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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MindTheGap Resource Report Resource Website 1+ mentions |
MindTheGap (RRID:SCR_024115) | data analysis software, data processing software, software application, software resource | Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. | perform detection and assembly of DNA insertion variants, NGS read datasets, reference genome, call insertions, donor genome, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_05472 | https://sources.debian.org/src/mindthegap/ | SCR_024115 | mindthegap | 2026-08-29 11:28:07 | 3 | |||||||
|
MafFilter Resource Report Resource Website 10+ mentions |
MafFilter (RRID:SCR_024105) | data analysis software, data processing software, software application, software resource | Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc. | genome alignments analysis, parse and manipulate MAF files, genome alignment processor, | is listed by: Debian | PMID:24447531 | Free, Available for download, Freely available, | OMICS_06743 | https://sources.debian.org/src/maffilter/, https://github.com/jydu/maffilter | SCR_024105 | MafFilter a genome alignment processor, maffilter | 2026-08-29 11:28:26 | 12 | ||||||
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sparta Resource Report Resource Website 10+ mentions |
sparta (RRID:SCR_024349) | data analysis software, data processing software, software application, software resource | Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms. | analyzing single-end Illumina RNA-seq data, | is listed by: Debian | PMID:26847232 | Free, Available for download, Freely available, | https://sources.debian.org/src/sparta/ | SCR_024349 | SPARTA | 2026-08-29 11:28:08 | 10 | |||||||
|
Maude Resource Report Resource Website |
Maude (RRID:SCR_024108) | data or information resource, portal, project portal, software library, software resource, software toolkit | Software high performance reflective language and system supporting both equational and rewriting logic specification and programming for wide range of applications.Supports equational specification and programming, rewriting logic computation. | equational and rewriting logic specification and programming, equational specification and programming, rewriting logic computation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/maude/, http://maude.cs.illinois.edu/w/index.php/Maude_download_and_installation | SCR_024108 | Maude, maude | 2026-08-29 11:28:07 | 0 | ||||||||
|
mPTP Resource Report Resource Website 1+ mentions |
mPTP (RRID:SCR_024121) | data analysis software, data processing software, software application, software resource | Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets. | single locus species delimitation, ML delimitation from inferred phylogenetic tree of the samples, ML delimitation, inferred phylogenetic tree, samples inferred phylogenetic tree, | is listed by: Debian | PMID:28108445 | Free, Available for download, Freely available, | OMICS_15264 | https://sources.debian.org/src/mptp/ | SCR_024121 | , mptp, multi-rate Poisson Tree Processes | 2026-08-29 11:28:33 | 2 | ||||||
|
Yanosim Resource Report Resource Website |
Yanosim (RRID:SCR_024363) | Yanosim | simulation software, software application, software resource | Software tool as read simulator for nanopore DRS datasets. | read simulator for nanopore DRS datasets, read simulator, nanopore DRS datasets, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/yanosim/ | SCR_024363 | yanosim, yet another nanopore simulator | 2026-08-29 11:28:08 | 0 | |||||||
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Molekel Resource Report Resource Website 1+ mentions |
Molekel (RRID:SCR_024122) | data processing software, data visualization software, software application, software resource | Open source multi platform molecular visualization program. | molecular visualization | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/molekel/ | SCR_024122 | molekel | 2026-08-29 11:28:26 | 1 | ||||||||
|
MRtrix3 Resource Report Resource Website 100+ mentions |
MRtrix3 (RRID:SCR_024123) | data analysis software, data processing software, software application, software resource | Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses. | diffusion MRI analyses, tractography, next generation group level analyses, | is listed by: Debian | PMID:31473352 | Free, Available for download, Freely available, | https://sources.debian.org/src/mrtrix3/ | SCR_024123 | mrtrix3 | 2026-08-29 11:28:07 | 335 | |||||||
|
MIA Resource Report Resource Website |
MIA (RRID:SCR_024081) | data processing software, image analysis software, software application, software resource | Software toolkit for gray scale medical image analysis. Provides combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in command shell and prototype algorithms as shell scripts. MIA is build around a plug-in structure that makes it easy to add functionality without compromising the original code base, and it makes use of wide variety of external libraries that provide additional functionality. | gray scale medical image analysis, interactive image processing, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/mia/ | https://sources.debian.org/src/libmialm/ | SCR_024081 | python3-mia, libmia-2.4-dev, mia-tools, mia-viewit, libvistaio-dev, libmialm-dev, libmiaviewit-dev, libmialm, mialmpick | 2026-08-29 11:28:33 | 0 | |||||||
|
PyMouseTracks Resource Report Resource Website |
PyMouseTracks (RRID:SCR_024453) | PMT | instrument resource, software resource, source code | Open source, adaptable tracking system for multiple rodents. Scalable and customizable system for tracking and behavior assessment consists of Raspberry Pi based video and RFID acquisition. Maximum of six rodents of any coat color can be tracked simultaneously in any user defined arena with few restrictions. For pose estimation and travel trajectory analysis, PyMouseTracks supports interfacing with open source packages such as DeepLabCut and Traja. | OpenBehavior, tracking system, tracking system for multiple rodents, Raspberry Pi based video, RFID acquisition, |
is listed by: OpenBehavior is related to: DeepLabCut |
Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/pymousetracks/ | SCR_024453 | 2026-08-29 11:28:35 | 0 | ||||||||
|
DataMares Resource Report Resource Website |
DataMares (RRID:SCR_024575) | data or information resource, portal, topical portal | Open source, and interactive platform to resolve trans disciplinary problems related to coastal and marine ecosystem. Data sharing and science communication portal holds amounts of fishery, reef, and mangrove data pertaining to Gulf of California and Mexico specific oceans, and delivers this information in interactive and easily digestible manner. Consistently expands library of datasets while improving functionality and overall usability of the platform. Facilitate access to scientific knowledge and data to promote transparency, education, and deeper understanding of Mexico’s ecosystems and their biodiversity to bridge gap between science and design process of conservation and resource management programs. | coastal and marine ecosystem data, fishery data, reef data, mangrove data, Gulf of California and Mexico, |
is listed by: DataCite has parent organization: University of California; California; USA |
Free, Freely available | https://api.datacite.org/dois?prefix=10.13022, https://library.ucsd.edu/dc/collection/bb3039464b | SCR_024575 | 2026-08-29 11:28:29 | 0 | |||||||||
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CodeMeta Generator Resource Report Resource Website 1+ mentions |
CodeMeta Generator (RRID:SCR_024601) | software resource | Web application that creates CodeMeta files. | CodeMeta files, CodeMeta files creation, exchange schema for software metadata files, | has parent organization: Software Heritage | Free, Freely available | SCR_024601 | 2026-08-29 11:28:29 | 2 | ||||||||||
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Software Heritage Resource Report Resource Website 1+ mentions |
Software Heritage (RRID:SCR_024602) | nonprofit organization | Software Heritage provides service for archiving and referencing historical and contemporary software with focus on human readable source code. The site was unveiled in 2016 by Inria and is supported by UNESCO. The project itself is structured as non‑profit multi‑stakeholder initiative. | UNESCO, Inria, archiving and referencing historical and contemporary software, | is parent organization of: CodeMeta Generator | SCR_024602 | 2026-08-29 11:28:17 | 2 | |||||||||||
|
ProPlot Resource Report Resource Website |
ProPlot (RRID:SCR_024584) | data processing software, data visualization software, software application, software resource | Software tool as succinct matplotlib wrapper for making publication quality graphics. | matplotlib wrapper, making publication quality graphics, | Free, Available for download, Freely available | https://zenodo.org/doi/10.5281/zenodo.3873878, https://github.com/proplot-dev/proplot | SCR_024584 | 2026-08-29 11:28:36 | 0 | ||||||||||
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Ocular Resource Report Resource Website 1+ mentions |
Ocular (RRID:SCR_024467) | data acquisition software, data processing software, software application, software resource | Photometrics acquisition software to capture, save and publish images and movies. Allows users of color and monochrome cameras to capture high quality images and videos from their microscope or lens system. | Teledyne Photometrics, photometrics acquisition, capture control, images and movies capture, microscope, lens system, image, video | Free, Freely available | SCR_024467 | Teledyne Photometrics Ocular | 2026-08-29 11:28:28 | 2 | ||||||||||
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Engineering Biology Research Consortium Resource Report Resource Website |
Engineering Biology Research Consortium (RRID:SCR_024578) | EBRC | nonprofit organization | Non-profit, public-private partnership dedicated to bringing together inclusive community committed to advancing engineering biology to address national and global needs. We showcase cutting-edge research in engineering biology, identify pressing challenges and opportunities in research and application, articulate compelling research roadmaps and programs to address them, and provide timely access to other key developments in engineering biology. | advancing engineering biology, national and global needs, engineering biology, |
is listed by: DataCite has parent organization: University of California; California; USA |
https://api.datacite.org/dois?prefix=10.25498 | SCR_024578 | The Engineering Biology Research Consortium (EBRC) | 2026-08-29 11:28:16 | 0 | ||||||||
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Customizable Multielectrode Array Resource Report Resource Website |
Customizable Multielectrode Array (RRID:SCR_024551) | CMEA | instrument resource | Simple, lightweight, and low cost customizable multielectrode array for Local Field Potential recordings. Used to collect LFP data from different brain regions simultaneously in rats. Can be modified to record single unit and multiunit activity in addition to LFP activity using both wired and wireless neural data acquisition systems. | OpenBehavior, instrument, multielectrode array, Local Field Potential Recordings, LFP recordings, collect LFP data, brain regions LFP data, record single unit and multiunit activity, wired neural data acquisition system, wireless neural data acquisition system, explore neural activity, | is listed by: OpenBehavior | Government of Canada Natural Sciences and Engineering Research Council of Canada | Free, Freely available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_024551.pdf | SCR_024551 | , CMEA: Customizable Multielectrode Arrays, 16-channel customizable multielectrode array | 2026-08-29 11:28:29 | 0 | ||||||
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Berkeley Seismological Laboratory Resource Report Resource Website |
Berkeley Seismological Laboratory (RRID:SCR_024552) | data or information resource, laboratory portal, organization portal, portal | Acts as part of statewide earthquake monitoring system, the California Integrated Seismic Network. Conducts essential research on earthquakes and solid earth processes while collecting and delivering high quality geophysical data. Data from these geophysical networks are recorded digitally and are archived at the Northern California Earthquake Data Center, which is located at the Berkeley Seismological Lab. | California Integrated Seismic Network, statewide earthquake monitoring system, research on earthquakes and solid earth processes, geophysical data, Northern California Earthquake Data Center, |
is listed by: DataCite has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: University of California; California; USA |
Free, Freely available | https://api.datacite.org/dois?prefix=10.7932 | SCR_024552 | Berkeley Seismological Lab | 2026-08-29 11:28:36 | 0 | ||||||||
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Sparrow-data Resource Report Resource Website |
Sparrow-data (RRID:SCR_024432) | data or information resource, database, software application, software resource | Software for managing geochemical data created by individual geochronology laboratory. Designed for flexibility and extensibility, so that it can be tailored to the needs of individual analytical labs that manage wide variety of data. Database set up for metadata tracking. | geology, managing geochemical data, individual geochronology laboratory, metadata tracking, | Free, Freely available | SCR_024432 | 2026-08-29 11:28:35 | 0 | |||||||||||
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Biocode Commons Resource Report Resource Website |
Biocode Commons (RRID:SCR_024553) | data or information resource, portal, topical portal | Platform provides resources for genomic observations from collection to analysis and publication. Works with standards community to ensure clear vocabularies and useful ontologies for biological resources and related assets. Biocode Commons is also collaborating on development of Biological Collections Ontology, working to better integrate ontologies, vocabularies, and relevant standards that are related to BCO. | Biological Collections Ontology, Biological Collections Ontology development, genomic observations, collection, analysis, publication, standards community, |
is listed by: DataCite is listed by: University of California; California; USA has parent organization: University of California; California; USA |
Free, Freely available | https://api.datacite.org/dois?prefix=10.7286 | SCR_024553 | 2026-08-29 11:28:15 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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