primate Research Center (RRID:SCR_012987) Copy   

•   Source: SciCrunch Registry

http://biositemaps.ncbcs.org/rds/search.html

Resource Discovery System is a web-accessible and searchable inventory of biomedical research resources. Powered by the Resource Discovery System (RDS) that includes a standards-based informatics infrastructure * Biositemaps Information Model * Biomedical Resource Ontology Extensions * Web Services distributed web-accessible inventory framework * Biositemap Resource Editor * Resource Discovery System Source code and project documentation to be made available on an open-source basis. Contributing institutions: University of Pittsburgh, University of Michigan, Stanford University, Oregon Health & Science University, University of Texas Houston. Duke University, Emory University, University of California Davis, University of California San Diego, National Institutes of Health, Inventory Resources Working Group Members

Proper citation: Resource Discovery System (RRID:SCR_005554) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/home/recombinase

Curated data about all recombinase-containing transgenes and knock-ins developed in mice providing a comprehensive resource delineating known activity patterns and allows users to find relevant mouse resources for their studies.

Proper citation: Recombinase (cre) Activity (RRID:SCR_006585) Copy   

•   Source: SciCrunch Registry

https://open.med.harvard.edu/display/SHRINE/Community

Software providing a scalable query and aggregation mechanism that enables federated queries across many independently operated patient databases. This platform enables clinical researchers to solve the problem of identifying sufficient numbers of patients to include in their studies by querying across distributed hospital electronic medical record systems. Through the use of a federated network protocol, SHRINE allows investigators to see limited data about patients meeting their study criteria without compromising patient privacy. This software should greatly enable population-based research, assessment of potential clinical trials cohorts, and hypothesis formation for followup study by combining the EHR assets across the hospital system. In order to obtain the maximum number of cases representing the study population, it is useful to aggregate patient facts across as many sites as possible. Cutting across institutional boundaries necessitates that each hospital IRB remain in control, and that their local authority is recognized for each and every request for patient data. The independence, ownership, and legal responsibilities of hospitals predetermines a decentralized technical approach, such as a federated query over locally controlled databases. The application comes with the SHRINE Core Ontology but it can be used with any ontology, even one that is disease specific. The Core Ontology is designed to enable the widest range of studies possible using facts gathered in the EMR during routine patient care. SHRINE allows multiple ontologies to be used for different research purposes on the same installed systems.

Proper citation: SHRINE (RRID:SCR_006293) Copy   

•   Source: SciCrunch Registry

http://www.wakehealth.edu/Research/WFUPC/Cynomolgus-Breeding-Colony-Request-Form-Instructions.htm

The Wake Forest Cynomolgus Breeding Colony (CBC) is a colony of cynomolgus macaques (crab-eating macaques, Macaca fascicularis). The cynomolgus colony is designed to produce specific pathogen free (SPF) cynomolgus monkeys for use in biomedical research. The colony, supported by a grant from the NCRR, addresses the growing need for investigators to use in their protocols animals defined for the absence of specific diseases including CHV-1 (Herpes B), simian immunodeficiency virus, and simian retroviruses. An additional important characteristic of this colony is that, unlike many breeding colonies, the NHPs will be fed two defined diets. The first diet is a soy-free diet, not commercial monkey chow. The second diet has the same macronutrients but the protein source is from soy; similar in isoflavone content. A drawback of chow diets is that the exact nutritional product composition is unknown from lot to lot. However, they are always rich in soy bean meal, isoflavones and other constituents of soy bean meal that are known confounders of several types of research projects. All research using the cynomolgus colony must be reviewed and approved by the colony''s scientific board and the Wake Forest Animal Care and Use Committee (ACUC) before any work can be initiated. The scientific board meets regularly to assess the scientific value of each request and to determine whether or not animals/samples/data can be made available. This includes all requests for: # The purchase of animals for use outside the colony # The use of animals within the colony for the collection of blood/tissue samples, behavioral observations or other kinds of testing # The use of the CBC sample/tissue repository # The use of the CBC data repository

Proper citation: Wake Forest Cynomolgus Breeding Colony (RRID:SCR_006605) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/lapdftext/

Software that facilitates accurate extraction of text from PDF files of research articles for use in text mining applications. It is intended for both scientists and natural language processing (NLP) engineers interested in getting access to text within specific sections of research articles. The system extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles. The current version of LA-PDFText is a baseline system that extracts text using a three-stage process: * identification of blocks of contiguous text * classification of these blocks into rhetorical categories * extraction of the text from blocks grouped section-wise.

Proper citation: lapdftext (RRID:SCR_006167) Copy   

•   Source: SciCrunch Registry

http://superfly.ucsd.edu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 23, 2013. Homophila utilizes the sequence information of human disease genes from the NCBI OMIM (Online Mendelian Inheritance in Man) database in order to determine if sequence homologs of these genes exist in the current Drosophila sequence database (FlyBase). Sequences are compared using NCBI's BLAST program. The database is updated weekly and can be searched by human disease, gene name, OMIM number, title, subtitle and/or allelic variant descriptions.

Proper citation: Homophila (RRID:SCR_007717) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.ucla.edu/ASAP2

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. An expanded version of the Alternative Splicing Annotation Project (ASAP) database with a new interface and integration of comparative features using UCSC BLASTZ multiple alignments. It supports 9 vertebrate species, 4 insects, and nematodes, and provides with extensive alternative splicing analysis and their splicing variants. As for human alternative splicing data, newly added EST libraries were classified and included into previous tissue and cancer classification, and lists of tissue and cancer (normal) specific alternatively spliced genes are re-calculated and updated. They have created a novel orthologous exon and intron databases and their splice variants based on multiple alignment among several species. These orthologous exon and intron database can give more comprehensive homologous gene information than protein similarity based method. Furthermore, splice junction and exon identity among species can be valuable resources to elucidate species-specific genes. ASAP II database can be easily integrated with pygr (unpublished, the Python Graph Database Framework for Bioinformatics) and its powerful features such as graph query, multi-genome alignment query and etc. ASAP II can be searched by several different criteria such as gene symbol, gene name and ID (UniGene, GenBank etc.). The web interface provides 7 different kinds of views: (I) user query, UniGene annotation, orthologous genes and genome browsers; (II) genome alignment; (III) exons and orthologous exons; (IV) introns and orthologous introns; (V) alternative splicing; (IV) isoform and protein sequences; (VII) tissue and cancer vs. normal specificity. ASAP II shows genome alignments of isoforms, exons, and introns in UCSC-like genome browser. All alternative splicing relationships with supporting evidence information, types of alternative splicing patterns, and inclusion rate for skipped exons are listed in separate tables. Users can also search human data for tissue- and cancer-specific splice forms at the bottom of the gene summary page. The p-values for tissue-specificity as log-odds (LOD) scores, and highlight the results for LOD >= 3 and at least 3 EST sequences are all also reported.

Proper citation: Alternative Splicing Annotation Project II Database (RRID:SCR_000322) Copy   

•   Source: SciCrunch Registry