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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BisoGenet Resource Report Resource Website 1+ mentions |
BisoGenet (RRID:SCR_018502) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18, 2020. Software package to create, visualize and analyze biological networks. Can include coding relations to distinguish between genes and their products. BisoGenet client is designed to work as Cytoscape plugin for querying server along with graph topology analysis and visualization options for easing interpretation process. | Center for Genetic Engineering and Biotechnology from Havana ; Cuba. ; INSPUR Electronic Information Industry ; Beijing |
PMID:20163717 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_018502 | 2026-09-19 12:53:52 | 4 | ||||||||||
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Campden Instruments: Vibroslice vibrating microtome Resource Report Resource Website 1+ mentions |
Campden Instruments: Vibroslice vibrating microtome (RRID:SCR_018460) | instrument resource | Vibrating microtome manufactured by Campden Instruments. 752 Vibroslice tissue cutter for manual tissue transport. | vibratome, vibrating microtome, Campden Instruments Inc., Vibroslice | Restricted | https://www.limef.com/Downloads/752-752M%20manual.pdf | SCR_018460 | 752 vibroslice tissue cutter | 2026-09-19 12:53:52 | 3 | |||||||||
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Fujifilm: FLA-5100 Scanner Resource Report Resource Website |
Fujifilm: FLA-5100 Scanner (RRID:SCR_018581) | instrument resource | EImaging scanner that images fluorescent and radioisotopic samples. It can be used for protein electrophoresis, genomics array analysis, fluorescence, radioisotope detection, and chemiluminescence detection by direct detection method. | Scanner, Instrument, Equipment, ABRF | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018581.pdf | Model_Number_FLA_1500, SCR_019925 | http://www.raytek.co.uk/Brochures/FLA5100%20UK-IE%20Brochure.pdf | SCR_018581 | 2026-09-19 12:53:54 | 0 | |||||||||
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Illumina: cBot Genetic Amplifier Resource Report Resource Website 1+ mentions |
Illumina: cBot Genetic Amplifier (RRID:SCR_018580) | instrument resource | Genetic amplifier that uses amplification to create single molecule DNA templates and dispense reagents. It also controls reaction times, flow rates, and temperatures. | Illumina, Genetic Amplifier, Instrument Equipment, USEDit | is listed by: USEDit | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018580.pdf | SCR_020129, Model_Number_cBot | https://www.illumina.com/documents/products/datasheets/datasheet_cbot.pdf | https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/cbot/cbot-system-guide-15006165-04.pdf | SCR_018580 | 2026-09-19 12:53:54 | 1 | ||||||
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Kent Scientific: Coda Blood Pressure System Resource Report Resource Website 10+ mentions |
Kent Scientific: Coda Blood Pressure System (RRID:SCR_018585) | instrument resource | CODA mouse rat tail-cuff system was designed to allow accurate blood pressure measurement in mice and rats. Blood pressure is measured in the tail of the mouse or rat using Volume Pressure Recording (VPR) sensor technology. Using the included software allows you to continuously view data in real-time. | Blood Pressure System, Instrument, Equipment, Mouse Blood Pressure Measuring Equipment, USEDit, Kent Scientific | is listed by: USEDit | Restricted | https://www.kentscientific.com/Customer-Content/www/products/Files/CODA_High_Thrpt_Manual_V2_00_02.pdf | SCR_018585 | 2026-09-19 12:53:54 | 13 | |||||||||
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LASTZ Resource Report Resource Website 50+ mentions |
LASTZ (RRID:SCR_018556) | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software package for sequence alignment. Pairwise aligner for aligning DNA sequences. Designed to handle sequences size of human chromosomes and from different species. Useful for sequences produced by NGS sequencing technologies. | Sequence, sequence alignment, pairwise aligner, DNA sequence alingning, human chromosome, Next Generation Sequencing technology data | has parent organization: Miller Lab at the Penn State Center for Comparative Genomics and Bioinformatics | Free, Available for download, Freely available | http://www.bx.psu.edu/~rsharris/lastz/, https://github.com/lastz/lastz | SCR_018556 | 2026-09-19 12:53:53 | 54 | |||||||||
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Agilent: 3100 OFFGEL Fractionator Resource Report Resource Website 1+ mentions |
Agilent: 3100 OFFGEL Fractionator (RRID:SCR_018433) | instrument resource | Agilent 3100 OFFGEL Fractionator performs isoelectric focusing of proteins or peptides in immobilized pH gradient (IPG) gel strips. | Fractionator, Instrument, Equipment, Electrophoresis, Agilent, USEDit, ABRF, | is listed by: USEDit | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018433.pdf | SCR_018442, SCR_019388 | https://www.agilent.com/Library/usermanuals/Public/G3100-90001_OFFGEL_UserManual_ebook.pdf | SCR_018433 | Agilent 3100 OFFGEL Fractionator | 2026-09-19 12:53:52 | 1 | |||||||
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Thermo Fisher: Applied Biosystems: ABI Voyager DE Pro MALDI-Mass Spectrometer Resource Report Resource Website |
Thermo Fisher: Applied Biosystems: ABI Voyager DE Pro MALDI-Mass Spectrometer (RRID:SCR_018432) | instrument resource | Benchtop MALDI TOF mass spectrometer that has linear and reflector analyzer. It is used to analyze organic and inorganic compounds, protein identification, synthetic peptide validation, and polymer analysis. | Benchtop Mass Spectrometer, MALDI TOF, Instrument, Equipment, ABI, MALDI, ABRF, USEDit | is listed by: USEDit | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018432.pdf | , SCR_018445 | https://tools.thermofisher.com/content/sfs/brochures/cms_039956.pdf | SCR_018432 | 2026-09-19 12:53:52 | 0 | ||||||||
|
Minimap2 Resource Report Resource Website 1000+ mentions |
Minimap2 (RRID:SCR_018550) | alignment software, data processing software, image analysis software, software application, software resource | Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences. | Pairwise alignment, nucleotide sequence, map DNA sequence, map mRNA sequence, reference database, spliced nucleotide sequence, bio.tools, FASEB list |
is used by: D-GENIES is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG010040 | PMID:29750242 | Free, Available for download, Freely available | OMICS_31658, biotools:minimap2 | https://bio.tools/minimap2, https://sources.debian.org/src/libminimap2-dev/ | SCR_018550 | 2026-09-19 12:53:53 | 1593 | ||||||
|
Nanotomy Resource Report Resource Website 10+ mentions |
Nanotomy (RRID:SCR_018565) | data or information resource, data repository, data set, database, image collection, service resource, storage service resource | Large scale electron microscopy datasets. Large scale electron microscopy database for Human Type 1 Diabetes. | Large scale, electron microscopy, data set, Human Type 1 Diabetes, image collection |
is related to: Golddigger has parent organization: University of Groningen; Groningen; Netherlands |
Type 1 diabetes, Diabetes | PMID:32424134 | Free, Freely available | SCR_020961 | SCR_018565 | nano-anatomy, Anatomy at nanoscale, nanotomy | 2026-09-19 12:53:53 | 30 | ||||||
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TimeZone Resource Report Resource Website 1+ mentions |
TimeZone (RRID:SCR_018564) | data analysis software, data processing software, software application, software resource | Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes. | Detect footprint, positive selection, functionally adaptive, point mutation, microbial genome | NIAID RC4 AI092828; NIGMS R01 GM084318 |
PMID:23471110 | Free, Available for download, Freely available | SCR_018564 | 2026-09-19 12:53:53 | 1 | |||||||||
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Doric Neuroscience Studio Resource Report Resource Website 10+ mentions |
Doric Neuroscience Studio (RRID:SCR_018569) | data acquisition software, data processing software, software application, software resource | Software tool which allows to control Doric hardware and acquire all required data simultaneously. Incorporates different modules for each devices connected. | Doric, Doric hardware control, data acquire | Restricted | SCR_018569 | 2026-09-19 12:53:53 | 23 | |||||||||||
|
ggtree Resource Report Resource Website 50+ mentions |
ggtree (RRID:SCR_018560) | data processing software, data visualization software, software application, software resource | Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses. | Phylogenetic tree visualization, phylogenetic tree annotation, data, bio.tools |
is listed by: CRAN is listed by: Bioconductor is listed by: Debian is listed by: bio.tools |
Seed Funding Programme for Basic Research | DOI:10.1111/2041-210X.12628 | Free, Available for download, Freely available | biotools:ggtree | https://bio.tools/ggtree | SCR_018560 | 2026-09-19 12:53:53 | 61 | ||||||
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DiANNA Resource Report Resource Website 50+ mentions |
DiANNA (RRID:SCR_018529) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Neural network and web server, which determines cysteine oxidation state and disulfide connectivity of protein, given only its amino acid sequence. Used to predict disulfide connectivity topology. Predicts which half-cystines are covalently bound to which other half-cystines. DiANNA 1.1 is extension of DiANNA web server for ternary cysteine classification. | Ternary cysteine classification, cysteine oxidation, disulfide protein connectivity, amino acid sequence, predict disulfide connectivity, connectivity topology, cysteine covalent bound, | Boston College ; NSF DBI 0543506 |
PMID:16844987 PMID:15980459 |
Free, Freely available | http://bioinformatics.bc.edu/clotelab/DiANNA/ | SCR_018529 | DiANNA 1.1 | 2026-09-19 12:53:53 | 55 | |||||||
|
DAMBE Resource Report Resource Website 10+ mentions |
DAMBE (RRID:SCR_018528) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers. | Data analysis, molecular sequence data, genomic data, phylogenetic data, data, anaysis, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Ottawa; Ontario; Canada |
Hong Kong Research Grant Council ; Natural Science and Engineering Research Council of Canada ; University of Hong Kong |
PMID:11535656 PMID:28379490 PMID:23564938 PMID:29669107 |
Free, Available for download, Freely available | biotools:dampe | https://bio.tools/dambe | SCR_018528 | DAMBE6, DAMBE5, DAMBE7, Data Analysis in Molecular Biology and Evolution | 2026-09-19 12:53:53 | 12 | |||||
|
BepiPred-2.0 Resource Report Resource Website 1+ mentions |
BepiPred-2.0 (RRID:SCR_018499) | analysis service resource, data access protocol, production service resource, service resource, software application, software resource, standalone software, web service | Sequential B-Cell Epitope Predictor. Web server predicts B-cell epitopes from protein sequence. Sequence-based B-cell epitope prediction using conformational epitopes. Sequences of protein of interest should be in fasta format. BepiPred 2.0 is available as stand alone software package, with same functionality as web service., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Sequential predictor, B cell epitope, B cell epitope predictor, B-cell epitope, protein sequence, protein, epitope, sequence | has parent organization: Technical University of Denmark; Lyngby; Denmark | NIH HHSN272201200010C | PMID:28472356 PMID:16635264 |
THIS RESOURCE IS NO LONGER IN SERVICE | http://www.cbs.dtu.dk/services/BepiPred-1.0/ | SCR_018499 | BepiPred-1.0, BepiPred | 2026-09-19 12:53:52 | 7 | ||||||
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JetFighter Resource Report Resource Website 1+ mentions |
JetFighter (RRID:SCR_018498) | analysis service resource, production service resource, service resource, software resource, web application | Web tool that automatically screens bioRxiv preprints for rainbow colormaps, which are not colorblind safe. Emails authors information on replacing these colormaps with colorblind safe alternatives. Screens preprints to improve data representation and colour-blind accessibility. | bioRxiv preprint screening, ranbow colormap, colorblind safe, replacing colormap, improve data, improve picture, ASWG | has parent organization: California Institute of Technology; Pasadena; USA | Free, Freely available | https://github.com/smsaladi/jetfighter | SCR_018498 | 2026-09-19 12:53:52 | 1 | |||||||||
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AmberTools Resource Report Resource Website 500+ mentions |
AmberTools (RRID:SCR_018497) | simulation software, software application, software resource, software toolkit | Software suite that works by themselves, and with Amber20 itself. Can be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. | Molecular dynamics simulation, water, Born solvent model, molecular dynamics, molecular modeling | DOI:10.1002/wcms.1121 | SCR_018497 | Amber, AmberTools20, AmberTools MD software packages | 2026-09-19 12:53:52 | 728 | ||||||||||
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DiscoTope Resource Report Resource Website 100+ mentions |
DiscoTope (RRID:SCR_018530) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server to predict discontinuous B cell epitopes from protein three dimensional structures. | B cell epitope, B cell epitope prediction, discontinous B cell epitope prediction, protein, protein three dimentional structure, protein structure, 3D | European Union Seventh Framework Programme | PMID:23300419 | Free, Freely available | SCR_018530 | 2026-09-19 12:53:53 | 109 | |||||||||
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AllerTop Resource Report Resource Website 100+ mentions |
AllerTop (RRID:SCR_018496) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for in silico prediction of allergens. Alignment free server for in silico prediction of allergens based on main physicochemical properties of proteins. Used to predict the route of allergen exposure: food, inhalant or toxin. | Allergen, allergen prediction, physicochemical protein property, protein, protein property, allergen exposure | National Research Fund of the Ministry of Education and Science ; Bulgaria |
PMID:23735058 | SCR_018496 | 2026-09-19 12:53:52 | 352 |
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