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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.
Software as branch of FieldTrip with added functionality for sleep analyses, like calculating sleep tables, descriptives, ploting hypnograms, detecting slow waves, sleep spindles, REMS and their cooccurrence etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SleepTrip (RRID:SCR_017318) Copy
https://github.com/BackofenLab/GraphClust-2
Software tool for scalable clustering of RNAs based on sequence and secondary structures similarities. Implemented within Galaxy framework. Used for studying RNA function.
Proper citation: GraphClust2 (RRID:SCR_017286) Copy
https://github.com/biocore/redbiom
Software tool for allowing samples that contain microbiome features to be rapidly identified. Rapid sample discovery and feature characterization system. Integrated with existing analysis tools to enable fast, large scale microbiome searches and discovery of new microbiome relationships. Service for sample metadata and sample data.
Proper citation: redbiom (RRID:SCR_017285) Copy
Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats.
Proper citation: PILER (RRID:SCR_017333) Copy
Software event based framework for processing and controlling data streams. Visual language designed for making software systems that require rich and rapid interaction with external world.
Proper citation: Bonsai (RRID:SCR_017218) Copy
http://rna.urmc.rochester.edu/RNAstructureWeb/Servers/Predict1/Predict1.html
Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program.
Proper citation: RNAstructure (RRID:SCR_017216) Copy
Software tool for statistical analysis by BellCurve that adds statistical analysis methods to Excel menu .
Proper citation: Excel Statistics (RRID:SCR_017294) Copy
http://bio3d.colorado.edu/SerialEM/
Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function.
Proper citation: SerialEM (RRID:SCR_017293) Copy
http://kim.bio.upenn.edu/software/pivot.shtml
Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows.
Proper citation: PIVOT software (RRID:SCR_017210) Copy
http://140.120.197.173/Ecology/prod02.htm
Software tool used to conduct life table analysis focused on development of cohort or population for animal species with two sexes. Parent organization is National Chung Hsing University, Taichung, Taiwan.
Proper citation: TWOSEX-MSChart (RRID:SCR_017298) Copy
https://github.com/BioInf-Wuerzburg/proovread
Software tool for PacBio hybrid error correction through iterative short read consensus.
Proper citation: Proovread (RRID:SCR_017331) Copy
Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms.
Proper citation: SynGO (RRID:SCR_017330) Copy
https://www.electrontomography.org/?page_id=446
Software tool for electron tomography and 3D image processing. Software package used in electron tomography for marker free alignment and 3D reconstruction of tilt series. Tomography software package distributed for linux operating system and developed by Hanspeter Winkler.
Proper citation: Protomo (RRID:SCR_017296) Copy
https://sites.google.com/site/3demimageprocessing/tomo3d
Software tool for fast tomographic reconstruction on multicore computers. Used for electron tomography studies with increasing resolution needs.
Proper citation: TOMO3D (RRID:SCR_017295) Copy
https://cran.r-project.org/web/packages/phangorn/index.html
Software R package for phylogenetic reconstruction and analysis. Used for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks.
Proper citation: Phangorn (RRID:SCR_017302) Copy
Medical image repository to store medical research data.
Proper citation: SICAS Medical Image Repository (RRID:SCR_017420) Copy
https://beast.community/tempest
Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019.
Proper citation: TempEst (RRID:SCR_017304) Copy
Facility serves students and faculty of University of Florida, and researchers from industry who use facility instruments to check outcome of reactions or characterize compounds. Instruments include Inova 500 MHz magnet with 2 RF Channels, Inova 500 MHz magnet with 3 RF Channels, Mercury 300 MHz (m4n and m8n), Mercury 300 MHz Broadband, Agilent 600 MHZ Magnet, and several NMR probes.
Proper citation: University of Florida Department of Chemistry Nuclear Magnetic Resonance Core Facility (RRID:SCR_017382) Copy
https://github.com/cwatson/braingraph/
Software R package for performing graph theory analyses of brain MRI data.
Proper citation: brainGraph (RRID:SCR_017260) Copy
https://software.broadinstitute.org/morpheus/
Software tool for versatile matrix visualization and analysis. Program to generate heatmaps from input data. JavaScript matrix visualization and analysis.
Proper citation: Morpheus by Broad Institute (RRID:SCR_017386) Copy
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