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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.
http://www.scripps.edu/florida/technologies/flowcytometry/index.html
Flow cytometry core to measure phenotypic, biochemical and molecular characteristics of individual cells or particles suspended in fluid stream.Flow Cytometry Core on Jupiter, Florida campus of Scripps Research provides services including Cell Sorting, Analytical Cytometry,Data Analysis,Microdissection and Imaging. Hematology services including:Cell Sorting on ARIA: violet, blue, green and red lasers and on FUSION: violet, blue, green and red lasers; Cell Analysis on LSR2: ultra-violet, violet, blue, green and red lasers, GALLIOS: violet, blue, green and red lasers,CANTO: violet, blue and red lasers;Laser Microdissection and Fluorescence Imaging using LEICA LMD 7000;Hematology using HEMAVET 950FS.
Proper citation: Scripps Research Institute - Florida Flow Cytometry Core Facility (RRID:SCR_017830) Copy
Collection of open chromatin regions from sequencing data. Metadata as entire curated DNase-I hypersensitive sites (DHS) on the whole genome datasets and data specific to each chromosome.
Proper citation: Database of Open Chromatin Regions (RRID:SCR_016614) Copy
http://omicslab.genetics.ac.cn/dred/index.php
Database of genes related to Repeat Expansion Diseases, as comprehensive manually curated database that covers all reported repeat expansion diseases included in PubMed and OMIM. Detailed information about each repeat and its related genes/diseases can be found in database, links to OMIM, NCBI and Ensembl are also provided. Provides list of predicted genes containing unstable tandem repeats that may cause diseases via abnormal repeat expansion by support vector machine and random forest.
Proper citation: Database of genes related to Repeat Expansion Diseases (RRID:SCR_018086) Copy
Data collection of large scale genome wide DNA methylation analysis of 1,000 mother-child pairs at serial time points across life course (ARIES).
Proper citation: mqtldb (RRID:SCR_018002) Copy
Open source object relational database system that uses and extends SQL language combined with many features that safely store and scale the most complicated data workloads. PostgreSQL runs on all major operating systems.
Proper citation: PostgreSQL (RRID:SCR_021067) Copy
Abstract and indexing database with full text links that is produced by Elsevier Co. Combines expertly curated abstract and citation database with enriched data and linked scholarly literature across wide variety of disciplines.
Proper citation: Scopus (RRID:SCR_022559) Copy
http://bioinfo.life.hust.edu.cn/EVmiRNA/#!/
Collection of comprehensive miRNA expression profiles in extracellular vesicles from tissues. Includes miRNA expression profiles, miRNA regulated pathways, miRNA function, miRNA related drugs and publications to support miRNA biomarker discovery.
Proper citation: EVmiRNA (RRID:SCR_018795) Copy
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
https://prokoplab.com/vistedd/
Database of SARS-CoV-2 and other viruses. Integrates structural and dynamic insights with viral evolution for proteins coded by virus. Each virus within database has workflow performed on each protein. Workflow consists of protein modeling, molecular dynamic simulations, evolutionary analysis, and mapping of protein-protein interactions. On page for each protein is link to individual protein data folder system, video of protein rotating with conservation, details of protein function, widget to purchase 3D print of protein at cost of production, amino acid movement from molecular dynamic simulations, and table of data for each amino acid of protein.
Proper citation: Viral Integrated Structural Evolution Dynamic Database (RRID:SCR_018793) Copy
https://github.com/clinwiki-org/clinwiki
Clinical trials database.
Proper citation: ClinWiki (RRID:SCR_021297) Copy
https://www.epicore.ualberta.ca/IsletCore/
Collection of data from all pancreatic islet isolations.
Proper citation: Alberta Diabetes Institute IsletCore database (RRID:SCR_018566) Copy
Network of healthcare organizations, together with data partners in Brazil, South Korea, and Japan, to bring clinical facts on more than 250 million patients around the world. Federated model so users of this data are ensured new patients, observations, and results every day, all harmonized to standard terminology like ICD-10 and LOINC without any data wrangling required at the point of care. The raw data is not available to authors of papers and papers in medicine are being retracted.
Proper citation: trinetx (RRID:SCR_022760) Copy
Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.
Proper citation: Bioconductor (RRID:SCR_006442) Copy
https://pynwb.readthedocs.io/en/latest/
Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information.
Proper citation: PyNWB (RRID:SCR_017452) Copy
http://download.ant-neuro.com/matlab/
Software as an EEGLAB tool used for LIBEEP recordings.
Proper citation: Libeep EEGLAB plugin (RRID:SCR_016334) Copy
https://github.com/BioDepot/nbdocker
Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment.
Proper citation: nbdocker (RRID:SCR_017159) Copy
http://www.cbrc.jp/htbin/show_tffactor_mw
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 13, 2016.
A dataset about transcriptional regulation in eukaryotic cells, including data such as transcription factors and their binding sites and profiles. Resource is in Chinese.
Proper citation: TFFACTOR (RRID:SCR_000519) Copy
https://www.igb.illinois.edu/corefacilities
Core for biological microscopy and image analysis. Offers high-end equipment,user training,ongoing support, including experiment design and data interpretation,twenty-four hour access Services,3D Printing, Transfer Files, Image Analysis,Histology,Instrument Training.
Proper citation: University of Illinois at Urbana-Champaign Core Facilities at IGB (RRID:SCR_017938) Copy
https://www.preventivemedicine.northwestern.edu/divisions/biostatistics/
Core where division members engage in statistical methods development and application, research design and statistical computing for health science research. Faculty interests encompass Bayesian methods, bioinformatics, causal inference, computational biology, clinical trials, diagnostic testing, longitudinal modeling, missing data modeling, observational data methods, semi-parametric models, spatial modeling, statistical genetics and survival analysis.
Proper citation: Northwestern University Biostatistics Collaborative Center (RRID:SCR_017943) Copy
https://bioconductor.org/packages/FlowSorted.Blood.450k/
Illumina HumanMethylation data on sorted blood cell populations.
Proper citation: FlowSorted.Blood.450k R package (RRID:SCR_018003) Copy
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