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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GROMACS topology editors Resource Report Resource Website 1+ mentions |
GROMACS topology editors (RRID:SCR_025013) | gmxtras | software resource, software application | Software tool as set of Python scripts to modify GROMACS topology files, by adding content from different topology files and other GROMACS input files. Useful, particularly when system components are assembled outside of GROMACS, or in different steps within GROMACS. This helps prevent users from having to copy and paste significantly large blocks of text within topology files. | GROMACS, topology files, force fields, modify GROMACS topology files, | Free, Available for download, Freely available | SCR_025013 | 2026-08-12 10:53:16 | 2 | ||||||||||
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ICA-PNM Resource Report Resource Website |
ICA-PNM (RRID:SCR_024952) | data processing software, software resource, software application | Software de-noising pipeline combines noise regressors identified by tools such as PNM and ICA (and FIX) and effectively prepares them for entry into single FEAT model, thus allowing the user to clean data in single step. | clean data, de-noising, clean data in single step, | is listed by: FSL | Free, Freely available | SCR_024952 | 2026-08-12 10:53:21 | 0 | ||||||||||
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Genotype Sparse Compression Resource Report Resource Website 1+ mentions |
Genotype Sparse Compression (RRID:SCR_025071) | GSC | software resource, software application | Software tool for lossless compression of VCF files, designed to efficiently store and manage VCF files in compressed format. It accepts VCF/BCF files as input and utilizes advanced compression techniques to significantly reduce storage requirements while ensuring fast query capabilities. | lossless compression of VCF files, store and manage VCF files, compressed format, | SCR_025071 | Genotype Sparse Compression (GSC) | 2026-08-12 10:53:23 | 1 | ||||||||||
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fsl-cluster Resource Report Resource Website |
fsl-cluster (RRID:SCR_024938) | software resource, software application | Software application used to form clusters, report information about clusters and/or perform cluster based inference. | FSL, form clusters, report information about clusters, perform cluster based inference, | is a plug in for: FSL | Free, Freely available | SCR_024938 | cluster | 2026-08-12 10:53:21 | 0 | |||||||||
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XTRACT Resource Report Resource Website 1+ mentions |
XTRACT (RRID:SCR_024933) | software resource, software application | Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain. | automated tractography, tractography, human, macaque, brain | is a plug in for: FSL | Medical Research Council PhD Studentship UK ; Marie Skłodowska-Curie Individual Fellowship Grant ; Biotechnology and Biological Sciences Research Council ; Netherlands Organization for Scientific Research NWO Netherlands ; Sir Henry Dale Wellcome Trust Fellowship UK ; MRC Career Development Fellowship UK ; Wellcome Trust Collaborative Award UK ; UK Engineering and Physical Sciences Research Council ; Wellcome Trust grant UK ; Human Connectome Project ; NIMH 1U54MH091657; McDonnell Center for Systems Neuroscience at Washington University ; NIH ; UK Biobank Resource ; Wellcome Trust |
PMID:32407993 | Free, Freely available | SCR_024933 | 2026-08-12 10:53:16 | 4 | ||||||||
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eddy Resource Report Resource Website 1+ mentions |
eddy (RRID:SCR_024934) | data processing software, software resource, software application | Software tool for correcting eddy currents and movements in diffusion data. Used to predict undistorted data, to which actual observed images can be aligned, to estimate and to correct for volume-to-volume movement and off-resonance fields, to signal dropout caused by movement during diffusion encoding, within-volume movement and movement-induced changes of susceptibility-induced off-resonance field. In addition to correcting for these effects, the output from this framework offers description of off resonance and subject movement effects present in uncorrected data. | correcting eddy currents and movements, diffusion data correction, | is a plug in for: FSL | Free, Freely available | SCR_024934 | 2026-08-12 10:53:14 | 9 | ||||||||||
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randomise Resource Report Resource Website 10+ mentions |
randomise (RRID:SCR_024937) | software resource, software application | Software tool for nonparametric permutation inference on neuroimaging data. | nonparametric permutation inference, neuroimaging data | is a plug in for: FSL | PMID:24530839 | Free, Freely available | SCR_024937 | 2026-08-12 10:53:14 | 12 | |||||||||
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snm3C Pipeline Resource Report Resource Website 1+ mentions |
snm3C Pipeline (RRID:SCR_025041) | snM3C | data processing software, software resource, software application | Software open-source, cloud-optimized computational workflow for processing single-nucleus methylome and chromatin contact (snm3C) sequencing data. The workflow is designed to demultiplex and align raw sequencing reads, call chromatin contacts, and generate summary metrics. | data processing, single-nucleus methylome data, single-cell data, chromatin contact data, single-cell methylome and chromatin contact sequencing data, |
is organization facet of: BICCN is organization facet of: BRAIN Initiative Cell Atlas Network |
Free, Freely available | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/snM3C | SCR_025041 | , Single Nucleus Methly-Seq and Chromatin Capture, single-nucleus Methylome and Chromatin Contact, Single Nucleus Methly-Seq and Chromatin Capture (snM3C) | 2026-08-12 10:53:22 | 2 | |||||||
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Numba Resource Report Resource Website 1+ mentions |
Numba (RRID:SCR_025056) | software resource, software application | Open source JIT compiler that translates subset of Python and NumPy code into fast machine code. Can compile large subset of numerically-focused Python, including many NumPy functions. Has support for automatic parallelization of loops, generation of GPU-accelerated code, and creation of ufuncs and C callbacks. | Accelerate Python functions, JIT compiler, translate subset of Python and NumPy code into fast machine code, | Anaconda ; Inc. |
Free, Available for download, Freely available, | https://numba.pydata.org, https://github.com/numba/numba/blob/c6da26929c7fc18b06dd2e5fc86982cea828df6c/docs/source/index.rst | SCR_025056 | 2026-08-12 10:53:23 | 8 | |||||||||
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LDbase Resource Report Resource Website |
LDbase (RRID:SCR_025052) | service resource, data repository, storage service resource | NIH funded collaboration between researchers and librarians to build behavioral project oriented data repository containing decades of knowledge from educational and developmental sciences on individuals across the full range of abilities. | behavioral project oriented data, learning disabilities, | has parent organization: Florida State University; Florida; USA | NICHD R01HD095193 | Free, Freely available | r3d100014160 | https://doi.org/10.17616/R31NJNF4 | SCR_025052 | Learning and Development data repository | 2026-08-12 10:53:22 | 0 | ||||||
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Abaqus FEA Resource Report Resource Website 10+ mentions |
Abaqus FEA (RRID:SCR_024997) | software resource, software application | Software suite for finite element analysis and computer aided engineering. | Simulia, finite element analysis, computer aided engineering, | Restricted | https://en.wikipedia.org/wiki/Abaqus | SCR_024997 | Simulia Abaqus FEA | 2026-08-12 10:53:22 | 28 | |||||||||
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OutLyzer Resource Report Resource Website 1+ mentions |
OutLyzer (RRID:SCR_025120) | software resource, source code | Software tool for extracting low-allele-frequency tumor mutations from sequencing background noise in clinical practice. Detects variations, specifically low allele frequency variation, in next generation sequencing data. | Detects variations, variant caller, low allele frequency variation, extracting low-allele-frequency tumor mutations, next generation sequencing data | Institut National du Cancer | PMID:27825131 | Free, Available for download, Freely available | https://github.com/EtieM/outLyzer | SCR_025120 | 2026-08-12 10:53:19 | 1 | ||||||||
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Natural Products Atlas Resource Report Resource Website 10+ mentions |
Natural Products Atlas (RRID:SCR_025107) | NP Atlas | data or information resource, atlas, knowledge base | Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles. | FAIR principles, microbial natural products discovery, natural product structures, bacterial and fungal natural products, visualize chemical diversity, | has parent organization: Simon Fraser University; British Columbia; Canada | NSERC Discovery ; NCCIH U41 AT008718; NIGMS R01 GM125943; NCCIH F31 AT010098; NCI F31 CA236237; NCCIH T32 AT007533; NIH D43 TW010530; NSF ; BBSRC ; Carnegie Trust for the Universities of Scotland ; Netherlands eScience Center ; Sao Paulo Research Foundation ; NCCIH AT008718; NIGMS GM124461; Natural Sciences and Engineering Research Council of Canada ; Ministry of Science ; Technology and Telecommunications of Costa Rica |
PMID:31807684 DOI:10.1093/nar/gkab941 |
Free, Freely available, | SCR_025107 | , The Natural Products Atlas, The Natural Products Atlas 2.0 | 2026-08-12 10:53:18 | 36 | ||||||
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JaCoP Resource Report Resource Website 10+ mentions |
JaCoP (RRID:SCR_025164) | JaCoP | software toolkit, software resource, source code | Software toolbox as plugin for ImageJ that supports colocalization analysis in light microscopy. Used for subcellular colocalization analysis under ImageJ that integrates current global statistic methods and novel object-based approach. | ImageJ, subcellular colocalization analysis, colocalization analysis, | is a plug in for: ImageJ | PMID:17210054 | Free, Available for download, Freely available | SCR_025164 | Just Another Colocalization Plugin | 2026-08-12 10:53:24 | 37 | |||||||
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bioKGQA-KGT Resource Report Resource Website 1+ mentions |
bioKGQA-KGT (RRID:SCR_025176) | software resource, source code | Software contains all scripts and instructions for running Knowledge Graph-based Thought model, which is knowledge graph enhanced LLMs framework for pan-cancer question answering. | pan-cancer knowledge graph, large language model, knowledge graph question answering, | Free, Available for download, Freely available | SCR_025176 | 2026-08-12 10:53:25 | 2 | |||||||||||
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krypto Resource Report Resource Website |
krypto (RRID:SCR_025179) | software resource, source code | Software C++ implementation of multivariate quadratic FHE. | C++ implementation, multivariate quadratic FHE, | Free, Available for download, Freely available | SCR_025179 | 2026-08-12 10:53:25 | 0 | |||||||||||
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PhysiCell Studio Resource Report Resource Website 10+ mentions |
PhysiCell Studio (RRID:SCR_025311) | software resource, source code | Software graphical tool to allow easy editing of (XML) model, create initial positions of cells, run simulation, and visualize results. To contribute, fork and make PRs to the development branch. Used to create, execute, and visualize multicellular model using PhysiCell. | create, execute, visualize, multicellular model, create initial positions of cells, | NSF ; NCI U01 CA232137; Breast Cancer Research Foundation ; Jayne Koskinas Ted Giovanis Foundation for Health and Policy ; European Commission |
PMID:37961612 | Free, Available for download, Freely available | SCR_025311 | 2026-08-12 10:53:24 | 15 | |||||||||
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Prisma/DB Resource Report Resource Website |
Prisma/DB (RRID:SCR_025246) | software resource, source code | Software application as cryptographic security layer for relational database systems, that currently supports Microsoft SQL Server, MySQL, MariaDB, PostgreSQL and CockroachDB. Security layer for relational database systems. | Security layer, security for relational database systems, | Free, Available for download, Freely available | SCR_025246 | 2026-08-12 10:53:22 | 0 | |||||||||||
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cameraCalibrationCMOS Resource Report Resource Website 1+ mentions |
cameraCalibrationCMOS (RRID:SCR_025339) | software resource, source code | Software for performing pixelwise calibration of sCMOS cameras. MATLAB code and instructions for routine camera calibration. | MATLAB code, instructions for routine camera calibration, performing pixelwise calibration, sCMOS cameras, | Free, Available for download, Freely available | SCR_025339 | 2026-08-12 10:53:28 | 2 | |||||||||||
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Winnowmap Resource Report Resource Website 10+ mentions |
Winnowmap (RRID:SCR_025349) | software resource, source code | Software tool as long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. Winnowmap2 computes each read mapping through collection of confident subalignments. This approach is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats. | long-read mapping, ONT and PacBio reads, repetitive reference sequences, paralog specific variants within repeats, | NHGRI ; Indian Institute of Science |
PMID:35365778 | Free, Available for download, Freely available | SCR_025349 | Winnowmap2 | 2026-08-12 10:53:28 | 26 |
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