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http://www.medibeacon.com/preclinical/

Software used to analyze glomerular filtration rate (GFR) measurement from MediBeacon GFR monitor. It is used with the Transdermal Continuous Renal Function Monitor.

Proper citation: MediBeacon Studio Software (RRID:SCR_016252) Copy   

•   Source: SciCrunch Registry
  

http://www.xenopus.com/

Supplier of Frogs and Tadpoles for the scientific community.

Proper citation: Xenopus Express (RRID:SCR_016373) Copy   

•   Source: SciCrunch Registry
  

http://sciscore.com

Text-mining software that reviews methods sections of scientific articles. It provides a numerical score to represent the "reproducibility" of the article's research.

Proper citation: SciScore (RRID:SCR_016251) Copy   

•   Source: SciCrunch Registry
  

https://bitbucket.org/nsegata/graphlan/wiki/Home

Software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. Used for concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation as a high-resolution microbial tree of life with taxonomic annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GraPhlAn (RRID:SCR_016130) Copy   

•   Source: SciCrunch Registry
  

http://www.cycif.org/

Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence.

Proper citation: CycIF.org (RRID:SCR_016267) Copy   

•   Source: SciCrunch Registry
  

http://bioplex.hms.harvard.edu/

Database of cell lines with each expressing a tagged version of a protein from the ORFeome collection. The overarching project goal is to determine protein interactions for every member of the collection.

Proper citation: BioPlex (RRID:SCR_016144) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/projects/vdb/

Virtual resource for neuroscience.

Proper citation: Virtual Digital Brain (RRID:SCR_016265) Copy   

•   Source: SciCrunch Registry
  

https://mentha.uniroma2.it/

Software that archives evidence collected from different sources, then analyzes and presents these data. Its data come from manually curated protein-protein interaction databases that have adhered to the IMEx consortium.

Proper citation: mentha (RRID:SCR_016148) Copy   

•   Source: SciCrunch Registry
  

https://metadatacenter.org

Develops information technologies that make authoring complete metadata more manageable. Its products aim to facilitate using the metadata in further research.Center to improve metadata and its use throughout biomedical sciences. Develops information technologies that make authoring complete metadata more manageable through better interfaces, terminology, metadata practices, and analytics. Optimizes metadata pathway from provider to end user. Provides way for funders to specify what metadata they want to collect as part of research life cycle.

Proper citation: Center for Expanded Data Annotation and Retrieval (RRID:SCR_016269) Copy   

•   Source: SciCrunch Registry
  

https://www.phc.ox.ac.uk/research/technology-outputs/easygv

Software for calculating different measures of glycaemic variability (GV). It analyzes continuous glucose monitoring data using a simple interface.

Proper citation: easyGV (RRID:SCR_016260) Copy   

•   Source: SciCrunch Registry
  

https://www.illumina.com/systems/sequencing-platforms/miseqdx.html

MiSeqDx System is FDA-regulated, CE-IVD-marked, NGS platform for in vitro diagnostic (IVD) testing. System offers both diagnostic and research modes.

Proper citation: Illumina: MiSeqDx System (RRID:SCR_016380) Copy   

•   Source: SciCrunch Registry
  

https://www.illumina.com/systems/sequencing-platforms/hiseq-x.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 15,2023. Sequencer for whole-genome sequencing. System consists of HiSeq X ultra-high-throughput instruments that deliver over 18,000 human genomes per year.

Proper citation: Illumina: HiSeq X (RRID:SCR_016385) Copy   

•   Source: SciCrunch Registry
  

https://support.illumina.com/sequencing/sequencing_instruments/hiseq_2500.html

High-throughput sequencing system. High-quality data using proven Illumina SBS chemistry has made it the instrument of choice for major genome centers and research institutions throughout the world.HiSeq 2500 System has been discontinued. Illumina will support the instrument and intends to supply the reagents through February 28, 2023.

Proper citation: Illumina: HiSeq 2500 System (RRID:SCR_016383) Copy   

•   Source: SciCrunch Registry
  

https://hirnetwork.org/consortium/chib

Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is combining advances in beta cell biology and cell biology with tissue engineering technologies to develop microdevices that support functional human islets.

Proper citation: HIRN Consortium on Human Islet Biomimetics (RRID:SCR_016199) Copy   

•   Source: SciCrunch Registry
  

http://www.fishbrowser.org/software/LR_Gapcloser/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th, 2023. Software that uses long reads to close gaps in the assemblies.

Proper citation: LR Gapcloser (RRID:SCR_016194) Copy   

•   Source: SciCrunch Registry
  

http://www.medwow.com/med/pulse_stimulator/grass-telefactor/s88_dual_output_square_pulse/31612.model-spec

Hardware that is a electrical pulse generator.

Proper citation: Grass Stimulator Model S88 (RRID:SCR_016192) Copy   

•   Source: SciCrunch Registry
  

https://hirnetwork.org/consortium/cbds

Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is using human tissues to discover highly specific biomarkers of beta cell injury in asymptomatic T1D and developing strategies to stop beta cell destruction early in the disease process.

Proper citation: HIRN Consortium on Beta Cell Death and Survival (RRID:SCR_016198) Copy   

•   Source: SciCrunch Registry
  

https://github.com/G-Node/nix/wiki

Software that defines a data model for annotated scientific datasets. It includes data together with metadata, and a corresponding file format based on HDF5 for storing and sharing such datasets.

Proper citation: NIX (RRID:SCR_016196) Copy   

•   Source: SciCrunch Registry
  

https://www.xlstat.com/en/

Software for commercial data analysis and statistical software package for Microsoft Excel.

Proper citation: XLSTAT (RRID:SCR_016299) Copy   

•   Source: SciCrunch Registry
  

http://interlex.org

The InterLex project - a core component of SciCrunch and supported by projects such as the Neuroscience Information Framework project (NIF), the NIDDK Information Network (dkNET), and the Open Data Commons for Spinal Cord Injury - is a dynamic lexicon of biomedical terms. Unlike an encyclopedia, a lexicon provides the meaning of a term, and not all there is to know about it. InterLex is being constructed to help improve the way that biomedical scientists communicate about their data, so that information systems like NIF and dkNET can find data more easily and provide more powerful means of integrating that data across distributed resources. One of the big roadblocks to data integration in the biomedical sciences is the inconsistent use of terminology in databases and other resources such as the literature. When we use the same terms to mean different things, we cannot easily ask questions that span across multiple resources. For example, if three databases have information about what genes are expressed in cortex, but they all use different definitions of cerebral cortex, then it is hard to compare them. InterLex allows for the association of data values (i.e. the value of a field or text within a field) to terminologies enabling the crowdsourcing of data-terminology mappings. InterLex was built on the foundation of NeuroLex (see Larson and Martone 2013 Neurolex: An online framework for neuroscience knowledge. Frontiers in Neuroinformatics, 7:18) and contains all of the existing NeuroLex terms. The initial entries in NeuroLex were built from the NIFSTD ontologies. NIFSTD currently has about 60,000 concepts (includes both classes and synonyms) that span gross anatomy, cells, subcellular structures, diseases, functions and techniques. InterLex models terms using primitives of the Web Ontology Language (OWL) and can export directly to a variety of standard ontology formats. A primary goal of interlex is to provide a stable layer on top of the many other existing terminologies, lexicons, and ontologies (i.e. provide a way to federate ontologies for data applications) and to provide a set of inter-lexical and inter-data-lexical mappings. In the future, InterLex will support user specific namespaces so that users can customize the exact definitions or ontologies they source from, as well as the relationships on those terms. Importantly, however, InterLex enforces a simple rule which is that terms which represent the same concept under the same superclass will maintain the same identifier fragment (i.e. 'ilx_1234567'). However, each user will be able to 'fork' a term into their own namespace (e.g. http://uri.interlex.org/user/ilx_1234567). This enables the various perspectives on a term or concept to have equal space so that the full diversity of views on a term can be seen and expressed. Sign-up for updates to get notified about updates to InterLex and when new features are available.

Proper citation: InterLex (RRID:SCR_016178) Copy   

•   Source: SciCrunch Registry