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https://opencontext.org/

Publishes documentation and data to make them discoverable and searchable on the Web. Publishing service archives data by integrating analyses, maps, media, and journals together. Open Context editors clean data and organize content. Every item receives unique identifier that allows citation of individual items. Your data publication receives DOI. Creative Commons licenses facilitate reuse. All Open Context data publications are preserved with California Digital Library.

Proper citation: Open Context (RRID:SCR_024604) Copy   

•   Source: SciCrunch Registry

https://imacel.net/en/

Artificial intelligence image analysis platform that facilitates life science research. It offers data analysis, processing functions, and security features to accelerate research productivity.

Proper citation: IMACEL (RRID:SCR_015868) Copy   

•   Source: SciCrunch Registry

http://www.detaibio.com/sms2/protein_gravy.html

Web protein hydrophilicity analysis tool.

Proper citation: protein hydrophilicity analysis tool (RRID:SCR_023015) Copy   

•   Source: SciCrunch Registry

https://online.kitp.ucsb.edu/

Most seminars, conferences, colloquia, and lectures at KITP since late 1997 have been archived on this website, in the form of slides, audio, video, and podcasts. Portal to foster scientific communication, education, and outreach.

Proper citation: Kavli Institute for Theoretical Physics Online Talks (RRID:SCR_024580) Copy   

•   Source: SciCrunch Registry

https://docs.google.com/presentation/d/13KqqDOFLbhCPRsCqf4zETdcjhZECIXD_/edit#slide=id.p1

MJFF in partnership with Aligning Science Across Parkinson’s are in the process of establishing data platform, CRN Cloud, leveraging Verily Workbench to share data generated by researcher labs funded through ASAP Collaborative Research Network. The data types include mainly raw and processed single cell RNA-seq, single nucleus RNA-seq, and bulk RNA-seq from both PD and healthy control samples.

Proper citation: Collaborative Research Network Cloud (RRID:SCR_023923) Copy   

•   Source: SciCrunch Registry

https://git.integromics.fr/published/predomics

Software package for metagenomics data. Discovers accurate predictive signatures and provides unprecedented interpretability. Package contains three methods for suppervised learning based on ternary coefficients. Used to discover classification models for quantitative metagenomics data.

Proper citation: Predomics (RRID:SCR_017415) Copy   

•   Source: SciCrunch Registry

https://jcr.clarivate.com/JCRLandingPageAction.action

Web tool with systematic, objective means to critically evaluate journals, with quantifiable, statistical information based on citation data. Provides information about academic journals in natural sciences and social sciences, including impact factors in database integrated with Web of Science. Sourced from Web of Science Core Collection,citation index on Web of Science platform.

Proper citation: Journal Citation Reports (RRID:SCR_017656) Copy   

•   Source: SciCrunch Registry

http://biocc.hrbmu.edu.cn/CellMarker/

Database provides cell markers for various cell types in tissues of human and mouse. Manually curated resource of cell markers in human and mouse. Provides user-friendly interface for browsing, searching and downloading markers of diverse cell types of different tissues. Summarized marker prevalence in each cell type is graphically presented., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CellMarker (RRID:SCR_018503) Copy   

•   Source: SciCrunch Registry

http://www.mirtoolsgallery.org/miRToolsGallery/node/1055

Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: miRanda (RRID:SCR_017496) Copy   

•   Source: SciCrunch Registry

https://www.fli.de/en/institutes/department-of-experimental-animal-facilities-and-biorisk-management-atb/bio-bank/#:~:text=Collection%20of%20Cell%20Lines%20in%20Veterinary%20Medicine%20(CCLV),the%20collection%20comprises%201%2C500%20lines.

Generates, characterises and collects cell lines which are of interest for veterinary research and diagnostics. Collection includes cell lines of farm animals such as cattle, pig, horse, sheep, goat and poultry and other mammals, birds, reptiles, fishes and insects (70 species).Authentication and quality-control tests (tests for contamination with mycoplasms, bacteria, BVDV) of the cultures are done routinely.Cell cultures are provided to scientists of the Friedrich-Loeffler-Institute and other non-commercial institutions worldwide after consultation of a scientific staff member of the CCLV.

Proper citation: Collection of Cell Lines in Veterinary Medicine (RRID:SCR_023182) Copy   

•   Source: SciCrunch Registry

http://www.people.fas.harvard.edu/~junliu/em/em.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program.

Proper citation: EM-DECODER (RRID:SCR_000023) Copy   

•   Source: SciCrunch Registry

https://github.com/wilsonGW/SomaDetection

Source code for a machine learning method to detect somas on confocal microscopic images of the Drosophila brain. The method can be applied to the original raw images where the noises are not removed and the number of somas is unknown.

Proper citation: SomaDetection (RRID:SCR_015717) Copy   

•   Source: SciCrunch Registry

http://viewer.shigen.info/cgi-bin/crispr/crispr.cgi

Web tool to show micro homology sequences striding over double strand break point created by CRISPR/Cas9 system. Used to search for CRISPR target site with micro-homology sequences. Used to predict deletion pattern.

Proper citation: NBRP Medaka CRISPR target site (RRID:SCR_018159) Copy   

•   Source: SciCrunch Registry

http://Bacterio.net

Database lists names of prokaryotes that have been validly published in International Journal of Systematic and Evolutionary Microbiology directly or by inclusion in Validation List, under Rules of International Code of Nomenclature of Bacteria. Has classification of prokaryotes and information on prokaryotic nomenclature and culture collections.

Proper citation: LPSN Database (RRID:SCR_018151) Copy   

•   Source: SciCrunch Registry

http://nucleobytes.com/index.php/4peaks

Software application for viewing and editing sequence trace files.

Proper citation: 4Peaks (RRID:SCR_000015) Copy   

•   Source: SciCrunch Registry

https://ist.medisapiens.com/

Database by Medisapiens Ltd. as fully integrated and annotated human gene expression data source. All genes are comparable across all samples. Provides data analysis options using database of human transcriptome.

Proper citation: IST Online (RRID:SCR_018794) Copy   

•   Source: SciCrunch Registry

http://cisbp.ccbr.utoronto.ca

Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs.

Proper citation: CIS-BP (RRID:SCR_017236) Copy   

•   Source: SciCrunch Registry

https://www.fastgenomics.org/

Open online platform for single cell RNA-seq. Provides data management and analytics. Used to analyze public and private datasets and you can choose between several best practices workflows and browse existing analyses.

Proper citation: FASTGenomics (RRID:SCR_022898) Copy   

•   Source: SciCrunch Registry

https://vertebrate.genenames.org/

Software resource for vertebrate gene nomenclature. Database of gene symbols. Coordinates with vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), AGNC (Anole green lizard), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are named in line with their human homologs.

Proper citation: VGNC (RRID:SCR_017514) Copy   

•   Source: SciCrunch Registry

https://www.robotreviewer.net/

Software tool as machine learning system that automatically assesses bias in clinical trials. From PDF formatted trial report determines risks of bias for domains defined by Cochrane Risk of Bias (RoB) tool, and extracts supporting text for these judgments.

Proper citation: Robot Reviewer (RRID:SCR_018961) Copy   

•   Source: SciCrunch Registry