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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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American Federation for Aging Research Resource Report Resource Website 1+ mentions |
American Federation for Aging Research (RRID:SCR_000806) | AFAR | non profit organization | A non-profit organization that supports the advance of healthy aging through biomedical research. | funding resource, healthy aging, late adult human, biotechnology | Aging | Crossref funder ID: 100005366, Wikidata: Q4743745, nlx_144115, grid.427612.4, ISNI: 0000 0001 0395 8845 | https://ror.org/000r61a05 | SCR_000806 | 2026-09-12 12:55:15 | 5 | ||||||||
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Yandell Lab Portal Resource Report Resource Website |
Yandell Lab Portal (RRID:SCR_000807) | data analysis software, data or information resource, data processing software, laboratory portal, organization portal, portal, software application, software resource | Sequenced genomes contain a treasure trove of information about how genes function and evolve. Getting at this information, however, is challenging and requires novel approaches that combine computer science and experimental molecular biology. My lab works at the intersection of both domains, and research in our group can be summarized as follows: generate hypotheses concerning gene function and evolution by computational means, and then test these hypotheses at the bench. This is easier said than done, as serious barriers still exist to using sequenced genomes and their annotations as starting points for experimental work. Some of these barriers lie in the computational domain, others in the experimental. Though challenging, overcoming these barriers offers exciting training opportunities in both computer science and molecular genetics, especially for those seeking a future at the intersection of both fields. Ongoing projects in the lab are centered on genome annotation and comparative genomics; exploring the relationships between sequence variation and human disease; and high-throughput biological image analysis. Current software tools available: VAAST (the Variant Annotation, Analysis & Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST builds upon existing amino acid substitution (AAS) and aggregative approaches to variant prioritization, combining elements of both into a single unified likelihood-framework that allows users to identify damaged genes and deleterious variants with greater accuracy, and in an easy-to-use fashion. VAAST can score both coding and non-coding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases. VAAST thus has a much greater scope of use than any existing methodology. MAKER 2 (updated 01-16-2012) MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources. RepeatRunner RepeatRunner is a CGL-based program that integrates RepeatMasker with BLASTX to provide a comprehensive means of identifying repetitive elements. Because RepeatMasker identifies repeats by means of similarity to a nucleotide library of known repeats, it often fails to identify highly divergent repeats and divergent portions of repeats, especially near repeat edges. To remedy this problem, RepeatRunner uses BLASTX to search a database of repeat encoded proteins (reverse transcriptases, gag, env, etc...). Because protein homologies can be detected across larger phylogenetic distances than nucleotide similarities, this BLASTX search allows RepeatRunner to identify divergent protein coding portions of retro-elements and retro-viruses not detected by RepeatMasker. RepeatRunner merges its BLASTX and RepeatMasker results to produce a single, comprehensive XML-based output. It also masks the input sequence appropriately. In practice RepeatRunner has been shown to greatly improve the efficacy of repeat identifcation. RepeatRunner can also be used in conjunction with PILER-DF - a program designed to identify novel repeats - and RepeatMasker to produce a comprehensive system for repeat identification, characterization, and masking in the newly sequenced genomes. CGL CGL is a software library designed to facilitate the use of genome annotations as substrates for computation and experimentation; we call it CGL, an acronym for Comparitive Genomics Library, and pronounce it Seagull. The purpose of CGL is to provide an informatics infrastructure for a laboratory, department, or research institute engaged in the large-scale analysis of genomes and their annotations. | software, gene, genome annotation, human |
has parent organization: University of Utah; Utah; USA is parent organization of: VAAST |
PMID:21700766 PMID:21700266 PMID:21325948 PMID:21347285 |
nlx_144364 | SCR_000807 | 2026-09-12 12:55:15 | 0 | |||||||||
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Open Biosystems Resource Report Resource Website 10+ mentions |
Open Biosystems (RRID:SCR_000808) | instrument manufacture, material service resource, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Open Biosystems offers products that span Genomics, RNAi and Antibodies. Building on the rapid sharing model that is at the core of the Human Genome Project, Open Biosystems collaborates with some of the most innovative life science investigators working today. We partner with them to bring to market new productsthey have often pioneered the new resources in their own lab, and we prepare it for widespread use and then provide access to the research community. Delivery of genetic content is our most recent technological breakthrough. Recently, we brought to market the Tranz-vector system, the safest human-based lentiviral delivery technology. Further supplementing our already strong line of RNA interference (RNAi) and complementary DNA (cDNA) products, this technology provides investigators with superior delivery capabilities for high-quality cellular screening. The combination or our unique Tranz-vector system and whole genome RNAi and cDNA content enables our customers to perform drug target validation on a large scale. With our genomics resources, Open Biosystems provides the content investigators utilize to unlock the functions of human genes and their relationships to normal and disease development. We offer the most complete gene library in the industry. This novel library consists of several full length cDNA and open reading frame collections. Most prominently among these is the Mammalian Gene Collection (MGC), the industry's gold standard gene catalog. The discovery of RNA interference has revolutionized the way investigators approach the studies of gene expression, regulation and interactions, particularly as it relates to drug development. Our collaboration with Drs. Greg Hannon (CSHL) and Steve Elledge (Harvard) has led the way in the evolution of the short hairpin RNA (shRNA) technologies to provide the life science community with whole genome resources for human, mouse and rat with a multitude of technology and delivery advantages. | open reading frame, cdna, antibody, commercial |
is related to: BMAP cDNA Resources is related to: Mammalian Gene Collection |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144444 | SCR_000808 | Open Biosystems - RNAi Gene Expression Antibodies | 2026-09-12 12:55:15 | 10 | ||||||||
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aTag Generator Resource Report Resource Website |
aTag Generator (RRID:SCR_000801) | aTag, aTags, | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 13, 2012. Snippets of HTML that capture the information that is most important in a machine-readable, interlinked format, making it easier to see the big picture. aTags work with any Web text and can store and connect any textual element that is highlighted in a browser. The structure of the embedded RDF/OWL is decidedly simple: a very short piece of human-readable text that is "tagged" with relevant ontological entities. An aTag generator can be easily added to any web browser and allows researchers to quickly generate aTags out of key statements from web pages, such as PubMed abstracts. The resulting aTags can be embedded anywhere on the web, for example on blogs, wikis, or biomedical databases. aTag demonstrates how the resulting statements that are distributed over the web can be searched, visualized and aggregated with Semantic Web / Linked Data tools, and discusses how aTags can be used to answer practically relevant biomedical questions even though their structure is very simple. aTags are based on Semantic Web standards and Linked Data practices. Specifically, they make use of RDFa, the SIOC vocabulary and various domain ontologies and taxonomies that are available in RDF/OWL format. The autocomplete functionality is based on Apache Solr. Reference: Simple, ontology-based representation of biomedical statements through fine-granular entity tagging and new web standards Matthias Samwald and Holger Stenzhorn. Bio-Ontologies 2009., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | semantic mark up, ontology, semantic tagging |
is listed by: FORCE11 has parent organization: Digital Enterprise Research Institute |
Konrad Lorenz Institute for Evolution and Cognition Research; Altenberg; Austria ; Science Foundation Ireland SFI/08/CE/I1380 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-37038 | SCR_000801 | associative tags, associated tags | 2026-09-12 12:55:15 | 0 | ||||||
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Ecole Normale Superieure; Paris; France Resource Report Resource Website |
Ecole Normale Superieure; Paris; France (RRID:SCR_000960) | ENS | university | A higher education institute for advanced undergraduate and graduate studies in France. The institute has fourteen teaching and research departments that span the humanities and sciences. | france, french, undergraduate, graduate |
is parent organization of: Brian Simulator is parent organization of: yMGV - Yeast microarray global viewer |
grid.5607.4, ISNI: 121105547, nlx_73418, Crossref funder ID: 100007649, Wikidata: Q83259 | https://ror.org/05a0dhs15 | SCR_000960 | Ecole Normale Superieure, �cole Normale Sup�rieure | 2026-09-12 12:55:16 | 0 | |||||||
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Catholic University of the Sacred Heart; Milan; Italy Resource Report Resource Website 100+ mentions |
Catholic University of the Sacred Heart; Milan; Italy (RRID:SCR_000958) | UCSC | university | An Italian private research university that offers undergraduate, graduate and postdoctoral level degrees in both Italian and English. | italy, private, research, undergraduate, graduate, english, italian | is related to: PharmaCog | ISNI:0000 0001 0941 3192, Wikidata:Q229022, nlx_158321, grid.8142.f, Crossref funder ID:501100005743 | https://ror.org/03h7r5v07 | SCR_000958 | Catholic University of the Sacred Heart, Universita Cattolica del Sacro Cuore, Universit� Cattolica del Sacro Cuore, Universit� Cattolica, Universita Cattolica | 2026-09-12 12:55:16 | 154 | |||||||
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Keyose Resource Report Resource Website |
Keyose (RRID:SCR_000798) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 5, 2014. Keyose is a project designed and led by a family physician. We are not IT focused, but health-care focused. Technology is just a tool, not our purpose. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31988 | http://www.keyose.com | SCR_000798 | Keyose | 2026-09-12 12:55:15 | 0 | |||||||||
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Australian Research Council Resource Report Resource Website 100+ mentions |
Australian Research Council (RRID:SCR_000952) | ARC | nonprofit organization | An Australian government agency that allocates research funding to academics and researchers at Australian universities. The mission of the council is to deliver policy and programs that advance Australian research, spur innovation and benefit the community. | funding, allocation, australia, research, academic, policy, public health, community, grant | is parent organization of: RAiD | ISNI: 0000 0004 0611 9213, Wikidata: Q4824612, nlx_156882, grid.413452.5, Crossref funder ID: 501100000923 | https://ror.org/05mmh0f86 | SCR_000952 | ARC | 2026-09-12 12:55:16 | 356 | |||||||
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Academia Sinica; Taipei; Taiwan Resource Report Resource Website |
Academia Sinica; Taipei; Taiwan (RRID:SCR_000950) | university | The national academy of Taiwan that supports research activities in a wide variety of disciplines, ranging from mathematical and physical sciences, to life sciences, and to humanities and social sciences. The institution plays a particularly important role in the academic field of Chinese Studies. | national, academy, research, math, physical science, life science, humanities, social science, chinese studies |
is parent organization of: HiPipe is parent organization of: FastSNP is parent organization of: Gene Ontology Browsing Utility (GOBU) is parent organization of: IGDB.NSCLC is parent organization of: CNVVdb - Copy Number Variations across Vertebrate genomes is parent organization of: Encyclopedia of Hepatocellular Carcinoma Genes Online is parent organization of: KnowPredsite |
THIS RESOURCE IS NO LONGER IN SERVICE | ISNI:0000 0001 2287 1366, Crossref funder ID:501100001869, grid.28665.3f, nlx_89460, Wikidata:Q337266 | https://ror.org/05bxb3784 | SCR_000950 | 2026-09-12 12:55:16 | 0 | ||||||||
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Brown University; Rhode Island; USA Resource Report Resource Website |
Brown University; Rhode Island; USA (RRID:SCR_000957) | university | A private, Ivy League research university in Rhode Island, USA. The university offers degrees at the undergraduate and graduate level in a wide variety of fields. | private, university, research, undergraduate, graduate |
uses: ReadCube is related to: Mnemiopsis Genome Project Portal is parent organization of: HapCompass is parent organization of: ASC is parent organization of: Laboratory for Neural Computation and Cognition is parent organization of: Basal Ganglia Model in Action is parent organization of: Mutation Annotation and Genomic Interpretation is parent organization of: Brown University Rhode Island Biobank Core Facility is parent organization of: GASVPro is parent organization of: Spliceman is parent organization of: Brown University Alpert Medical School Department of Molecular Pharmacology Physiology and Biotechnology is parent organization of: Brown University Department of Neuroscience is parent organization of: Brown Alpert Medical School; Rhode Island; USA is parent organization of: Rnnotator is parent organization of: Brown University Genomics Core Facility is parent organization of: Brown Proteomics Shared Resource Facility is parent organization of: Brown University Labs and Facilities is parent organization of: THetA is parent organization of: North East Cyberinfrastructure Consortium is parent organization of: GASV is parent organization of: Human Neocortical Neurosolver is parent organization of: Brown Alpert Medical School Women and Infants Hospital of Rhode Island Kilguss Research Institute Molecular Biology and Imaging Core Facility is parent organization of: RepEnrich is parent organization of: Brown University Clinical Laboratory Core Facility is parent organization of: Brown University Health Center of Biomedical Research Excellence on Opioids and Overdose Admin Core Facility is parent organization of: Brown University BUH-OPIOID-COBRE Community Engagement Core Facility is parent organization of: Brown University BUH-COBRE Translational and Transformative Core Facility is parent organization of: Brown University BUH-OPIOID COBRE Data and Research Methods Core Facility |
ISNI:0000 0004 1936 9094, Crossref funder ID:100006418, grid.40263.33, Wikidata:Q49114, nlx_78147 | https://ror.org/05gq02987 | SCR_000957 | Brown | 2026-09-12 12:55:16 | 0 | ||||||||
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Austrian Agency for Health and Food Safety Resource Report Resource Website |
Austrian Agency for Health and Food Safety (RRID:SCR_000955) | AGES | nonprofit organization | A company based in Austria that supports the management of federal agencies relating to public health, animal health, food safety, medical and drug safety, food security and consumer protection. They provide professional and scientific expertise. | public health, animal health, food safety, medical and drug safety, food security, consumer protection, research, austria, | grid.414107.7, ISNI: 0000 0001 2224 6253, nlx_157916 | https://ror.org/055xb4311 | http://www.ages.at/ages/en/ | SCR_000955 | Austrian Agency for Health and Food Safety (AGES) | 2026-09-12 12:55:16 | 0 | |||||||
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University of Utah; Utah; USA Resource Report Resource Website |
University of Utah; Utah; USA (RRID:SCR_001003) | university | Public university in Utah, USA that provides undergraduate, master's, post graduate, graduate, and professional degree programs. | public, university, graduate, post graduate, undergraduate, master's |
is related to: International AMD Genetics Consortium is related to: Clinical and Translational Science Awards Consortium is parent organization of: University of Utah School of Medicine; Utah; USA is parent organization of: ShapeWorks is parent organization of: Pathline is parent organization of: Yandell Lab Portal is parent organization of: University of Utah Labs and Facilities is parent organization of: SLOPE is parent organization of: University of Utah Genetic Science Learning Center - Learn Genetics is parent organization of: Center for Integrative Biomedical Computing is parent organization of: SCIRun is parent organization of: Seg3D is parent organization of: TumorSim is parent organization of: SSU rRNA Modification Database is parent organization of: MMAPPR is parent organization of: MAKER is parent organization of: MAKER Web Annotation Service is parent organization of: Viking Viewer for Connectomics is parent organization of: VisTrails is parent organization of: Mouse Party is parent organization of: Atlases of the Brain is parent organization of: Schmidtea mediterranea Genome Database is parent organization of: Medical Biochemistry Resource is parent organization of: Georgie Project is parent organization of: BioMesh3D is parent organization of: ImageVis3D is parent organization of: map3d is parent organization of: MizBee is parent organization of: GNomEx is parent organization of: University of Utah Microarray and Genomic Analysis Core Facility is parent organization of: University of Utah Flow Cytometry Core Facility is parent organization of: BioPSE is parent organization of: RNA Modification Database is parent organization of: Nornir is parent organization of: ABC (Atlas Based Classification) is parent organization of: DTIProcess ToolKit is parent organization of: SCORE is parent organization of: Neoseg is parent organization of: FluoRender is parent organization of: Ir-tweak is parent organization of: GEMINI is parent organization of: Center for Iron and Heme Disorders at the University of Utah Iron and Heme Core is parent organization of: peddy is parent organization of: ITK-SNAP is parent organization of: University of Utah Cell Imaging Core Facility |
nlx_26775, Wikidata:Q168515, grid.223827.e, ISNI:0000 0001 2193 0096, Crossref funder ID:100007747 | https://ror.org/03r0ha626 | SCR_001003 | University of Utah | 2026-09-12 12:55:17 | 0 | ||||||||
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ROSTLAB Resource Report Resource Website 1+ mentions |
ROSTLAB (RRID:SCR_000792) | group | A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research. | protein, structure, function, dna, rna, gene, machine learning, statistics, analysis, protein, biomedical |
has parent organization: Columbia University; New York; USA is parent organization of: PredictNLS is parent organization of: SNPdbe |
NLM LM007329; NLM GM50291 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31417 | http://cubic.bioc.columbia.edu/services/disis | SCR_000792 | Rost Group | 2026-09-12 12:55:15 | 1 | ||||||
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Aarhus University; Aarhus; Denmark Resource Report Resource Website |
Aarhus University; Aarhus; Denmark (RRID:SCR_000948) | AU | university | A public university in Denmark that offers degrees at the undergraduate and graduate level in fields such as engineering, nanotechnology, medicine and modern languages. | university, undergraduate, graduate, public, nanotechnology, engineering, medicine, modern languages, archaeology |
is parent organization of: EMI is parent organization of: FaBox is parent organization of: FastGap is parent organization of: Aarhus University Fluorescence Activated Cell Sorting Core Facility is parent organization of: Aarhus University Bioimaging Core Facility |
nlx_156945 | SCR_000948 | Aarhus Universitet, Aarhus University, University of Aarhus | 2026-09-12 12:55:16 | 0 | ||||||||
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Functional Annotation of the Mammalian Genome Resource Report Resource Website 10+ mentions |
Functional Annotation of the Mammalian Genome (RRID:SCR_000788) | FANTOM | consortium, data or information resource, database, organization portal, portal | International collaborative research project and database of annotated mammalian genome. Used to improve estimates of total number of genes and their alternative transcript isoforms in both human and mouse. Consortium to assign functional annotations to full length cDNAs that were collected during Mouse Encyclopedia Project at RIKEN. | mammal, genome, isoform, human, gene, transcriptome, regulatory network, FASEB list |
is related to: CAGE Basic Viewer for Mus musculus is related to: RIKEN integrated database of mammals has parent organization: RIKEN Brain Science Institute |
NIMH MH062261 | PMID:20211142 PMID:33211864 |
nif-0000-30552 | http://fantom.gsc.riken.jp | SCR_000788 | Functional Annotation of the Mammalian Genome, FANTOM, Functional Annotation of the Mammalian Genome (FANTOM) | 2026-09-12 12:55:14 | 43 | |||||
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HapCompass Resource Report Resource Website 1+ mentions |
HapCompass (RRID:SCR_000942) | algorithm | Software that utilizes a fast cycle basis algorithm for the accurate haplotype assembly of sequence data. It is able to create pairwise SNP phasings. | algorithm, haplotype, sequence, genome, dna, rna, snp |
is listed by: OMICtools has parent organization: Brown University; Rhode Island; USA |
NSF 1048831; NSF 1321000 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00197 | SCR_000942 | 2026-09-12 12:55:16 | 1 | ||||||||
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FAS Center For Systems Biology Resource Report Resource Website 1+ mentions |
FAS Center For Systems Biology (RRID:SCR_000789) | group | A group dedicated to combining a variety of experimental and theoretical approaches to find general principles that explain the structure, behavior and evolution of cells and organisms. The center hosts a variety of fellows and faculty from various backgrounds such as biology, physics, chemistry, mathematics, computer science and engineering. | cell, organism, evolution, biology, physics, chemistry, mathematics, computer science, engineering, hybridization | has parent organization: Harvard University; Cambridge; United States | National Science Foundation DEB 0415718; National Science Foundation DEB 0640512 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30555 | SCR_000789 | FAS Center | 2026-09-12 12:55:15 | 2 | |||||||
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Macquarie University Labs and Facilities Resource Report Resource Website |
Macquarie University Labs and Facilities (RRID:SCR_000944) | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Set of facilities based out of Macquarie University in New South Wales. Some facilities provide services such as proteome analysis or resources of various academic departments like engineering, biological sciences, and geography. | proteome, analysis, research, university, biological science, engineering, geography |
is listed by: ScienceExchange is related to: MQ Australian Proteome Analysis Facility is related to: MQ Animal Behaviour Laboratory is related to: MQ Ramaciotti Centre for Gene Function Analysis is related to: MQ BioFocus Research Centre is related to: MQ ARC Centre of Excellence for Engineered Quantum Systems is related to: Macquarie University MQ Research Centre in Quantum Science and Technology is related to: MQ Research Centre for Astronomy Astrophysics and Astrophotnics has parent organization: Macquarie University; Sydney; Australia |
THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_9680 | https://www.mq.edu.au/ | SCR_000944 | Macquarie University Labs Facilities | 2026-09-12 12:55:16 | 0 | |||||||
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cbiNifti: Matlab/Octave Nifti library Resource Report Resource Website 1+ mentions |
cbiNifti: Matlab/Octave Nifti library (RRID:SCR_000860) | cbiNifti | software library, software resource, software toolkit | An I/O library for Matlab/Octave Matlab and Octave library for reading and writing Nifti-1 files. cbiNifti is intended to be a small, self-contained library that makes minimal assumptions about what Nifti files should look like and allow users easy access to the raw data. cbiNifti handles compressed file formats for reading and writing, using Unix pipes for compression and decompression. More information and code examples at: http://www.pc.rhul.ac.uk/staff/J.Larsson/software.html | computed tomography, magnetic resonance, pet, spect, matlab, octave | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155680 | SCR_000860 | 2026-09-12 12:55:15 | 1 | ||||||||
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National Institute of Health Sciences; Tokyo; Japan Resource Report Resource Website |
National Institute of Health Sciences; Tokyo; Japan (RRID:SCR_000981) | NIHS | government granting agency | Japanese national institute that conducts testing, research, and studies toward the proper evaluation of the quality, safety, and efficacy of pharmaceutical products, foods, and numerous chemicals in the living environment. Its major responsibilities involve extensive testing and research to ensure the quality, efficacy, and safety of chemical substances (including pharmaceuticals and food) that are closely related to people's lives. | nihs, national institute, health science, japan, research, pharmaceutical products, environment, testing, Drugs-Medical Devices, chemicals | nlx_157927 | SCR_000981 | National Institute of Health Sciences - Japan, National Institute of Health Sciences (Japan), National Institute of Health Sciences | 2026-09-12 12:55:17 | 0 |
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