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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.
http://www.broadinstitute.org/gsea/
Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.
Proper citation: Gene Set Enrichment Analysis (RRID:SCR_003199) Copy
Non profit bioscience research organization in Seattle, Washington dedicated to accelerating research globally and sharing that data within the science community. Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, and The Paul G. Allen Frontiers Group are four divisions of this Institute with commitment to open science model within its research institutes.
Proper citation: Allen Institute (RRID:SCR_005435) Copy
International, curated, digital repository that makes the data underlying scientific publications discoverable, freely reusable, and citable. Particularly data for which no specialized repository exists. Provides the infrastructure for, and promotes the re-use of, data underlying the scholarly literature. Governed by a nonprofit membership organization. Membership is open to any stakeholder organization, including but not limited to journals, scientific societies, publishers, research institutions, libraries, and funding organizations. Most data are associated with peer-reviewed articles, although data associated with non-peer reviewed publications from reputable academic sources, such as dissertations, are also accepted. Used to validate published findings, explore new analysis methodologies, repurpose data for research questions unanticipated by the original authors, and perform synthetic studies.UC system is member organization of Dryad general subject data repository.
Proper citation: Dryad Digital Repository (RRID:SCR_005910) Copy
http://ucsd.researchaccelerator.org/
Software platform that allows researchers to easily collaborate on research and share reagents, antibodies, cell lines and more. It is designed to increase scientific collaboration across disciplines and geographical boundaries. Among the institutions now using the platform include Yale University, U of Pennsylvania, U of Chicago, Washington U, Cambridge University, University College London. The platform is licensed to select institutions. ResearchAccelerator.org allows researchers to form targeted, data driven collaborations. Researchers can search for data based on gene, disease and pathway, and they can post data which would otherwise be orphaned. The resulting collaborations, which are likely to be transdisciplinary, can greatly amplify impact and research productivity.
Proper citation: Research Accelerator (RRID:SCR_006051) Copy
http://www.nitrc.org/projects/itk-snap/
Open source interactive software application for three dimentional medical images, manual delineation of anatomical regions of interest, and performing automatic image segmentation. Used for delineating anatomical structures and regions in MRI, CT and other 3D biomedical imaging data.WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons).
Proper citation: ITK-SNAP (RRID:SCR_002010) Copy
https://datashare.nida.nih.gov
Website which allows data from completed clinical trials to be distributed to investigators and public. Researchers can download de-identified data from completed NIDA clinical trial studies to conduct analyses that improve quality of drug abuse treatment. Incorporates data from Division of Therapeutics and Medical Consequences and Center for Clinical Trials Network.
Proper citation: NIDA Data Share (RRID:SCR_002002) Copy
https://scicrunch.org/resolver/SCR_002250
THIS RESOURCE IS NO LONGER IN SERVICE. Documented Jul 19, 2024. Metadatabase manually curated that provides web accessible tools related to genomics, transcriptomics, proteomics and metabolomics. Used as informative directory for multi-omic data analysis.
Proper citation: OMICtools (RRID:SCR_002250) Copy
Independent international facilitator catalyzing and coordinating global development of neuroinformatics aiming to advance data reuse and reproducibility in global brain research. Integrates and analyzes diverse data across scales, techniques, and species to understand brain function and positively impact the health and well being of society.
Proper citation: International Neuroinformatics Coordinating Facility (RRID:SCR_002282) Copy
Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
Proper citation: Ensembl (RRID:SCR_002344) Copy
http://brainproducts.com/productdetails.php?id=17
Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more.
Proper citation: BrainVision Analyzer (RRID:SCR_002356) Copy
https://t1dexchange.org/pages/
Provides access to resources T1D researchers need to conduct clinical studies. Data sets from their clinic registry is openly available, as are new study results. They also offer use of T1D Discovery Tool, which allows users to search different fields from registry data, and T1D Exchange Biobank, which offers specimen types such as serum, plasma, white blood cells, DNA, and RNA.
Proper citation: T1D Exchange (RRID:SCR_014532) Copy
http://factominer.free.fr/index.html
Software R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables.
Proper citation: FactoMineR (RRID:SCR_014602) Copy
http://www.heka.com/downloads/downloads_main.html#down_tida
A software which is used to acquire physiological data from the HEKA Patch Clamp Amplifiers and HEKA interfaces.
Proper citation: TIDA (RRID:SCR_014582) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 11132025. Facility that provides database development and management and bioinformatic network building services by utilizing on-site hardware and software. Three members of the facility are available to assist researchers with advanced bioinformatics and biostatistics analysis to help put data into biological context across various disease areas to create testable hypotheses and understand biology of the process. The bulk of support includes connecting functional genomic data with pathways and networks, connecting gene/protein expression and disease state and consultations on statistical aspects of the research with the team statistician.
Proper citation: Sanford Burnham Prebys Medical Discovery Institute Bioinformatics and Data Management Facility (RRID:SCR_014868) Copy
Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification.
Proper citation: MetaboAnalyst (RRID:SCR_015539) Copy
http://www.ime.fraunhofer.de/en.html
Provides assistance with consulting on experimental design, training on bioinformatics tools and databases, data quality assessment, data processing, data visualization, data interpretation, data mining of published datasets, and assistance with preparation of manuscripts and grant proposals.
Proper citation: Mainz Institute of Molecular Biology Bioinformatics Core Facility (RRID:SCR_011244) Copy
Non profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request.
Proper citation: Wellcome Trust Sanger Institute; Hinxton; United Kingdom (RRID:SCR_011784) Copy
Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.
Proper citation: ImageJ (RRID:SCR_003070) Copy
http://www.type2diabetesgenetics.org/
Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease.
Proper citation: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) (RRID:SCR_003743) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse.
Proper citation: BioMart Project (RRID:SCR_002987) Copy
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