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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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Google Forms Resource Report Resource Website 10+ mentions |
Google Forms (RRID:SCR_023174) | software resource, software application | Software for creating surveys and questionnaires. | creating surveys, creating questionnaires | Free, Freely available | SCR_023174 | 2026-08-12 10:52:59 | 40 | |||||||||||
|
VCF2Dis Resource Report Resource Website 10+ mentions |
VCF2Dis (RRID:SCR_022513) | data analytics software, software resource, software application | Software to calculate p-distance matrix based Variant Call Format. | calculate p-distance matrix based Variant Call Format | Free, Available for download, Freely available | SCR_022513 | 2026-08-12 10:52:44 | 22 | |||||||||||
|
Tonkaz Resource Report Resource Website 1+ mentions |
Tonkaz (RRID:SCR_023206) | software resource, software application | Software CLI tool to verify workflow reproducibility. | workflow reproducibility, workflow reproducibility verification | DOI:10.1101/2022.10.11.511695 | Free, Available for download, Freely available | SCR_023206 | 2026-08-12 10:52:51 | 1 | ||||||||||
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Yevis cli Resource Report Resource Website 1+ mentions |
Yevis cli (RRID:SCR_023204) | software resource, software application | Software CLI tool to support building and maintaining Yevis workflow registry. | Yevis workflow registry, Yevis, workflow registry with automated quality control, | is related to: Yevis web | Free, Available for download, Freely available | https://sapporo-wes.github.io/yevis-cli/getting_started | SCR_023204 | Yevis-cli | 2026-08-12 10:52:59 | 2 | ||||||||
|
FLIC Monitor Resource Report Resource Website 1+ mentions |
FLIC Monitor (RRID:SCR_018387) | software resource, software application | Software tool as user interface for running Fly Liquid Food Interaction Counter experiments. | Monitoring FLIC experiment, monitor fly liquid food experiment, fly liquid food interaction | PMID:24978054 | Free, Available for download, Freely available | SCR_018387 | Fly Liquid Food Interaction Counter Monitor | 2026-08-12 10:52:07 | 2 | |||||||||
|
Docker based GPU enabled Jupyterlab Resource Report Resource Website 1+ mentions |
Docker based GPU enabled Jupyterlab (RRID:SCR_022695) | software resource, software application | Open source, docker based, and GPU enabled jupyterlab notebook infrastructure that runs on public compute infrastructure of Galaxy Europe for rapid prototyping and developing end-to-end AI projects. Jupyterlab notebook in GPU enabled docker container for machine learning and deep learning. | Jupyterlab, GPU enabled jupyterlab notebook infrastructure, Galaxy Europe, public compute infrastructure | is related to: Jupyter Notebook | DOI:10.1101/2022.07.08.499333 | Free, Available for download, Freely available | biotools:gpu-enabled_docker_container_with_jupyterlab_for_ai | https://bio.tools/gpu-enabled_docker_container_with_jupyterlab_for_ai | SCR_022695 | 2026-08-12 10:52:46 | 2 | |||||||
|
Pyani Resource Report Resource Website 50+ mentions |
Pyani (RRID:SCR_021088) | data analytics software, software resource, software application | Software package and script for calculation of genome scale average nucleotide identity. Python3 module that provides support for calculating average nucleotide identity and related measures for whole genome comparisons, and rendering relevant graphical summary output. Where available, it takes advantage of multicore systems, and can integrate with SGE/OGE-type job schedulers for the sequence comparisons. | Genome scale average nucleotide identity calculation, nucleotide identity calculation, nucleotide, identity calculation | Free, Available for download, Freely available | SCR_021088 | 2026-08-12 10:52:28 | 90 | |||||||||||
|
org.Rn.eg.db Resource Report Resource Website 1+ mentions |
org.Rn.eg.db (RRID:SCR_018358) | software resource, software application | Software R tool for genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers. | Genome annotation, rat, mapping, Entrez Gene identifier | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_018358 | 2026-08-12 10:52:06 | 1 | ||||||||||
|
zmax_edf_merge_converter Resource Report Resource Website |
zmax_edf_merge_converter (RRID:SCR_022567) | software resource, software application | Software tool for comprehensive conversion of folder with Hypnodyne zmax EDF files into merged European Data Format. | hypnodyne, Zmax, converter, EDF, merge, python, windows | Free, Available for download, Freely available | SCR_022567 | 2026-08-12 10:52:54 | 0 | |||||||||||
|
GeCo3 Resource Report Resource Website 1+ mentions |
GeCo3 (RRID:SCR_018877) | software resource, software application | Software tool as DNA compressor that uses neural network to do mixing of experts. | DNA compressor, neural network, expert mixing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:geco3 | https://bio.tools/geco3 | SCR_018877 | 2026-08-12 10:52:15 | 2 | ||||||||
|
FluCalc Resource Report Resource Website 1+ mentions |
FluCalc (RRID:SCR_019322) | data analytics software, software resource, software application | Software tool as MSS-MLE calculator for Luria–Delbrück fluctuation analysis. | Estimator, fluctuation calculation, MSS-MLE, Ma-Sandri-Sarkar Maximum Likelihood Estimator, calculator, fluctuation analysis | has parent organization: Tufts University; Massachusetts; USA | NIGMS GM105473; NIGMS GM60987 |
PMID:29043640 | Free, Available for download, Freely available | SCR_019322 | flucalc, fluctuation calculation | 2026-08-12 10:52:14 | 1 | |||||||
|
OpenSCAD Resource Report Resource Website 10+ mentions |
OpenSCAD (RRID:SCR_018870) | software resource, software application | Software tool for creating solid 3D CAD objects. Used for creating 3D models focusing on CAD aspects of 3D modeling of machine parts. Reads in script file that describes object and renders 3D model from this script file. | Creating solid 3D objects, CAD object, 3D CAD object, creating objects, creating 3D models, 3D modeling, machine part modeling | Free, Available for download, Freely available | https://github.com/openscad/openscad/ | SCR_018870 | Solid 3D CAD Modeller | 2026-08-12 10:52:14 | 23 | |||||||||
|
1KA Resource Report Resource Website 10+ mentions |
1KA (RRID:SCR_019283) | software resource, software application | Open source software application that enables services for online surveys. Provides advanced support for all steps of web survey process. Conduct research and analysis from beginning to end. | Online surveys service, web survey process support | has parent organization: University of Ljubljana; Ljubljana; Slovenia | Restricted | SCR_019283 | 2026-08-12 10:52:14 | 13 | ||||||||||
|
BayesEpiModels Resource Report Resource Website 1+ mentions |
BayesEpiModels (RRID:SCR_019291) | software resource, software application | Software tool for accessing performance of different epidemiological models, including both growth and compartmental models, in Bayesian framework. | Stochastic growth model, Stochastic SIR model, Bayesian inference, epidemiological models, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:bayesepimodels | https://bio.tools/bayesepimodels | SCR_019291 | 2026-08-12 10:52:25 | 1 | ||||||||
|
FastANI Resource Report Resource Website 100+ mentions |
FastANI (RRID:SCR_021091) | data analytics software, software resource, software application | Software tool for fast alignment free computation of whole genome Average Nucleotide Identity . Supports pairwise comparison of both complete and draft genome assemblies. to calcualte the average nucleotide identity (ANI) between your samples. | whole genome, Average Nucleotide Identity, ANI, alignment identity estimates, whole genome, similarity estimation | Free, Available for download, Freely available | SCR_021091 | Fast Whole Genome Similarity Estimation | 2026-08-12 10:52:28 | 336 | ||||||||||
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Color Oracle Resource Report Resource Website 1+ mentions |
Color Oracle (RRID:SCR_018400) | software resource, software application | Software tool as free color blindness simulator for Windows, Mac and Linux. Design for Color Impaired. Takes guesswork out of designing for color blindness by showing you in real time what people with common color vision impairments will see.Color Oracle is open source, available on GitHub for Mac and Windows/Java. | Color blindness simulator, color imapried, color blind, color vision impairement | Free, Available for download, Freely available | https://github.com/nvkelso/color-oracle, https://github.com/nvkelso/color-oracle-java | SCR_018400 | 2026-08-12 10:52:07 | 8 | ||||||||||
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OmicsGAN Resource Report Resource Website 1+ mentions |
OmicsGAN (RRID:SCR_022976) | software resource, software application | Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals. | integrate two omics data, interaction network, generate one synthetic data corresponding to each omics profile, phenotype prediction | NSF III1755761; NIGMS R01GM113952; NIDA DK097771 |
PMID:34415323 | Free, Available for download, Freely available | SCR_022976 | Omics Generative Adversarial Network | 2026-08-12 10:52:58 | 1 | ||||||||
|
Bio-Chado-Schema Resource Report Resource Website |
Bio-Chado-Schema (RRID:SCR_024059) | software resource, software application | Standard object-relational mapping layer for use with GMOD Chado database schema. This layer is implemented with DBIx::Class, generated with the help of DBIx::Class::Schema::Loader module. | Standard object-relational mapping layer, GMOD Chado database schema, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-chado-schema-perl/ | SCR_024059 | libbio-chado-schema-perl, Bio-Chado-Schema - A standard DBIx-Class layer for the Chado database schema | 2026-08-12 10:53:09 | 0 | ||||||||
|
VOSviewer Resource Report Resource Website 100+ mentions |
VOSviewer (RRID:SCR_023516) | software resource, software application | Software tool for constructing and visualizing bibliometric networks. These networks may for instance include journals, researchers, or individual publications, and they can be constructed based on citation, bibliographic coupling, co-citation, or co-authorship relations. Offers text mining functionality that can be used to construct and visualize co-occurrence networks of important terms extracted from body of scientific literature. | constructing and visualizing bibliometric networks, text mining functionality, co-occurrence networks, | has parent organization: Leiden University; Leiden; Netherlands | PMID:36589296 | Free, Available for download, Freely available | SCR_023516 | VOSviewer version 1.6.19 | 2026-08-12 10:53:03 | 293 | ||||||||
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pyomo Resource Report Resource Website 1+ mentions |
pyomo (RRID:SCR_024188) | software resource, software application | Open source Python-based optimization modeling language with diverse set of optimization capabilities. | Python, optimization modeling language, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pyomo/ | SCR_024188 | 2026-08-12 10:53:11 | 5 |
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