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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GOanna Resource Report Resource Website 10+ mentions |
GOanna (RRID:SCR_005684) | GOanna | service resource, analysis service resource, data analysis service, production service resource | GOanna is used to find annotations for proteins using a similarity search. The input can be a list of IDs or it can be a list of sequences in FASTA format. GOanna will retrieve the sequences if necessary and conduct the specified BLAST search against a user-specified database of GO annotated proteins. The resulting file contains GO annotations of the top BLAST hits. The sequence alignments are also provided so the user can use these to access the quality of the match. Platform: Online tool | agriculture, annotation, protein, ontology or annotation search engine, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: AgBase |
USDA ; Mississippi State University; Mississippi; USA ; MSU Office of Research ; MSU Bagley College of Engineering ; MSU College of College of Veterinary Medicine ; MSU Life Science and Biotechnology Institute |
PMID:17135208 PMID:16961921 |
Free for academic use | nlx_149139 | SCR_005684 | AgBase GOanna | 2026-08-11 09:41:10 | 17 | |||||
|
Kismeth Resource Report Resource Website 50+ mentions |
Kismeth (RRID:SCR_005444) | Kismeth | service resource, analysis service resource, data analysis service, production service resource | A web-based tool for bisulfite sequencing analysis that was designed to be used with plants, since it considers potential cytosine methylation in any sequence context (CG, CHG, and CHH). It provides a tool for the design of bisulfite primers as well as several tools for the analysis of the bisulfite sequencing results. Kismeth is not limited to data from plants, as it can be used with data from any species. | plant, methylation, bisulfite sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:18786255 | Free for academic use, Contact for commercial use | biotools:kismeth, OMICS_00602 | https://bio.tools/kismeth | SCR_005444 | 2026-08-11 09:41:08 | 55 | ||||||
|
Spliceman Resource Report Resource Website 1+ mentions |
Spliceman (RRID:SCR_005354) | Spliceman | service resource, analysis service resource, data analysis service, production service resource | An online tool that takes a set of DNA sequences with point mutations and returns a ranked list to predict the effects of point mutations on pre-mRNA splicing. The current implementation includes 11 genomes: human, chimp, rhesus, mouse, rat, dog, cat, chicken, guinea pig, frog and zebrafish. | dna sequence, pre-mrna, splicing, pre-mrna splicing, point mutation, mutation, sequence variation, fasta |
is listed by: OMICtools has parent organization: Brown University; Rhode Island; USA |
PMID:22328782 | Free, Non-commercial, Commercial use requires license | OMICS_02259 | SCR_005354 | 2026-08-11 09:41:16 | 5 | |||||||
|
omniBiomarker Resource Report Resource Website 1+ mentions |
omniBiomarker (RRID:SCR_005750) | omniBiomarker | service resource, analysis service resource, data analysis service, production service resource | omniBiomarker is a web-application for analysis of high-throughput -omic data. Its primary function is to identify differentially expressed biomarkers that may be used for diagnostic or prognostic clinical prediction. Currently, omniBiomarker allows users to analyze their data with many different ranking methods simultaneously using a high-performance compute cluster. The next release of omniBiomarker will automatically select the most biologically relevant ranking method based on user input regarding prior knowledge. The omniBiomarker workflow * Data: Gene Expression * Algorithms: Knowledge-Driven Gene Ranking * Differentially expressed Genes * Clinical / Biological Validation * Knowledge: NCI Thesaurus of Cancer, Cancer Gene Index * back to Algorithms | gene, gene expression, algorithm, cancer, cancer gene, cancer gene index, biocomputing, biomarker, clinical, gene ranking |
has parent organization: Georgia Institute of Technology; Georgia; USA has parent organization: Emory University; Georgia; USA |
Cancer | Georgia Cancer Coalition ; NCI U54CA119338; NCI R01CA108468 |
PMID:19695674 | nlx_149210 | SCR_005750 | omniBiomarker: Knowledge-Driven Biomarker Identification and Data Combination | 2026-08-11 09:41:11 | 3 | |||||
|
ScienceBlogs Resource Report Resource Website 1+ mentions |
ScienceBlogs (RRID:SCR_005197) | Sb | data or information resource, database, blog, narrative resource | From climate change to intelligent design, HIV/AIDS to stem cells, science education to space exploration, science is figuring prominently in our discussions of politics, religion, philosophy, business and the arts. New insights and discoveries in neuroscience, theoretical physics and genetics are revolutionizing our understanding of who are are, where we come from and where we''re heading. Launched in January 2006, ScienceBlogs is a portal to this global dialogue, a digital science salon featuring the leading bloggers from a wide array of scientific disciplines. Today, ScienceBlogs is the largest online community dedicated to science. We believe in providing our bloggers with the freedom to exercise their own editorial and creative instincts. We do not edit their work and we do not tell them what to write about. We have selected our 80+ bloggers based on their originality, insight, talent, and dedication and how we think they would contribute to the discussion at ScienceBlogs. Our role, as we see it, is to create and continue to improve this forum for discussion, and to ensure that the rich dialogue that takes place at ScienceBlogs resonates outside the blogosphere. ScienceBlogs is always interested in bringing new contributors into our community. If you''re interested in blogging with us, please fill out our application, and we''ll be in touch. | science, life science, physical science, environment, humanities, education, politics, medicine, brain, behavior, technology, information science, job, peer review |
is parent organization of: ScienceBlogs: Life Science is parent organization of: ScienceBlogs: Brain and Behavior is parent organization of: ScienceBlogs: Medicine and Health is parent organization of: ScienceBlogs: Jobs is parent organization of: Neurophilosophy is parent organization of: ScienceBlogs Neurotopia is parent organization of: Common Knowledge is parent organization of: Cognitive Daily |
nlx_144212 | SCR_005197 | 2026-08-11 09:41:16 | 6 | |||||||||
|
Chromas Resource Report Resource Website 10+ mentions |
Chromas (RRID:SCR_000598) | Chromas | software resource, commercial organization | Software ideal for the most basic of sequencing projects, where assembly of multiple sequences is not required., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01016, biotools:chromas | https://bio.tools/chromas | SCR_000598 | 2026-08-11 09:40:11 | 16 | |||||||
|
HMS NERCE FACSCalibur Flow Cytometer Resource Resource Report Resource Website 10+ mentions |
HMS NERCE FACSCalibur Flow Cytometer Resource (RRID:SCR_000879) | service resource, core facility, access service resource |
Core facility that provides the following services: Flow cytometry assay service, Data management system. The BD FACSCalibur system combines unique dual-laser technology, an automated sample loader option, and powerful software to provide the high throughput necessary to meet productivity requirements of clinical laboratories. The modularity and innovative technology designed into the BD FACSCalibur system also offers investigators the performance and flexibility required for a variety of research applications. Please note that since the NERCE program will end in February 2014, our ability to support new requests for services is limited. |
flow cytometry assay, data management |
is listed by: Eagle I is related to: HMS East Quad NMR Core Facility has parent organization: Harvard Medical School; Massachusetts; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156273 | http://nerce.med.harvard.edu/facs.html | SCR_000879 | 2026-08-11 09:40:14 | 20 | ||||||||
|
University of California at Davis Mutant Mouse Resource and Research Center Resource Report Resource Website 100+ mentions |
University of California at Davis Mutant Mouse Resource and Research Center (RRID:SCR_016448) | MMRRC UCD, UCD MMRRC | biomaterial supply resource, material resource | Center that imports, archives, maintains, and distributes mutant mouse alleles as live mice, frozen germplasm, stem cells, and molecular vectors for use in biomedical research. The MMRRC Davis receives transgenics, knockouts, and other kinds of mutant mouse lines at no cost to the donor, and after re-derivation and cryopreservation, distributes breeding stock, germplasm, cells, or tissues of genetically-defined and pathogen-free mice for a small fee to requesting investigators. | ABRF, USEDit, mouse, mice, research, genetic, mutant, mutation, transgenic, knockout, research, animal, behavior |
is listed by: ABRF CoreMarketplace is related to: USEDit is organization facet of: Mutant Mouse Resource and Research Center |
NIH Office of the Director U42 OD012210; NIH Office of the Director U42 OD010983 |
ABRF_1650 | https://coremarketplace.org/?FacilityID=1650&citation=1 | SCR_016448 | Mutant Mouse Resource and Research Center UC Davis, Davis MMRRC, UCD Mutant Mouse Resource and Research Center, UC Davis MMRRC, UC Davis Mutant Mouse Resource and Research Center, Mutant Mouse Resource and Research Center - UCD, Mutant Mouse Resource and Research Center - University of California at Davis, California MMRRC | 2026-08-11 09:43:19 | 189 | ||||||
|
Mutant Mouse Resource and Research Center - University of Missouri Resource Report Resource Website 50+ mentions |
Mutant Mouse Resource and Research Center - University of Missouri (RRID:SCR_016447) | UM MMRRC, MMRRC UM | biomaterial supply resource, material resource | Center that supplies mice and conducts research projects focused on the role of mice as animal models. Some of these projects include refinement of models to ensure study reproducibility, as well as development and improvement of economical methods for cryopreservation of mouse strains. | mice, mouse, supply, genetic, transgenic, knockout, research, mutant | is organization facet of: Mutant Mouse Resource and Research Center | NIH Office of the Director U42 OD010918 | SCR_016447 | Mutant Mouse Resource and Research Center - UM, UM Mutant Mouse Resource and Research Center, University of Missouri MMRRC, MMRRC University of Missouri | 2026-08-11 09:43:23 | 53 | ||||||||
|
golang Resource Report Resource Website 10+ mentions |
golang (RRID:SCR_017096) | GO | software resource, programming language | Software tool as open source programming language to build simple, reliable, and efficient software. Developed by team at Google and many contributors from open source community. | programming, language |
is related to: SciPipe has parent organization: Google |
Free, Available for download, Freely available | SCR_017096 | The Go Programming Language, GO programming language | 2026-08-11 09:43:37 | 13 | ||||||||
|
Laser Biomedical Research Center Resource Report Resource Website 1+ mentions |
Laser Biomedical Research Center (RRID:SCR_000106) | LBRC | biomedical technology research center, access service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Biomedical technology research center that develops basic scientific understanding and new techniques required for advancing clinical applications of lasers and spectroscopy. LBRC merges optical spectroscopy, imaging, scattering, and interferometry techniques to study biophysics and biochemistry of healthy and diseased biological structures from subcellular to entire-organ scale. | spectroscopy, laser, biomedicine, optical spectroscopy, imaging, scattering, interferometry, optical probe, microscopy | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | Pre-cancer, Cancer, Atherosclerosis, Healthy, Diseased | NIBIB 4P41EB015871-30 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152645 | SCR_000106 | MIT Laser Biomedical Research Center, Laser Biomedical Research Center (LBRC) | 2026-08-11 09:40:06 | 4 | |||||
|
Perl Programming Language Resource Report Resource Website 100+ mentions |
Perl Programming Language (RRID:SCR_018313) | software resource, programming language | Software tool to accompany existing resources such as Python programming language resource and comprehensive Perl archive network (CPAN) resource. Perl is family of two high level, general purpose, interpreted, dynamic programming languages. Perl refers to Perl 5, but from 2000 to 2019 it also referred to its redesigned sister language, Perl 6, before name was officially changed to Raku in October 2019. | Programming language | Free, Available for download, Freely available | SCR_018313 | Perl 5, Perl 6, Raku | 2026-08-11 09:43:43 | 382 | ||||||||||
|
ATLAS.ti Resource Report Resource Website 500+ mentions |
ATLAS.ti (RRID:SCR_022920) | software application, software resource, data analytics software | Software qualitative analysis tool. Used by researchers and practitioners to uncover and systematically analyze complex phenomena hidden in unstructured data including text, multimedia, geospatial. Provides tools that let the user locate, code, and annotate findings in primary data material, to weigh and evaluate their importance, and to visualize relations between them. Consolidates documents and keeps track of all notes, annotations, codes and memos in all fields that require close study and analysis of primary material consisting of text, images, audio, video, and geo data. Provides analytical and visualization tools designed to open new interpretative views on material. | ATLAS.ti Scientific Software Development GmbH, unstructured data analysis, text, images, audio, video, geo data, analytical and visualization tools, locate, code, and annotate findings in primary data material | Restricted | SCR_022920 | ATLAS.ti version no. 5. 2 | 2026-08-11 09:44:30 | 581 | ||||||||||
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NutriSurvey Resource Report Resource Website 10+ mentions |
NutriSurvey (RRID:SCR_022655) | software application, software resource, data analytics software | Software tool for nutrition calculations and surveys. | Nutrition calculation, nutrition surveys | Free, Available for download, Freely available | SCR_022655 | 2026-08-11 09:44:26 | 17 | |||||||||||
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calN50 Resource Report Resource Website 1+ mentions |
calN50 (RRID:SCR_022015) | software application, software resource, data analytics software | Software tool as simple script to calculate N50/NG50 and auN/auNG. | calculate N50/NG50, calculate auN/auNG | Free, Available for download, Freely available | SCR_022015 | 2026-08-11 09:44:16 | 8 | |||||||||||
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SAS JMP Pro Resource Report Resource Website 500+ mentions |
SAS JMP Pro (RRID:SCR_022199) | JMP Pro | software application, software resource, data analytics software | Statistical software tool. Predictive analytics software. Offers all tools in JMP plus advanced features for more sophisticated analyses. | Predictive analytics, statistics, visualizing data, building graphs, JMP | Restricted | SCR_022199 | JMP Pro from SAS | 2026-08-11 09:44:19 | 569 | |||||||||
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VCF2Dis Resource Report Resource Website 10+ mentions |
VCF2Dis (RRID:SCR_022513) | software application, software resource, data analytics software | 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 | 2026-08-11 09:44:22 | 22 | |||||||||||
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Pyani Resource Report Resource Website 50+ mentions |
Pyani (RRID:SCR_021088) | software application, software resource, data analytics software | 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 | 2026-08-11 09:44:07 | 90 | |||||||||||
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Libeep EEGLAB plugin Resource Report Resource Website 1+ mentions |
Libeep EEGLAB plugin (RRID:SCR_016334) | software application, software resource, software toolkit | Software as an EEGLAB tool used for LIBEEP recordings. | plugin, library, recording, electrophysiological, data, neuroscience |
is related to: LIBEEP is related to: EEGLAB is related to: MATLAB |
Free, Available for download, Freely available | SCR_016334 | ANTeepimport | 2026-08-11 09:43:17 | 1 | |||||||||
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FLIMfit Resource Report Resource Website 1+ mentions |
FLIMfit (RRID:SCR_016298) | software application, software resource, software toolkit | Software package for quantitative analysis of large Fluorescence Lifetime Imaging Microscopy (FLIM) data, including global analysis. It is able to routinely analyse multi-well plate FLIM datasets on conventional PC workstations in a reasonable time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | fluorescence, lifetime, imaging, microscopy, dataset, global, analysis, multiwell, plate, routine | United Kingdom Biotechnology and Biological Sciences Research Council BBSRC BB/E003621/1; United Kingdom Technology Strategy Board Technology Award CHBT/007/00030; Wellcome Trust WT 095931/Z/11/Z |
PMID:23940626 DOI:10.1371/journal.pone.0070687 |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/flimfit/FLIMfit | SCR_016298 | 2026-08-11 09:43:17 | 6 |
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