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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Software toolkit for the visualization, segmentation, registration and analysis of multidimensional biomedical imaging data. With Analyze, both anatomic structure and associated function can be studied and fused together for synergistic display and measurement of important structure-to-function relationships.
Proper citation: Analyze Software System (RRID:SCR_005988) Copy
http://www.nitrc.org/projects/arctic
An end-to-end application allowing individual regional analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line. * Operating System: MacOS, Linux * Programming Language: C++ * Supported Data Format: ANALYZE, Nrrd, Other Format * build requires: Insight Toolkit
Proper citation: ARCTIC (RRID:SCR_005989) Copy
http://www.bioconductor.org/packages/2.14/bioc/html/h5vc.html
Software package that contains functions to interact with tally data from Next-Generation Sequencing (NGS) experiments that is stored in HDF5 files.
Proper citation: h5vc (RRID:SCR_006039) Copy
http://compbio.charite.de/phenexplorer/
The PhenExplorer allows you to browse the Human Phenotype Ontology (HPO) in different ways, using the tabs ''''by features'''', ''''by disease'''', ''''by ontology'''' or ''''by genes''''. Clicking on a particular phenotypic feature (HPO-term) you can get a list of disease entries that are linked to it (i.e. diseases that are annotated with this HPO-term). You can also visualize this term in the context of the ontological structure. Finally, a lists of genes can be displayed, that are known to cause (when mutated) the linked diseases mentioned above. For each disease you can get the list of linked HPO-terms and genes. You can also search for specific genes and explore to which HPO-terms and diseases they are linked.
Proper citation: Phenexplorer (RRID:SCR_006156) Copy
http://hannonlab.cshl.edu/index.html
The Hannon laboratory comprises a broad spectrum of programs in small RNA biology, mammalian genetics and genomics. We study RNAi and related pathways in a wide variety of organisms to extract common themes that define both the mechanisms by which small RNAs act and the biological processes which they impact. Currently, we focus on microRNAs, endogenous siRNAs and piRNAs and their roles in gene regulation, cancer biology, stem cell biology and in defense of the genome against transposons. In collaboration with Steve Elledge (Harvard) and Scott Lowe (CSHL), we develop genome-wide shRNA tools for RNAi-based genetics in mammalian cells, and we are now producing similar collections of artificial microRNAs for Arabidopsis with Detlef Weigel (MPI), Dick McCombie (CSHL) and Rob Martienssen (CSHL) as part of the 2010 project (see 2010.cshl.edu). Our genomic efforts include the application of RNAi-based genetic screens to cancer biology and stem cells. We also make heavy use of next generation sequencing methodologies for probing small RNA populations, in part as a member of the ENCODE consortium (with Tom Gingeras, CSHL). Finally, we develop (with Dick McCombie) and apply focal re-sequencing methods for identifying disease relevant mutations, for probing the epigenetic landscape and for the study of human evolution.
Proper citation: CSHL - Hannon Lab (RRID:SCR_005982) Copy
https://bitbucket.org/cob87icW6z/cafe/wiki/Home
R software package for the detection of gross chromosomal abnormalities from gene expression microarray data.
Proper citation: CAFE (RRID:SCR_005983) Copy
http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl
Ontology that describes the different types of associations between a gene and a disease. It was developed to integrate information from different databases that contain gene-disease associations such as UniProt, CTD, Orphanet, the GWAS Catalog, GAD, MGD, RGD, and LHGDN.
Proper citation: Gene-Disease Association Type Ontology (RRID:SCR_006159) Copy
An open-membership International community to promote mechanisms that standardize the description of genomes and the exchange and integration of genomic data. Community-driven standards have the best chance of success if developed within the auspices of international working groups. Participants in the GSC include biologists, computer scientists, those building genomic databases and conducting large-scale comparative genomic analyses, and those with experience of building community-based standards. The mission of the GSC is to work with the wider community towards: * the implementation of new genomic standards * methods of capturing and exchanging metadata * harmonization of metadata collection and analysis efforts across the wider genomics community
Proper citation: Genomic Standards Consortium (RRID:SCR_006273) Copy
University in Norway, located in Oslo. Its faculties include Lutheran Theology, Law, Medicine, Humanities, Mathematics, natural sciences, social sciences, Dentistry, and Education.
Proper citation: University of Oslo; Oslo; Norway (RRID:SCR_006275) Copy
Collegiate university based in Dunedin, Otago, New Zealand.
Proper citation: University of Otago; Dunedin; New Zealand (RRID:SCR_006276) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 13, 2012. Cell Press continues to evolve the way scientific information is conveyed, and has made Article of the Future available for all review article formats, in addition to the research article format launched in January. With this latest release, all articles are also now more customizable, giving users added flexibility and control over how they read research and reviews. Readers can now: * Adjust the widths of the text and figure panels using a horizontal slider, allowing text and figures to be viewed side-by-side in a way that best suits the readers' needs. (Available in the Summary and Main Text tabs for reviews, and in the Results tab for research articles) * Easily identify proteins and small molecules and access additional information about these compounds with Reflect, winner of the 2009 Elsevier Grand Challenge * Reveal greater detail in figures with improved zoom functionality * Search across all tabs within an article * View the article in the standard, linear format with one click
Proper citation: Article of the Future (RRID:SCR_006270) Copy
http://www.australianphenomics.org.au/
Mouse models for the study of human and animal disease for Australian and international researchers. It has reduced the cost to researchers of accessing mouse models of disease, and provides equipment and expertise to undertake characterization and further research of these models. The APN brought together mouse production, strain storage and pathology capabilities, later extending the core services of the network, and include new services (RNAi and genomics services). Twelve Australian facilities and institutions currently constitute the APN. The APN partners contribute their expertise and infrastructure for the production of mouse models, as well as providing cryopreservation and pathology services. * Walter and Eliza Hall Institute of Medical Research * Monash University * Queensland Institute of Medical Research * Animal Resources Centre * Institute of Medical and Veterinary Science * University of Melbourne * Institute of Molecular Bioscience * Menzies Research Institute * Peter MacCallum Cancer Centre * Australian National University * Western Australian Institute of Medical Research * Centenary Institute In addition, the APN is working with the Atlas of Living Australia to develop a framework for Australia''''s e-science infrastructure to improve the capture, annotation and dissemination of research data. The APN''''s core expertise and infrastructure is also extended by key national and international partnerships. These include the Garvan Institute, the National Institutes of Health (United States), the Wellcome Trust (United Kingdom), and the University of Manitoba (Canada). Services * ES Cell to Mouse: Create a mouse model from embryonic stem cells * RNAi: Screen full genomes to identify novel gene targets * ENU Mutagenesis - Produce chemically-induced mouse models * Pathology - Investigate mouse models using clinical and histopathology * Genomics - Further mouse mutant identification via new discovery pipeline * NHMRC Australian PhenomeBank - a non-profit repository of mouse strains used in Medical Research.
Proper citation: Australian Phenomics Network (RRID:SCR_006150) Copy
http://purl.bioontology.org/ontology/VO
A biomedical ontology in the vaccine domain
Proper citation: Vaccine Ontology (RRID:SCR_006271) Copy
http://www.nitrc.org/projects/toads-cruise/
A collection of software plug-ins developed for the automatic segmentation of magnetic resonance brain images. The tools include multiple published algorithms developed at Johns Hopkins University. The SPECTRE algorithm performs brain extraction. The TOADS algorithm generates a topology-preserving tissue classification into cortical, subcortical, and cerebellar structures. The CRUISE algorithm produces inner, central, and outer cortical surfaces suitable for computing thickness and other geometric measures. Tools are also included for performing gyral labeling, lesion segmentation, thickness computation, surface visualization, and surface file conversion. All tools are released as plug-ins for the MIPAV software package and were developed using the Java Image Science Toolkit (both available at NITRC: http://nitrc.org). They are therefore cross-platform and compatible with a wide variety of file formats.
Proper citation: TOADS-CRUISE Brain Segmentation Tools (RRID:SCR_005977) Copy
http://mousetracker.jbfreeman.net
A free, user-friendly software package that allows researchers to record and analyze hand movements traveling toward potential responses on the screen (via the x, y coordinates of the computer mouse). By looking at the dynamics of how participants' hand movements settle into a response alternative--and how they may be partially pulled toward other alternatives--researchers glean valuable information about real-time cognitive processing. It's like opening up a single reaction time into a continuous stream of rich cognitive output. MouseTracker has impressive temporal resolution, comparable to eye-tracking and event-related brain potential (ERP) measures. Experiments can incorporate images, letter strings, sounds, and videos. Once recorded, mouse trajectories can be visualized, averaged, and explored, and measures of attraction/curvature, complexity, velocity, and acceleration can be computed. Precise characterizations of mouse trajectories' temporal and spatial dynamics are available, and these can shed light on a variety of important empirical questions across psychology, cognitive science, and beyond.
Proper citation: MouseTracker (RRID:SCR_005979) Copy
http://researchdata.4tu.nl/en/home/
Multidisciplinary data repository for a consortium of universities in the Netherlands housing over datasets with a focus on scientific and technical data. Most data were produced by Dutch researchers including datasets from doctoral research. Users can deposit up to 1G by completing an upload form. Collection development foci include applied sciences, biomedical technology, earth sciences, and technology and construction. 4TU.Datacentrum is a collaboration of the libraries of the three leading technical universities - Delft University of Technology, Eindhoven University of Technology and the University of Twente.
Proper citation: 4TU.Datacentrum (RRID:SCR_006295) Copy
http://www.megasoftware.net/mega-md/mega-md.php
Software to forecast the deleteriousness of non-synonymous single nucleotide variants (nsSNVs) using multiple methods and explore them in the context of the variability permitted in the long-term evolution of the affected positions. A web version (MEGA-MDW) is also available.
Proper citation: MEGA-MD (RRID:SCR_006403) Copy
http://www.uni-koeln.de/med-fak/cgars/
Software package to dissect random from non-random patterns in copy number data and thereby to assess significantly enriched somatic copy number aberrations (SCNA) across a set of tumor specimens or cell lines.
Proper citation: CGARS (RRID:SCR_006404) Copy
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