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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.
Open source software framework that includes the necessary building blocks for surgical simulations, such as native device support, haptic feedback, graphics, discrete collision detection and physics simulation. Developers can refactor the physics engine, swap models, ODE solvers, or linear system solvers.
Proper citation: OpenSurgSim (RRID:SCR_024147) Copy
Open source software network communication interface for image guided interventions.Provides plug-and-play unified real-time communications in operating rooms for image-guided interventions, where imagers, sensors, surgical robots,and computers from different vendors work cooperatively to ensure seamless data flow among those components and enable a closed loop process of planning, control, delivery, and feedback.
Proper citation: OpenIGTLink (RRID:SCR_024148) Copy
https://github.com/mbillingr/libgdf
Software library for processing of biomedical signals. Provides generic storage for biosignals, such as EEG, ECG, MEG. C++ implementation of GDF - " general dataformat for biosignals" version V2.20.
Proper citation: libGDF (RRID:SCR_024075) Copy
https://psignifit.sourceforge.net/
Software toolbox to fit psychometric functions and to test hypotheses about psychometric data.
Proper citation: psignifit (RRID:SCR_024196) Copy
https://github.com/husonlab/jloda
Software Java library of data structures and algorithms.Provides some basic data structures and algorithms used by SplitsTree, Dendroscope and MEGAN.
Proper citation: JLODA (RRID:SCR_024076) Copy
https://gitlab.com/german.tischler/libmaus2
Software collection of data structures and algorithms. Contains I/O classes (single byte and UTF-8), bitio classes (input, output and various forms of bit level manipulation), text indexing classes (suffix and LCP array, fulltext and minute (FM), ...), BAM sequence alignment files input/output (simple and collating) and many lower level support classes.
Proper citation: libmaus2 (RRID:SCR_024077) Copy
http://metabarcoding.org/sumaclust
Software tool aims to cluster sequences in a way that is fast and exact at the same time.
Proper citation: sumaclust (RRID:SCR_024352) Copy
http://swissknife.sourceforge.net
Software object oriented Perl library to handle Swiss-Prot entries
Proper citation: libswiss-perl (RRID:SCR_024356) Copy
https://www.aquamaniac.de/rdm/projects/libchipcard
Software library for generic access to chipcard readers and cards
Proper citation: Libchipcard (RRID:SCR_024071) Copy
https://github.com/vcflib/tabixpp
Software C++ wrapper around tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.Wrapper to tabix indexer
Proper citation: tabixpp (RRID:SCR_024107) Copy
https://sw-tools.rcsb.org/apps/CORE-WRAPPER/index.html
Software library that exports C++ mmCIF accessors to Python.
Proper citation: Core Wrapper (RRID:SCR_024087) Copy
https://github.com/wdecoster/nanolyse
Software package to remove reads mapping to the lambda phage genome from a fastq file.
Proper citation: NanoLyse (RRID:SCR_024125) Copy
https://graphics.stanford.edu/software/volpack/
Portable software library for volume rendering.
Proper citation: VolPack (RRID:SCR_024367) Copy
https://github.com/mtholder/ncl
Software C++ class library for interpreting data files in NEXUS format. NEXUS Class Library software package is collection of C++ classes designed to simplify interpreting data files written in the NEXUS format used by many computer programs for phylogenetic analyses.NEXUS format allows different programs to share the same data files, even though none of the programs can interpret all of the data stored.
Proper citation: libncl (RRID:SCR_024080) Copy
https://github.com/kdm9/libqes
Software C library with bioinformatic focus optimised for speed and clean API.
Proper citation: libqes (RRID:SCR_024083) Copy
https://github.com/toddy15/medicalterms
Software package to create specialized dictionaries for medical terms used in various languages.German medical dictionary words.
Proper citation: medicalterms (RRID:SCR_024117) Copy
http://www.homozygositymapper.org/
A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software)
Proper citation: HOMOZYGOSITYMAPPER (RRID:SCR_001714) Copy
Database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It is an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Sponsors: VIPERdb is funded by the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: VIPERdb (RRID:SCR_002853) Copy
An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways.
Proper citation: Human Gene Connectome Server (RRID:SCR_002627) Copy
A system providing resolvable persistent Uniform Resource Identifiers (URIs) used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative. It provides direct access to the identified data using one chosen physical location (or resource). If more than one physical locations providing the data are recorded in the Registry, then you can access them via the top banner or by using a profile.
Proper citation: Identifiers.org (RRID:SCR_003735) Copy
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