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http://fairbydesign.nl

Software metadata ingestion platform that helps to improve quality of metadata. Station allows users to record meta-data according to minimum information standards thereby ensuring FAIR scientific data management from the start.

Proper citation: FAIR Data Station (RRID:SCR_023239) Copy   

•   Source: SciCrunch Registry

https://www.piirus.com

A database and collaboration tool which allows researchers to make contacts or find collaborators within their field or from a different discipline. Users can create a profile detailing their collaboration interests, research areas, and methodologies as well as add links to external sites such as LinkedIn and Academia.edu. Piirus takes the information from users' profiles to suggest researchers with whom they may be interested in collaborating with. Users can also search for users with particular interests, expertise, or techniques.

Proper citation: Piirus (RRID:SCR_013964) Copy   

•   Source: SciCrunch Registry

https://github.com/linnarsson-lab/loom-viewer

Software tool for sharing, browsing and visualizing single-cell data stored in the Loom file format.

Proper citation: loom-viewer (RRID:SCR_016683) Copy   

•   Source: SciCrunch Registry

https://cell-innovation.nig.ac.jp/maser/Tools/visualization_top_en.html

One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGffToGe_db for custom genome software loads GFF files of custom genomes to a database for Genome Explorer. It allows the user to browse the results through the GE.

Proper citation: loadGffToGe_db for custom genome (RRID:SCR_015997) Copy   

•   Source: SciCrunch Registry

http://www.mricro.com

Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.

Proper citation: MRIcron (RRID:SCR_002403) Copy   

•   Source: SciCrunch Registry

https://developers.google.cn/earth-engine/

Web application as public data catalog, compute infrastructure, geospatial APIs and interactive app server. Geospatial processing service.

Proper citation: Google Earth Engine (RRID:SCR_023224) Copy   

•   Source: SciCrunch Registry

http://www.uchicagoddrcc.org

Center whose goals include fostering collaboration among basic and clinical investigators, facilitating the use of new technologies in the study of treatment of digestive diseases, and providing education and training for improved treatment and diagnosis.

Proper citation: University of Chicago Digestive Diseases Research Core Center (RRID:SCR_015601) Copy   

•   Source: SciCrunch Registry

http://openneu.ro/metasearch

Web application search tool intended to help users find MRI data shared publicly on the Web, particularly from projects organized under the 1000 Functional Connectomes Project (FCP) and International Neuroimaging Data-sharing Initiative (INDI). Users can perform queries visually to select a cohort of participants with brain imaging data based on their demographics and phenotypic information and then link out to imaging measures.

Proper citation: MetaSearch (RRID:SCR_014751) Copy   

•   Source: SciCrunch Registry

http://www.bsc.gwu.edu/dpp/index.htmlvdoc

Multicenter clinical research study aimed at discovering whether modest weight loss through dietary changes and increased physical activity or treatment with the oral diabetes drug metformin (Glucophage) could prevent or delay the onset of type 2 diabetes in study participants. At the beginning of the DPP, all 3,234 study participants were overweight and had blood glucose levels higher than normal but not high enough for a diagnosis of diabetesa condition called prediabetes. In addition, 45 percent of the participants were from minority groups-African American, Alaska Native, American Indian, Asian American, Hispanic/Latino, or Pacific Islander-at increased risk of developing diabetes. The DPP found that participants who lost a modest amount of weight through dietary changes and increased physical activity sharply reduced their chances of developing diabetes. Taking metformin also reduced risk, although less dramatically. In the DPP, participants from 27 clinical centers around the United States were randomly divided into different treatment groups. The first group, called the lifestyle intervention group, received intensive training in diet, physical activity, and behavior modification. By eating less fat and fewer calories and exercising for a total of 150 minutes a week, they aimed to lose 7 percent of their body weight and maintain that loss. The second group took 850 mg of metformin twice a day. The third group received placebo pills instead of metformin. The metformin and placebo groups also received information about diet and exercise but no intensive motivational counseling. A fourth group was treated with the drug troglitazone (Rezulin), but this part of the study was discontinued after researchers discovered that troglitazone can cause serious liver damage. The participants in this group were followed but not included as one of the intervention groups. In the years since the DPP was completed, further analyses of DPP data continue to yield important insights into the value of lifestyle changes in helping people prevent type 2 diabetes and associated conditions. For example, one analysis confirmed that DPP participants carrying two copies of a gene variant, or mutation, that significantly increased their risk of developing diabetes benefited from lifestyle changes as much as or more than those without the gene variant. Another analysis found that weight loss was the main predictor of reduced risk for developing diabetes in DPP lifestyle intervention group participants. The authors concluded that diabetes risk reduction efforts should focus on weight loss, which is helped by increased exercise.

Proper citation: Diabetes Prevention Program (RRID:SCR_001501) Copy   

•   Source: SciCrunch Registry

https://amstar.ca/

Guide tool to assess methodological quality of systematic reviews. Used to evaluate systematic reviews of randomised trials. AMSTAR 2 enables more detailed assessment of systematic reviews that include randomised or non-randomised studies of healthcare interventions, or both.

Proper citation: AMSTAR (RRID:SCR_023194) Copy   

•   Source: SciCrunch Registry

https://cinema.ispm.unibe.ch/

Web application that simplifies evaluation of confidence in findings from network meta analysis.

Proper citation: Confidence in network meta analysis (RRID:SCR_023193) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/RMassBank.html

Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Proper citation: RMassBank (RRID:SCR_002797) Copy   

•   Source: SciCrunch Registry

https://www.standardbio.com/products-services/instruments/hyperion

Imaging system enables comprehensive analysis of cellular phenotypes. Allows access to single cell insights. This includes deeper understanding of intricate spatial relationships of cells, pathways and phenotypes in tissue microenvironment.

Proper citation: Fluidigm: Hyperion Imaging System (RRID:SCR_023195) Copy   

•   Source: SciCrunch Registry

https://www.licor.com/bio/support/answer-portal/imaging-systems/odyssey-fc.html

System used to image and analyze Western blots. Odyssey Fc imager has been discontinued.

Proper citation: LI-COR: Odyssey Fc Imaging System (RRID:SCR_023227) Copy   

•   Source: SciCrunch Registry

https://upsetplot.readthedocs.io/en/stable/

Software Python implementation of UpSet plots to visualize set overlaps.

Proper citation: UpSetPlot (RRID:SCR_023225) Copy   

•   Source: SciCrunch Registry

http://www.ugr.es/local/abfr/tiempojm/

Web application that records the time devoted to each of the actions that are performed while playing motor games or active games. This recording system has applications in physical activity research and physical education.

Proper citation: Time in Motor Games (Tiempo en Juegos Motores) (RRID:SCR_015819) Copy   

•   Source: SciCrunch Registry

http://crispor.tefor.net

Web application that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. This sgRNA design tool assists with guide selection in a variety of genomes and pre-calculated results for all human coding exons as a UCSC Genome Browser track.

Proper citation: CRISPOR (RRID:SCR_015935) Copy   

•   Source: SciCrunch Registry

https://www.childrenshospitals.org/content/analytics/product-program/pediatric-health-information-system

Comparative database with clinical and resource utilization data for inpatient, ambulatory surgery, emergency department and observation unit encounters for more than 49 children's hospitals.

Proper citation: Children's Hospital Association Pediatric Health Information System (RRID:SCR_023168) Copy   

•   Source: SciCrunch Registry

http://blimp.cs.queensu.ca/

Bibliography covering all publications related to the fast-growing field of biomedical literature and text mining. This forum for collecting, compiling and sharing is a one-stop resource, letting researchers find out who-does-what in the area and where it is published, bridging across the many discipline-specific venues in which biomedical text-mining papers are published. If you know of a relevant paper that is missing from BLIMP, or have an accepted-for-publication paper, PhD/MSc thesis or a technical report, that you believe is relevant to biomedical text mining, fill in the submission form. The fast-growing field of biomedical literature mining is highly-interdisciplinary. Publications appear in forums ranging from the SIGIR conferences (the ACM Special Interest group on Information Retrieval) to journals such as Nature and Science, with the whole range of bioinformatics forums in-between. To substantially contribute, one must know what was/is being done in this diverse area, and place the work in context - both biologically and computationally. Instead of starting a journal fully dedicated to biomedical literature mining, thus creating yet another publication venue, this site offers an alternative: It holds in one place a compilation of references to relevant papers that have been published or accepted for publication.

Proper citation: BLIMP: Biomedical LIterature Mining Publications (RRID:SCR_007112) Copy   

•   Source: SciCrunch Registry

https://andor.oxinst.com/products/ixon-emccd-cameras-for-life-science

Scientific camera with EMCCD image sensor that is capable of detecting single photon events without image intensifier, achievable by way of unique electron multiplying structure built into the chip.

Proper citation: Andor: iXon Ultra EMCCD camera (RRID:SCR_023166) Copy   

•   Source: SciCrunch Registry