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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.
https://commonfund.nih.gov/hmp/
NIH Project to generate resources to characterize the human microbiota and to analyze its role in human health and disease at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract using metagenomic and traditional approach to genomic DNA sequencing studies.HMP was supported by the Common Fund from 2007 to 2016.
Proper citation: Human Microbiome Project (RRID:SCR_012956) Copy
Platform for Secure Access to Research Data and E-Infrastructure based on European Standards for Health Case information. Used for secure processing of sensitive personal data in research in health and care sector.
Proper citation: Secure Access to Research Data and E-Infrastructure (RRID:SCR_017246) Copy
https://gitlab.com/KHanghoj/DamMet
Software tool as a full probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen.
Proper citation: DamMet (RRID:SCR_016959) Copy
Open source resources to execute stop signal task and analyze resulting data. Simulation code is provided, and can be used in planning stage for investigation of response inhibition and impuls control.
Proper citation: stop-signal task resources (RRID:SCR_017137) Copy
http://ophid.utoronto.ca/mirDIP/
microRNA data integration portal to find microRNAs that target a gene, or genes targeted by a microRNA, in Homo sapiens. Software to integrate prediction databases to elucidate accurate microRNA:target relationships. Used for human microRNA prediction studies.
Proper citation: mirDIP (RRID:SCR_016770) Copy
https://www.schrodinger.com/maestro
Software tool for all purpose molecular modeling environment. Maestro is the portal to all of Schrödinger's computational technology. Helps researchers organize and analyze data.
Proper citation: Maestro (RRID:SCR_016748) Copy
http://www.nitrc.org/projects/brainlife_io/
Platform for publishing reproducible code and datasets and providing access to national supercomputers, private clouds, and institutional high-performance computer systems to promote open software and data sharing to advance understanding of the human brain.
Proper citation: brainlife.io (RRID:SCR_016513) Copy
https://openknowledgemaps.org/
Software tool as an open source knowledge mapping software that increases the visibility of research findings for science and society. Visual interface to the world's scientific knowledge.
Proper citation: Open Knowledge Maps (RRID:SCR_016470) Copy
http://www.reproducibleimaging.org
Center to help neuroimaging researchers to find and share data in FAIR fashion, to describe their data and analysis workflows in replicable fashion, to manage their computational resource options so that outcomes of neuroimaging research are more reproducible.
Proper citation: ReproNim: A Center for Reproducible Neuroimaging Computation (RRID:SCR_016001) Copy
Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions.
Proper citation: Oufti (RRID:SCR_016244) Copy
Software as an open source informatics platform to facilitate the implementation and operation of distributed health data networks. Consists of a web-based portal for distributing requests and administering the network, and the DataMart Client. Designed by the Therapeutics Research and Infectious Disease Epidemiology (TIDE) group at the Department of Population Medicine (DPM) of the Harvard Pilgrim Health Care Institute (HPHCI) to enable creation, operation, and governance of distributed health data networks.
Proper citation: PopMedNet (RRID:SCR_016456) Copy
Software integrated platform used for obtaining 3D structural information from single particle cryo-EM data. Enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery.
Proper citation: cryoSPARC (RRID:SCR_016501) Copy
https://github.com/mcapuccini/mare
Software tool to leverage power of Docker and Spark to run and scale your serial tools in MapReduce fashion.
Proper citation: MaRe (RRID:SCR_018069) Copy
Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility.
Proper citation: Whole Tale (RRID:SCR_017537) Copy
Data analytics company that operates a collection of services: Web of Science (EndNote, InCites, Journal Citation Reports, Publons, Kopernio), Cortellis, Derwent, Derwent World Patents Index, CompuMark, MarkMonitor, Techstreet, Publons, EndNote, Kopernio, and ScholarOne. Deliver critical data, information, workflow solutions and deep domain expertise to innovators everywhere.
Proper citation: Clarivate Analytics (RRID:SCR_017657) Copy
Nonhuman Primate reference transcriptome resource consisting of deep sequencing complete transcriptomes (RNA-seq) from multiple NHP species.
Proper citation: Nonhuman Primate Reference Transcriptome Resource (RRID:SCR_017534) Copy
Portal provides list of genetic resources such as Brain Atlases and genomes for various species provided by National Institute of Drug Abuse.
Proper citation: Compilation of Genetics Resource Databases (RRID:SCR_017501) Copy
https://www.jax.org/research-and-faculty/resources/optogenetics-resource
Mouse lines expressing proteins that activate, inhibit or detect neuronal activity are available from The Jackson Laboratory Repository. Many of these strains have been generated by HHMI Janelia Farm GENIE Project or by Allen Institute for Brain Science.
Proper citation: Optogenetics Resource at JAX (RRID:SCR_017508) Copy
https://www.lungepigenome.org/
Project to provide data on genome and epigenome of human lung to facilitate research efforts of investigators studying diseases of lung including COVID-19.Collaboration among multiple groups at University of California including Center for Epigenomics, Gaulton lab and Sun lab at UCSD Department of Pediatrics. This work is conducted as part of LungMAP consortitum.
Proper citation: Lung Genome Browser (RRID:SCR_019255) Copy
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
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