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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BeatBox Resource Report Resource Website 10+ mentions |
BeatBox (RRID:SCR_015780) | simulation software, software application, software resource | Simulation environment that combines flexible script language user interface with computational tools in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level. It aims to include cell excitation, tissue/anatomy models, and stimulation protocols in BeatBox scripts so that simulation run either sequentially or in parallel (MPI) without re-compilation. | simulation, cardiac electrophysiology, computation, script language, c, ecg, heart, cardiology, simulation protocol | EPSRC EP/I029664; EPSRC EP/N014391/1; EPSRC EP/P008690/1 |
PMID:28467407 | Free, Available for download | https://github.com/beatbox-heart/beatbox-public/tree/v1.7.982 | SCR_015780 | SciCrunch Registry | BeatBox—HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology. | 2026-09-26 02:15:37 | 11 | |||||||
|
statsmodel Resource Report Resource Website 100+ mentions |
statsmodel (RRID:SCR_016074) | data analysis software, data processing software, software application, software resource | Statistical software that provides classes and functions for the estimation of many different models, as well as for conducting statistical tests, and statistical data exploration. The results are tested against existing statistical packages to ensure that they are correct. http://conference.scipy.org/proceedings/scipy2010/seabold.html | python, statistic, estimate, econometric, model, library, class, function, r | Open source, Available for download | SCR_016074 | SciCrunch Registry | Statsmodels: Econometric and Statistical Modeling with Python | 2026-09-26 02:15:41 | 253 | ||||||||||
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Dotter Resource Report Resource Website 50+ mentions |
Dotter (RRID:SCR_016080) | alignment software, data analysis software, data processing software, data visualization software, image analysis software, sequence analysis software, software application, software resource | Software for sequence alignment that is a graphical dot-matrix program for detailed comparison of two sequences. | sequence, alignment, graphical, dot-matrix, program, comparison, two, detail |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
NHGRI U54 HG00455; Wellcome Trust Grant 098051 |
PMID:26801397 | Free, Available for download | SCR_016080 | SciCrunch Registry | Seqtools Dotter | 2026-09-26 02:15:41 | 84 | |||||||
|
LI-COR Image Studio Software Resource Report Resource Website 100+ mentions |
LI-COR Image Studio Software (RRID:SCR_015795) | data acquisition software, data processing software, image analysis software, software application, software resource | Image analysis software that acquires, analyzes, and archives research data without altering raw findings. It integrates data and changes how pixels are mapped to the screen for clearer display, rather than altering the pixels of the image data itself. | image studio, image analysis, raw data, image acquisition, pixel mapping, image viewer | Commercially available, Available for purchase, Free version available, Runs on Windows, Runs on MAC OS | https://www.licor.com/bio/products/software/image_studio | SCR_015795 | SciCrunch Registry | LI-COR Image Studio, Image Studio™ Software | 2026-09-26 02:15:37 | 223 | |||||||||
|
Falcon Resource Report Resource Website 100+ mentions |
Falcon (RRID:SCR_016089) | alignment software, data processing software, image analysis software, software application, software resource | Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes. | fast, aligner, sequencing, diploid, genome, assembly, non-inbred, rearranged, heterozygous, single-molecule |
is listed by: Debian is listed by: OMICtools is related to: Howard Hughes Medical Institute |
Gordon and Betty Moore Foundation GBMF 3034; National Science Foundation DBI-1350041; National Science Foundation IOS-1237880; National Science Foundation MCB 0929402; National Science Foundation MCB 1122246; NHGRI R01 HG006677 |
PMID:27749838 | Free, Available for download, Freely available | OMICS_13514 | https://sources.debian.org/src/falcon/ | SCR_016089 | SciCrunch Registry | 2026-09-26 02:15:41 | 293 | ||||||
|
Sigma: Millicell Cell Culture Inserts Resource Report Resource Website 10+ mentions |
Sigma: Millicell Cell Culture Inserts (RRID:SCR_015799) | instrument resource | Equipment that provides physical support for cell cultures. These cell culture inserts feature attachment and suspension cells that can access media from both their apical and basolateral sides. | cell culture, culture insert, hardware, attachment, suspension cell, apical side, basolateral side, instrument, equipment | Commercially available, Available for purchase | https://drive.google.com/file/d/1iKvbwq8VXv1PtD0ItetDiDk8tUv0RwlR/view?usp=drivesdk | https://www.emdmillipore.com/US/en/product/Millicell-Cell-Culture-Inserts, MM_NF-C10504?amp%3Bbd=1&bd=1#documentation | http://www.merckmillipore.com/ES/es/product/Millicell-Cell-Culture-Inserts, MM_NF-C10504?ReferrerURL=https%3A%2F%2Fwww.google.es%2F&bd=1 | SCR_015799 | SciCrunch Registry | Millicell® Cell Culture Inserts | 2026-09-26 02:15:37 | 10 | |||||||
|
Adobe Audition Resource Report Resource Website 1+ mentions |
Adobe Audition (RRID:SCR_015796) | authoring tool, data analysis software, data processing software, software application, software resource, software toolkit | Software for sound analysis, audio editing, and audio recording. It features multitrack, waveform, and spectral display for creating, mixing, editing, and restoring audio content for research or non-research purposes. | audio, editing, recording, sound analysis, audio analysis, audio editing, adobe | Commercially available, Available for purchase | SCR_015796 | SciCrunch Registry | Adobe Audition CC | 2026-09-26 02:15:37 | 8 | ||||||||||
|
Exonerate Resource Report Resource Website 100+ mentions |
Exonerate (RRID:SCR_016088) | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence, alignment, pairwise, comparison, dynamic, programming, heuristic, bio.tools |
is used by: ExonerateTransferAnnotation is listed by: Debian is listed by: bio.tools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:15713233 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:exonerate | https://bio.tools/exonerate | SCR_016088 | SciCrunch Registry | 2026-09-26 02:15:42 | 376 | |||||||
|
DOMALIGN Resource Report Resource Website |
DOMALIGN (RRID:SCR_016085) | alignment software, data processing software, image analysis software, software application, software resource | Software commands for Extra EMBOSS and protein domain alignment. The DOMALIGN programs were developed by Jon Ison and colleagues at MRC HGMP for their protein domain research. They are included as an EMBASSY package as a work in progress. | protein, domain, alignment, embassy, dhf, daf, fragment, redundancy, psi-blast | is listed by: Debian | Free, Available for download | https://sources.debian.org/src/embassy-domalign/ | SCR_016085 | SciCrunch Registry | Embassy-domalign | 2026-09-26 02:15:41 | 0 | ||||||||
|
NAPR: Neuroanatomical Age Prediction using R Resource Report Resource Website 1+ mentions |
NAPR: Neuroanatomical Age Prediction using R (RRID:SCR_015759) | NAPR | data repository, service resource, storage service resource | Cloud-based framework that allows users to estimate the age of individual subjects using cortical thickness maps derived from their own locally processed T1-weighted whole brain MRI scans. The provided age prediction models were trained using (i) relevance vector machines and (ii) Gaussian processes machine learning methods applied to cortical thickness surfaces obtained using Freesurfer v5.3. | neuroanatomy, prediction, r, neuroimaging, mri scan, cortical thickness, relevance vector | DOI:10.1101/099309 | Free, Available for download | http://www.cloudneuro.org/ | SCR_015759 | SciCrunch Registry | Neuroanatomical Age Prediction using R | 2026-09-26 02:15:37 | 1 | |||||||
|
Real time localization system for autonomous robots Benchmark Dataset Resource Report Resource Website |
Real time localization system for autonomous robots Benchmark Dataset (RRID:SCR_015756) | Dataset that can be used to analyze cyber-attacks to an indoor real time localization system for autonomous robots. Data have been gathered in an indoor mock-up apartment using an autonomous robot with an on-board Real Time Location System (RTLS). | benchmark, neural network, machine learning, autonomous robot, real time location system, rtls, training data, cyber-attack | is related to: Range-based people tracker classifiers Benchmark Dataset | Freely available, Available for download | SCR_015756 | SciCrunch Registry | Benchmark dataset for analysis of cyber-attacks to an indoor real time localization system for autonomous robots | 2026-09-26 02:15:37 | 0 | ||||||||||
|
Brain-CODE Resource Report Resource Website 10+ mentions |
Brain-CODE (RRID:SCR_015877) | data repository, service resource, storage service resource | Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders. | informatics, data storage, brain disorder | brain disorder, neurological disorder, informatics platform, data repository, data storage service, neuroscience | Public, Freely available, The research community can contribute to this resource | r3d100012181 | https://doi.org/10.17616/R3CK9G | SCR_015877 | SciCrunch Registry | 2026-09-26 02:15:38 | 49 | ||||||||
|
Antha Resource Report Resource Website |
Antha (RRID:SCR_015761) | software resource | Software language for methods to simplify protocols into reusable components that can be exchanged or removed to produce simple, reproducible, and scalable workflows. It allows users to develop, execute, and analyse biological experiments faster, while also introducing standardization and modularity to bioengineering. | software language, programming language, method, protocol, bioengineering, standardization, robot, robotics software | Freely available | https://github.com/antha-lang/antha | SCR_015761 | SciCrunch Registry | Synthace Antha | 2026-09-26 02:15:37 | 0 | |||||||||
|
MetaNetX Resource Report Resource Website 50+ mentions |
MetaNetX (RRID:SCR_015882) | data access protocol, software resource, web service | Web application to perform automated model construction and genome annotation for large-scale metabolic networks. Platform for accessing, analyzing and manipulating genome-scale metabolic networks (GSM) as well as biochemical pathways. | automated model construction, genome annotation, model, construction, genome, annotation, metabolic network, repository, gsm, biochemical, pathway | SIB Swiss Institute of Bioinformatics ; Swiss Federal Government ; Swiss National Science Foundation |
PMID:26527720 PMID:23357920 PMID:23172809 |
Free, Freely available | SCR_015882 | SciCrunch Registry | MNXref, MetaNetX: Automated Model Construction and Genome Annotation for Large-Scale Metabolic Networks | 2026-09-26 02:15:39 | 94 | ||||||||
|
Canu Resource Report Resource Website 1000+ mentions |
Canu (RRID:SCR_015880) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Canu is a fork of the Celera Assembler and is designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). | long-read, assembly, k-mer, weighting, repeat separation, adaptive, pacbio, single-molecule, sequencing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Celera assembler |
National Human Genome Research Institute ; National Science Foundation NSF IOS-1237993; US Department of Homeland Security (DHS) HSHQDC-07-C-00020 |
PMID:28298431 DOI:10.1101/071282 |
Free, Available for download | OMICS_14592, biotools:canu | http://canu.readthedocs.io/en/latest/, https://bio.tools/canu, https://sources.debian.org/src/canu/ | SCR_015880 | SciCrunch Registry | 2026-09-26 02:15:38 | 2451 | ||||||
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Cassiopee Resource Report Resource Website |
Cassiopee (RRID:SCR_016056) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity. | genomic, sequence, DNA, RNA, protein, scan, subsequence, search, match, substitution, distance, Hamming, insertion, deletion |
is listed by: Debian is listed by: OMICtools has parent organization: Durham University; Durham; England |
Free, Available for download | OMICS_19794 | https://sources.debian.org/src/cassiopee/ | SCR_016056 | SciCrunch Registry | cassiopee-c | 2026-09-26 02:15:41 | 0 | |||||||
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Cdbfasta Resource Report Resource Website |
Cdbfasta (RRID:SCR_016057) | CDB | data compression software, data processing software, data transfer software, software application, software resource, software toolkit | Software tool for indexing and retrieval of nucleotide sequences from FASTA (DNA and protein sequence alignment software) record databases. It has the option to compress data records. | index, retrieval, nucleotide, sequence, fasta, database, multi file, compress, record |
is listed by: Debian is listed by: OMICtools has parent organization: Carnegie Mellon University; Pennsylvania; USA has parent organization: University of Pittsburgh; Pennsylvania; USA |
The Free Software Foundation (FSF) | Free, Available for download | OMICS_19793 | https://github.com/gpertea/cdbfasta, https://sources.debian.org/src/cdbfasta/ | SCR_016057 | SciCrunch Registry | Constant DataBase | 2026-09-26 02:15:41 | 0 | |||||
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eHistology Resource Report Resource Website 1+ mentions |
eHistology (RRID:SCR_015887) | atlas, data or information resource, data repository, image repository, service resource, storage service resource | Image repository that allows researchers to interactively explore a collection of cellular-resolution colour histology images detailing mouse development. The original histological sections have been re-digitised at high resolution, in colour and in collaboration with Elsevier, the eHistology Atlas provides the annotations as presented in the original printed version. | histology, embryo, mouse, section, atlas, anatomy, imaging, 2d, spatial, image, repository, annotation | has parent organization: University of Edinburgh; Scotland; United Kingdom | Medical Research Council | PMID:26015534 | Free, Public | http://www.emouseatlas.org/emap/about/what_is_eHistology.html | SCR_015887 | SciCrunch Registry | 2026-09-26 02:15:39 | 1 | |||||||
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Autoprotocol Resource Report Resource Website 1+ mentions |
Autoprotocol (RRID:SCR_015764) | software resource | Language standard for automating English language protocols. Autoprotocol specifies experimental protocols for biological research as a way to define experiments that could be run over the internet on remote robotic automation. | language, protocol, research publication, automation, translation | Freely available | SCR_015764 | SciCrunch Registry | BioIO | 2026-09-26 02:15:37 | 3 | ||||||||||
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Stimfit Resource Report Resource Website 10+ mentions |
Stimfit (RRID:SCR_016050) | data analysis software, data processing software, software application, software resource | Software for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy. | electrophysiology, python, numpy, scipy, numerical, library, stimulus, analysis |
uses: NumPy uses: SciPy |
European Research Council ; Gatsby Charitable Foundation ; Wellcome Trust |
PMID:24600389 | Free, Available for download | SCR_016050 | SciCrunch Registry | 2026-09-26 02:15:41 | 41 |
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