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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MetMap Resource Report Resource Website 1+ mentions |
MetMap (RRID:SCR_006954) | MetMap | software resource | A computational pipeline for the analysis of MethylSeq experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00618 | SCR_006954 | 2026-09-05 06:26:04 | 9 | |||||||||
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Comparative Sequencing of Plant Small RNAs Resource Report Resource Website 1+ mentions |
Comparative Sequencing of Plant Small RNAs (RRID:SCR_007003) | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | This project has developed a sequence dataset of plant small RNAs based on the hypothesis that most if not all plants utilize important small RNA signaling networks. Different plant families are likely to have both common and lineage-specific miRNAs or other small RNAs with important biological roles. Comparative genomics approaches can be applied to distinguish potential miRNAs from siRNAs and to match the miRNAs to the target sequences. This project develops an unparalleled resource of millions of plant small RNAs for comparative analyses. The project includes sequencing of small RNAs from a diverse and agronomically-relevant set of plant species, focused analyses of important members of the Solanaceae and Poaceae, and development of a small RNA database and web interface for public access and analysis of data. These data will allow the experimental characterization of the majority of biologically important small RNAs for a range of plant species, and will be tremendously useful to a broad set of plant biologists interested in development, stress responses, epigenetics, evolution, RNA biology and other traits impacted by small RNAs. We offer a variety of tools to query the small RNA data set, with options to identify sequences based on homology, expression levels, conservation, or potential function: 1. Small RNA mapping tool: searches for small RNAs perfectly matching a genomic sequence provided by the user. 2. Small RNA mismatch tool: searches the database for small RNAs or other short sequences provided by the user, allowing mismatches. 3. Library-comparison tool to identify conserved small RNAs. 4. Library-comparison tool to identify differentially regulated small RNAs. 5. Reverse Target Prediction. | has parent organization: University of Delaware; Delaware; USA | NSF 0638525 | nlx_37749 | SCR_007003 | 2026-09-05 06:26:05 | 1 | ||||||||||
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Myrna Resource Report Resource Website 1+ mentions |
Myrna (RRID:SCR_006951) | Myrna | software resource | A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. It uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible. | mapreduce, hadoop, cloud computing, differential expression, gene expression, rna-seq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets has parent organization: Johns Hopkins University; Maryland; USA |
PMID:20701754 | Artistic License | OMICS_01310, biotools:myrna | https://github.com/BenLangmead/myrna, https://bio.tools/myrna | SCR_006951 | Myrna: Cloud-scale differential gene expression for RNA-seq | 2026-09-05 06:26:04 | 2 | |||||
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CCDB Image Converter Resource Report Resource Website |
CCDB Image Converter (RRID:SCR_007005) | Image Converter | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. A command line program in Unix to convert images to a variety of formats (PNG, TIFF, JPEG, PPM..etc). It is uniquely different from other programs such as Adobe Photoshop or ImageMagick because it is designed for dealing with the high-resolution images with file sizes of several gigabytes. Image Converter does not require any additional RAM or virtual memory to run. Also, run-time is relatively fast for high resolution data. | image | has parent organization: Cell Centered Database | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156720 | SCR_007005 | 2026-09-05 06:26:05 | 0 | ||||||||
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Minnesota Center for Twin and Family Research Resource Report Resource Website 1+ mentions |
Minnesota Center for Twin and Family Research (RRID:SCR_006948) | MCTFR | data or information resource, disease-related portal, portal, research forum portal, topical portal | Composed of many projects, including the Minnesota Twin Family Study (MTFS) and The Sibling Interaction and Behavior Study (SIBS), this research center seeks to identify genetic and environmental influences on development and psychological traits. Both projects are longitudinal research studies including twins, siblings, and parents. Over 9800 individuals have contributed to these exciting projects! By studying twins and siblings and their families, we can estimate how genes and environment interact to influence character, strengths, vulnerabilities and values. Participants in the MTFS include families with same-sex identical or fraternal twins who were born in Minnesota. The SIBS study is comprised of adoptive and biological siblings and their parents. Most participants partake in day-long visits to the MCTFR, and due to the longitudinal nature of our projects, they return every 3-4 years for follow-up visits. | longitudinal study, clinical study, twin, sibling, parent, longitudinal, gene, environment, adolescent, development, behavior, dna | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | Identical twin, Fraternal twin, Sibling, Parent, Twin | NIH | nlx_151990 | SCR_006948 | SIBS, Minnesota Twin Study, MTFS, Sibbling Interaction and Behavior Study, Minnesota Twin Family Study | 2026-09-05 06:26:04 | 3 | ||||||
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SimSeq Resource Report Resource Website 10+ mentions |
SimSeq (RRID:SCR_006947) | SimSeq | simulation software, software application, software resource | An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Free | biotools:simseq, OMICS_00258 | https://bio.tools/simseq | SCR_006947 | 2026-09-05 06:26:04 | 30 | |||||||
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Australian Government Bureau of Meteorology Resource Report Resource Website 100+ mentions |
Australian Government Bureau of Meteorology (RRID:SCR_007158) | AU BOM | nonprofit organization | The Bureau of Meteorology is Australia''s national weather, climate and water agency. Its expertise and services assist Australians in dealing with the harsh realities of their natural environment, including drought, floods, fires, storms, tsunami and tropical cyclones. Through regular forecasts, warnings, monitoring and advice spanning the Australian region and Antarctic territory, the Bureau provides one of the most fundamental and widely used services of government. The Bureau contributes to national social, economic, cultural and environmental goals by providing observational, meteorological, hydrological and oceanographic services and by undertaking research into science and environment related issues in support of its operations and services. The Bureau of Meteorology operates under the authority of the Meteorology Act 1955 and the Water Act 2007 which provide the legal basis for its activities, while its operation is continually assessed in accordance with the national need for climatic records, water information, scientific understanding of Australian weather and climate and effective service provision to the Australian community. The Bureau of Meteorology must also fulfill Australia''s international obligations under the Convention of the World Meteorological Organization (WMO) and related international meteorological treaties and agreements. | meteorology, weather, climate, water, natural, environment, flood, fire, strom, tsunami, tropical, cyclone, economic, social, cultural, environmental, oceanographic, research, science, environment | Commonwealth of Australia | nif-0000-30228, ISNI: 000000011086859X, grid.1527.1, Wikidata: Q923429 | https://ror.org/04dkp1p98 | SCR_007158 | AU BOM | 2026-09-05 06:26:07 | 175 | |||||||
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Association for the Scientific Study of Consciousness Resource Report Resource Website 1+ mentions |
Association for the Scientific Study of Consciousness (RRID:SCR_007154) | ASSC | community building portal, data or information resource, portal, topical portal |
An academic society that promotes rigorous research directed toward understanding the nature, function, and underlying mechanisms of consciousness. The ASSC includes members working in the fields of cognitive science, medicine, neuroscience, philosophy, and other relevant disciplines in the sciences and humanities. The ASSC web site has several main functions: * coordinating annual conferences on aspects of the scientific study of consciousness. * promotion of other activities in the field (smaller conferences, mailing lists, bibliographic resource, etc). * facilitate consciousness research with awards for new investigators. * publication of papers relevant to the scientific study of consciousness in the inter-disciplinary journal Psyche. The ASSC Students community''s aim is to foster greater involvement of graduate students within the Association for the Scientific Study of Consciousness (ASSC) and improve ways in which the ASSC serves the needs of its student members. Its primary goal is to promote research and debate about consciousness among new researchers. It organizes activities like the current essay contest, details of which are on the news page. It also manage the student pages of the ASSC website and conduct occasional surveys of the ASSC student members. |
cognitive, consciousness, humanities, medicine, neuroscience, philosophy, cognitive science | nif-0000-10156 | http://assc.caltech.edu/index.htm | SCR_007154 | 2026-09-05 06:26:07 | 3 | |||||||||
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Automatic Primer Design Resource Report Resource Website 1+ mentions |
Automatic Primer Design (RRID:SCR_007155) | data acquisition software, data processing software, production service resource, service resource, software application, software resource | This automatic primer design service uses the Primer3 Software (through EMBOSS primer3 interface) to design two sets of primers for doing a nested PCR. The input can either be in Fasta format or in GENOTRACE output format. You will have to indicate with square brackets which region should be included in the amplicon. Primers for multiple amplicons (for example all exons) can be designed in a single run. | primer, design, service, software, pcr | has parent organization: Royal Netherlands Academy of Arts and Sciences; Amsterdam; Netherlands | nif-0000-30136 | SCR_007155 | Primer Design Form | 2026-09-05 06:26:07 | 1 | |||||||||
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Mouse Genome Databases Resource Report Resource Website 1+ mentions |
Mouse Genome Databases (RRID:SCR_007147) | MGD | data or information resource, data set, database, organism-related portal, portal, topical portal | A mouse-related portal of genomic databases and tables of mouse brain data. Most files are intended for you to download and use on your own personal computer. Most files are available in generic text format or as FileMaker Pro databases. The server provides data extracted and compiled from: The 2000-2001 Mouse Chromosome Committee Reports, Release 15 of the MIT microsatellite map (Oct 1997), The recombinant inbred strain database of R.W. Elliott (1997) and R. W. Williams (2001), and the Map Manager and text format chromosome maps (Apr 2001). * LXS genotype (Excel file): Updated, revised positions for 330 markers genotyped using a panel of 77 LXS strain. * MIT SNP DATABASE ONLINE: Search and sort the MIT Single Nucleotide Polymorphism (SNP) database ONLINE. These data from the MIT-Whitehead SNP release of December 1999. * INTEGRATED MIT-ROCHE SNP DATABASE in EXCEL and TEXT FORMATS (1-3 MB): Original MIT SNPs merged with the new Roche SNPs. The Excel file has been formatted to illustrate SNP haplotypes and genetic contrasts. Both files are intended for statistical analyses of SNPs and can be used to test a method outlined in a paper by Andrew Grupe, Gary Peltz, and colleagues (Science 291: 1915-1918, 2001). The Excel file includes many useful equations and formatting that will help in navigating through this large database and in testing the in silico mapping method. * Use of inbred strains for the study of individual differences in pain related phenotypes in the mouse: Elissa J. Chesler''s 2002 dissertation, discussing issues relevant to the integration of genomic and phenomic data from standard inbred strains including genetic interactions with laboratory environmental conditions and the use of various in silico inbred strain haplotype based mapping algorithms for QTL analysis. * SNP QTL MAPPER in EXCEL format (572 KB, updated January 2002 by Elissa Chesler): This Excel workbook implements the Grupe et al. mapping method and outputs correlation plots. The main spreadsheet allows you to enter your own strain data and compares them to haplotypes. Be very cautious and skeptical when using this spreadsheet and the technique. Read all of the caveates. This excel version of the method was developed by Elissa Chesler. This updated version (Jan 2002) handles missing data. * MIT SNP Database (tab-delimited text format): This file is suitable for manipulation in statistics and spreadsheet programs (752 KB, Updated June 27, 2001). Data have been formatted in a way that allows rapid acquisition of the new data from the Roche Bioscience SNP database. * MIT SNP Database (FileMaker 5 Version): This is a reformatted version of the MIT Single Nucleotide Polymorphism (SNP) database in FileMaker 5 format. You will need a copy of this application to open the file (Mac and Windows; 992 KB. Updated July 13, 2001 by RW). * Gene Mapping and Map Manager Data Sets: Genetic maps of mouse chromosomes. Now includes a 10th generation advanced intercross consisting of 500 animals genetoyped at 340 markers. Lots of older files on recombinant inbred strains. * The Portable Dictionary of the Mouse Genome, 21,039 loci, 17,912,832 bytes. Includes all 1997-98 Chromosome Committee Reports and MIT Release 15. * FullDict.FMP.sit: The Portable Dictionary of the Mouse Genome. This large FileMaker Pro 3.0/4.0 database has been compressed with StuffIt. The Dictionary of the Mouse Genome contains data from the 1997-98 chromosome committee reports and MIT Whitehead SSLP databases (Release 15). The Dictionary contains information for 21,039 loci. File size = 4846 KB. Updated March 19, 1998. * MIT Microsatellite Database ONLINE: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. ONLINE. Updated July 12, 2001. * MIT Microsatellite Database: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. File size = 3.0 MB. Updated March 19, 1998. * OurPrimersDB: A small database of primers. Download this database if you are using numerous MIT primers to map genes in mice. This database should be used in combination with the MITDB as one part of a relational database. File size = 149 KB. Updated March 19, 1998. * Empty copy (clone) of the Portable Dictionary in FileMaker Pro 3.0 format. Download this file and import individual chromosome text files from the table into the database. File size = 231 KB. Updated March 19, 1998. * Chromosome Text Files from the Dictionary: The table lists data on gene loci for individual chromosomes. | gene, genetic, chromosome, genotype, inbred mouse strain, pain, phenotype, polygenic, recombinant, trait, genome, genomic, single nucleotide polymorphism, primer, brain, recombinant inbred mouse strain |
has parent organization: University of Tennessee Health Science Center; Tennessee; USA is organization facet of: Alliance of Genome Resources |
nif-0000-20982 | SCR_007147 | 2026-09-05 06:26:07 | 2 | |||||||||
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Cellular Imaging and Analysis Resource Report Resource Website 10+ mentions |
Cellular Imaging and Analysis (RRID:SCR_007149) | data or information resource, portal, topical portal | PerkinElmer designs, manufactures and delivers advanced technology solutions that address the world''s most critical health and safety concerns, including maternal and fetal health, clean water and air, and safe food and toys. It''s expertise combines science, innovation and a culture of operational excellence to offer our customers technology services and support that improve the quality of people''s lives worldwide. | manufacture, deliver, technology, solution, health, safety, material, fetal, clean, water, air, food, toy, science, innovation, culture | nif-0000-30319 | SCR_007149 | 2026-09-05 06:26:07 | 37 | |||||||||||
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Lyngby Resource Report Resource Website 1+ mentions |
Lyngby (RRID:SCR_007143) | Lyngby | data analysis software, data processing software, software application, software resource | Matlab toolbox for the analysis of functional neuroimages (PET, fMRI). The toolbox contains a number of models: FIR-filter, Lange-Zeger, K-means clustering among others, visualizations and reading of neuroimaging files. | functional, statistical, fmri, pet, matlab, neuroimaging |
is listed by: Biositemaps has parent organization: THOR Center for Neuroinformatics |
Human Brain Project ; Danish Research Council ; European Union ; BIOMED2 ; MAPAWAMO ; NASA ; NSF ; DOE ; NIDA R01 DA09246; NIMH P20 MH57180 |
Free, Non-commercial | nif-0000-00324 | SCR_007143 | Lyngby Toolbox, Lyngby - A Toolbox for Functional Neuroimaging | 2026-09-05 06:26:07 | 2 | ||||||
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Swami: The Next Generation Biology Workbench Resource Report Resource Website 1+ mentions |
Swami: The Next Generation Biology Workbench (RRID:SCR_007217) | NGBW | service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The Next Generation Biology Workbench is a free resource for research and education in Bioinformatics, Genomics, Proteomics, and Phylogenetics. The NGBW is a re-engineering of the Biology Workbench which was designed by Shankar Subramaniam and his group to provide an integrated environment where tools, user data, and public data resources can be easily accessed. The NGBW is designed to be an organic tool that evolves with the needs of the Biomedical research and education communities. The Next Generation Biology Workbench (NGBW) is now available for public use, in its production release. | has parent organization: University of California at San Diego; California; USA | IBM Corporation ; Microsoft Research ; NIGMS 5R01GM073931 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_14257 | http://www.ngbw.org/ | SCR_007217 | Next Generation Biology Workbench, Swami | 2026-09-05 06:26:08 | 2 | ||||||
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ESTIMA - Expressed Sequence Tag Information Management and Annotation Resource Report Resource Website 1+ mentions |
ESTIMA - Expressed Sequence Tag Information Management and Annotation (RRID:SCR_007216) | ESTIMA | data or information resource, database, service resource, software resource | A web application called Expressed Sequence Tag Information Management and Annotation (ESTIMA) has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against arbitrary reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for management of EST projects of many species, including honeybee (Apis mellifera), cattle (Bos taurus), songbird (Taeniopygia guttata), corn rootworm (Diabrotica vergifera), catfish (Ictalurus punctatus, Ictalurus furcatus), and apple (Malus x domestica). The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects. The scripts used to create the ESTIMA interface are freely available to academic users in an archived format from http://titan.biotec.uiuc.edu/ESTIMA/download/. The entity-relationship (E-R) diagrams and the programs used to generate the Oracle database tables are also available. Presently the chromatograms, EST databases and their annotations have been made available for cattle and honeybee. | has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA | nlx_22117 | SCR_007216 | ESTIMA: a Tool for EST Management in a Multi-Project Environment | 2026-09-05 06:26:08 | 1 | |||||||||
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Boston University Department of Neuroscience Resource Report Resource Website |
Boston University Department of Neuroscience (RRID:SCR_007218) | data or information resource, department portal, organization portal, portal | Neuroscience research at BU is coordinated through unified community of investigators from multiple research groups of Charles River and MED campuses.Neuroscience faculty support Undergraduate Program in Neuroscience and Graduate Program for Neuroscience. Students can get specialized training in additional disciplines while carrying out neuroscience thesis research (Anatomy & Neurobiology, Biology, and Pharmacology and Experimental Therapeutics). | has parent organization: Boston University; Massachusetts; USA | nif-0000-01897 | SCR_007218 | BU Neuroscience | 2026-09-05 06:26:08 | 0 | ||||||||||
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BioRobotics Laboratory Resource Report Resource Website 50+ mentions |
BioRobotics Laboratory (RRID:SCR_007176) | data or information resource, laboratory portal, organization portal, portal | This is portal takes you to the BioRobotics Laboratory website. Keywords: Laboratory, Software, Robot, Robotics, Biology, | has parent organization: Carnegie Mellon University; Pennsylvania; USA | nif-0000-30189 | SCR_007176 | BioRobotics | 2026-09-05 06:26:07 | 84 | ||||||||||
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American Heart Association Resource Report Resource Website 10000+ mentions |
American Heart Association (RRID:SCR_007210) | data or information resource, disease-related portal, portal, research forum portal, topical portal | The American Heart Association (AHA) publishes medical scientific statements on various cardiovascular disease and stroke topics. AHA volunteer scientists and healthcare professionals write the papers. The statements are supported by scientific studies published in recognized journals and have a rigorous review and approval process. Scientific statements generally include a review of data available on a specific subject, an evaluation on its relationship to overall cardiovascular disease science, and often an American Heart Association position on the basis of that evaluation. The American Heart Association sponsors accredited scientific conferences and professional development seminars to disseminate new and emerging scientific knowledge and stimulate discussion on future research and the application of knowledge. Keywords: Heart, Cardiovascular, Disease, Stroke, Volunteer, Scientist, Healthcare, Development, Knowledge, | is listed by: Duke Human Heart Repository | nif-0000-30095 | SCR_007210 | AHA | 2026-09-05 06:26:08 | 10045 | ||||||||||
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The NeuroCommons Project Resource Report Resource Website |
The NeuroCommons Project (RRID:SCR_007171) | community building portal, data or information resource, portal, software application, software development tool, software resource, systems interoperability software, topical portal | The Neurocommons project is an Open Source knowledge management platform for biological research. It seeks to make all scientific research materials - research articles, annotations, data, physical materials - as available and as usable as they can be. We do this by both fostering practices that render information in a form that promotes uniform access by computational agents - sometimes called interoperability. We want knowledge sources to combine meaningfully, enabling semantically precise queries that span multiple information sources. Our work covers general data and knowledge sources used in computational biology as well as sources specific to neuroscience and neuromedicine. The practices that we develop and promote are designed to play well on the Semantic Web. We view our technical work not as creating a new service or content library, although we do both, but rather as helping to promote the growth of semantically linked scientific information. | analytic tools, bundles, common naming), documenting, installer, interoperation, ontologies, protocol, rdf, rdf distribution, semantic web, software repository, sparql - protocol for querying triple stores, text processing - automated text to rdf, triple store, uris (manifesto, user interface, ontology, owl | nif-0000-01644 | SCR_007171 | NeuroCommons | 2026-09-05 06:26:07 | 0 | ||||||||||
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Cerrado concepts and plant community dynamics Resource Report Resource Website 1+ mentions |
Cerrado concepts and plant community dynamics (RRID:SCR_007174) | CCON | controlled vocabulary, data or information resource, ontology | Ontology of Cerrado wood plant dynamics to represent the set of concepts about the dynamics, that is, changes over time of the wood vegetation structure, of Cerrado. Ccon describes the main parameters used to measure the changes, such as mortality rate and recruitment rate. | owl | is listed by: BioPortal | nlx_157361 | SCR_007174 | 2026-09-05 06:26:07 | 2 | |||||||||
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Professor Anne Chaos Website Resource Report Resource Website 10+ mentions |
Professor Anne Chaos Website (RRID:SCR_007205) | data or information resource, portal, software resource, topical portal | This portal takes you to the website of Professor Anne Chao of the National Tsing Hua University, China. She studies birds. The portal offers Software, course information, publications and teaching. There are about 458 bird species in Taiwan. We have observed 155 species in our neighboring Ker-Yar estuary. We would estimate the total number of species in this area to be 180 including those unobserved. The more we discover about birds, the more we realize how intimately and closely our lives are entwined with those of birds. When the habitats of birds are destroyed and birds become extinct, we human beings are losing the land.... | bird, research, collection, speciation, speciman | has parent organization: National Tsing Hua University; Hsinchu; Taiwan | nif-0000-30106 | SCR_007205 | Professor Anne Chao''s Website | 2026-09-05 06:26:08 | 13 |
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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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