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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.
The Center develops conceptual models, computational infrastructure, an integrated knowledge repository, and query and analysis tools that enable scientists to effectively access and integrate the wealth of biological data. The National Center for Integrative Biomedical Informatics (NCIBI) was founded in October 2005 and is one of seven National Centers for Biomedical Computing (NCBC) in the NIH Roadmap. NCIBI is based at the University of Michigan as a part of the Center for Computational Medicine and Biology (CCMB). NCIBI is composed of biomedical researchers, computational biologists, computer scientists, developers and human-computer interaction specialists organized into seven major core functions. They work in interdisciplinary teams to collectively develop tools that are not only computationally powerful but also biologically relevant and meaningful. The four initial Driving Biological Projects (prostate cancer progression, Type 1 and type 2 diabetes and bipolar disorder) provide the nucleation point from which tool development is informed, launched, and tested. In addition to testing tools for function, a separate team is dedicated to testing usability and user interaction that is a unique feature of this Center. Once tools are developed and validated the goal of the Center is to share and disseminate data and software throughout the research community both internally and externally. This is achieved through various mechanisms such as training videos, tutorials, and demonstrations and presentations at national and international scientific conferences. NCIBI is supported by NIH Grant # U54-DA021519.
Proper citation: National Center for Integrative Biomedical Informatics (RRID:SCR_001538) Copy
https://jmorp.megabank.tohoku.ac.jp/
Japanese multi omics reference panel. Provides multidimensional approach to diversity of Japanese population. Public database for plasma metabolome and proteome analyses. Updated to metabolome, genome, transcriptome, metagenome, number of samples, analysis methods of each dataset, expanding links between each layer and links between hierarchies.
Proper citation: jMORP (RRID:SCR_024755) Copy
Manually curated database of relations between phase separation and diseases.
Proper citation: PhaSeDis (RRID:SCR_024963) Copy
https://pxdata.stat.fi/PxWeb/pxweb/en/StatFin/
Finland's statistical database contains collection of statistical tables on Finnish society and population of Finland including economy, housing, transport, tourism, consumption, prices, wages and salaries, energy, enterprises and other topics.
Proper citation: StatFin database (RRID:SCR_024843) Copy
Provides a collection of manually curated phase separation (PS) proteins and Membraneless organelles (MLOs) related proteins. Annotated phase separation-related proteins with droplet states, co-phase separation partners and other experimental information.
Proper citation: PhaSepDB (RRID:SCR_024964) Copy
National Prostate Cancer Register of Sweden database.
Proper citation: National Prostate Cancer Register of Sweden (RRID:SCR_024844) Copy
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145660/
Integrative database for proteins involved in liquid-liquid phase separation. Data resource of liquid–liquid phase separation in eukaryotes.
Proper citation: DrLLSP (RRID:SCR_024967) Copy
https://maayanlab.cloud/drugmonizome/#/
Database with search engine for querying annotated sets of drugs and small molecules for performing drug set enrichment analysis.
Proper citation: Drugmonizome (RRID:SCR_024821) Copy
Database of protein components of mammalian stress granules.
Proper citation: Mammalian Stress Granules Proteome (RRID:SCR_024946) Copy
Comprehensive database of RNAs involved in liquid-liquid phase separation.
Proper citation: RPS (RRID:SCR_024960) Copy
http://disphasedb.leloir.org.ar/#/home
Database of mutations found in proteins involved in membrane-less organelles and liquid-liquid phase separation in human diseases.
Proper citation: DisPhaseDB (RRID:SCR_024962) Copy
https://resources.aertslab.org/cistarget/
Web application to download database for motif enrichment, motif annotations,cluster-buster implementation, precomputed regions for creating gene-based databases and to download lists of transcription factors for human, mouse and fly, chip-seq tracks annotations.
Proper citation: cisTarget (RRID:SCR_024808) Copy
Database of digitized plant specimens. Used for finding plant name, type, specimens and their label data.The collection also includes partner contributed reference works and primary sources. Used for research and teaching in botany, ecology, and conservation studies.
Proper citation: JStor Global Plants (RRID:SCR_025018) Copy
Collection of in situ hybridization data of gene expression in the brain of adult fish. Data can be viewed and downloaded.
Proper citation: Adult Zebrafish Brain Gene Expression Database (RRID:SCR_025122) Copy
http://tide.dfci.harvard.edu/login/
Web platform for large-scale public data reuse to model immunotherapy response and resistance. Provides integrated large-scale omics data and biomarkers on published ICB trials, non-immunotherapy tumor profiles, and CRISPR screens.
Proper citation: TIDE (RRID:SCR_026350) Copy
https://www.polebio.lrsv.ups-tlse.fr/WallProtDB/
Database resource for plant cell wall proteomics. Aims at collecting cell wall proteomic experimental data. For each experiment, a scheme summarizing the strategy used for protein isolation and identification is provided.
Proper citation: WallProtDB (RRID:SCR_026506) Copy
https://www.plasticsurgeryhome.in
Website serves as digital resource for plastic surgery professionals. Educational and resource platform dedicated to plastic surgeons, trainees, and researchers. Provides access to curated content, including links to major plastic surgery societies, journal repositories, clinical resources, and upcoming events. Serves as comprehensive hub for continuous professional development and collaboration in the field of plastic surgery.
Proper citation: Plastic Surgery Home (RRID:SCR_026487) Copy
https://www.iana.org/time-zones
Database contains code and data that represent the history of local time for many representative locations around the globe. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight-saving rules.
Proper citation: Time Zone Database (RRID:SCR_026492) Copy
https://endomap.hms.harvard.edu/
Structural interactome viewer. Interactive database of endosomal protein-protein interactions identified by cross-linking mass spectrometry and modeled by AlphaFold multimer. Structural protein interactome of human early endosomes.
Proper citation: EndoMap (RRID:SCR_026690) Copy
Database that attempts to consolidate information on known clinical and selected set of pre-clinical biomarkers into single resource. Database includes five major types of biomarkers (condition specific, protein, chemical, karyotypic and genetic) and six biomarker categories (diagnostic, risk, prognostic, safety, monitoring, and response). Provides information such as: biomarker names and synonyms, associated conditions or pathologies, detailed disease descriptions, detailed biomarker descriptions, biomarker specificity, sensitivity and ROC curves, standard reference values (for protein and chemical markers), variants (for SNP or genetic markers), sequence information (for genetic and protein markers), molecular 2D and 3D structures (for protein and chemical markers), tissue or biofluid sources (for protein and chemical markers), chromosomal location and structure (for genetic and karyotype markers), clinical approval status and relevant literature references. Users can browse the data by conditions, condition categories, biomarker types, biomarker categories or search by sequence similarity through the advanced search function.
Proper citation: MarkerDB (RRID:SCR_026817) Copy
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