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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Whole Brain Atlas Resource Report Resource Website 10+ mentions |
Whole Brain Atlas (RRID:SCR_005390) | atlas, data or information resource, data repository, image repository, narrative resource, service resource, storage service resource, training material | An atlas of normal and abnormal brain images intended as an introduction to basic neuroanatomy, with emphasis on the pathoanatomy of several leading central nervous system diseases that integrates clinical information with magnetic resonance (MR), x-ray computed tomography (CT), and nuclear medicine images. A range of brain abnormalities are presented including examples of certain brain disease presented with various combinations of image type and imaging frequency. Submissions of concise, exemplary, clinically driven examples of neuroimaging are welcome. | atlas, brain, human, abnormal brain image, neuroanatomy, imaging |
is listed by: re3data.org has parent organization: Harvard Medical School; Massachusetts; USA |
Inflammatory disease, Infectious disease, Degenerative disease, Neoplastic disease, Brain tumor, Cerebrovascular disease, Stroke | American Academy of Neurology ; Brigham and Womens Hospital; Massachusetts; USA ; Departments of Radiology and Neurology ; Countway Library of Medicine |
Copyrighted, Acknowledgement required, Non-commercial, The community can contribute to this resource | r3d100010274, nif-0000-00079 | https://doi.org/10.17616/R34P4F | SCR_005390 | 2026-09-05 06:25:34 | 28 | ||||||
|
MuGeX Resource Report Resource Website |
MuGeX (RRID:SCR_005306) | MuGeX | service resource | Service that automatically extracts mutation-gene pairs from MEDLINE abstracts for a given disease. | disease, gene, mutation |
is listed by: OMICtools is related to: MEDLINE has parent organization: Sabanci University; Istanbul; Turkey |
PMID:18172928 | Acknowledgement requested | OMICS_01189 | SCR_005306 | MuGeX - Mutation Gene Extractor, Mutation Gene Extractor | 2026-09-05 06:25:33 | 0 | ||||||
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Synergizer Resource Report Resource Website 1+ mentions |
Synergizer (RRID:SCR_005308) | Synergizer | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | The Synergizer database is a growing repository of gene and protein identifier synonym relationships. This tool facilitates the conversion of identifiers from one naming scheme (a.k.a namespace) to another. The Synergizer is a service for translating between sets of biological identifiers. It can, for example, translate Ensembl Gene IDs to Entrez Gene IDs, or IPI IDs to HGNC gene symbols, and much more. Unlike some other tools for this purpose, The Synergizer is simple and easy to learn. The Synergizer works via a web interface (for users who are not programmers) or through a web service (for programmatic access). | gene, protein, json | has parent organization: University of Toronto; Ontario; Canada | nlx_144380 | SCR_005308 | The Synergizer | 2026-09-05 06:25:33 | 9 | ||||||||
|
Scripture Resource Report Resource Website 10+ mentions |
Scripture (RRID:SCR_005269) | Scripture | software resource | Software for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has modules for ChIP-Seq peak calling. | transcriptome, rna-seq read, genome sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Alt Event Finder has parent organization: Broad Institute |
PMID:20436462 | biotools:scripture, OMICS_01265 | https://bio.tools/scripture | SCR_005269 | 2026-09-05 06:25:32 | 11 | |||||||
|
Hmmer Resource Report Resource Website 5000+ mentions |
Hmmer (RRID:SCR_005305) | HMMER | analysis service resource, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource | Tool for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. | homolog, protein sequence, source code, FASEB list |
is used by: Mantis is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: SoftCite is related to: VectorBase has parent organization: Janelia Research |
Howard Hughes Medical Institute | PMID:21593126 DOI:10.1093/bioinformatics/14.9.755 |
OMICS_00996, nlx_144358 | https://sources.debian.org/src/hmmer/ | SCR_005305 | HMMER - biosequence analysis using profile hidden Markov models | 2026-09-05 06:25:33 | 9520 | |||||
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SpliceSeq Resource Report Resource Website 100+ mentions |
SpliceSeq (RRID:SCR_005267) | SpliceSeq | data analysis software, data processing software, software application, software resource | A Java application to investigate alternative mRNA splicing patterns in data from high-throughput mRNA sequencing studies. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing. This tool may be used on a single RNASeq sample to identify genes with multiple spliceforms, on a pair of samples to identify differential splicing between the two, or on groups of samples to identify statistically significant group level differences in splicing patterns. SpliceSeq can be run from the install page as a java web start application to explore the sequencing data on their server or can be installed locally to analyze your own mRNA-Seq data. | rna-seq, mrna splicing pattern |
is listed by: OMICtools has parent organization: University of Texas MD Anderson Cancer Center |
OMICS_01267 | SCR_005267 | 2026-09-05 06:25:32 | 179 | |||||||||
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NBIA Disorders Association Resource Report Resource Website 1+ mentions |
NBIA Disorders Association (RRID:SCR_005382) | NBIA Disorders Association | institution | The NBIA Disorders Association, formerly known as Hallervorden-Spatz Syndrome Association, (HSSA) was originally founded in 1996 by President, Patricia Wood. The goals of the association are to raise funds to support research pertinent to NBIA; to provide emotional support to those afflicted with NBIA and their families; and to raise public awareness of NBIA. The NBIA Disorders Association is accepting applications for one-year grants for clinical and translational research studies related to the early detection, diagnosis, or treatment of patients with NBIA. Neurodegeneration with Brain Iron Accumulation (NBIA) is a group of rare, genetic, neurological disorders characterized by the accumulation of iron deposits in the brain and progressive degeneration of the nervous system. It typically first appears in childhood. Presenting signs and symptoms may include difficulty walking, loss of balance, and problems related to speech. Those affected suffer a progressive loss of muscle control, sudden involuntary muscle spasms, and uncontrolled tightening of the muscles. Symptoms may also include disorientation, seizures, and deterioration of intellectual ability. Approximately half of the cases diagnosed have been linked to a mutation of a gene known as PANK2. At the present time, symptoms may be treated but there is no cure. The purpose of the NBIA Disorders Association Research Grant Program is to encourage meritorious research studies designed to improve the diagnosis or treatment of NBIA. The research can be conducted in the United States, countries of the European Union, Canada, Australia, New Zealand, Brazil, Argentina, Chile, South Africa, Japan, or Israel, and in other countries where adequate supervision of grant administration is possible. Grants will be awarded to qualified researchers to initiate pilot studies, the results of which are intended to be used to obtain larger multi-year grant funding. Evaluation of proposals will follow NIH guidelines and include careful consideration of experimental or protocol design, objectivity or relevance of parameters measured, and statistical analysis plan. Proposals that address the following areas will be given priority: * Therapeutics Development: ** Development of pantethine and its derivatives ** Development of other rational therapeutics * Animal & Cellular Models: ** Development of a new rodent disease model by targeted insertion of a ''human disease'' mutation into Pank2 ** Development of induced pluripotent stem cell lines. *** Development of animal and cellular models will be considered for multi-year funding with adequate budget justification. Proposals should detail a research plan and a budget for the initial phase of the work, with the option to contract further work out to a commercial enterprise. * Biomarker Discovery and Assay Development: ** Metabolomics ** Coenzyme A / acyl coenzyme A measurement using accessible (peripheral and central) tissue/fluid * New NBIA gene discovery | hallervorden-spatz disease, neurodegeneration with brain iron accumulation, rare disease, pantothenate kinase-associated neurodegeneration, genetic, neurological disorder, brain, neurodegeneration, pank2 | Crossref funder ID: 100009582, grid.469792.7, nlx_144453 | https://ror.org/008421332 | SCR_005382 | NBIA Disorders Association: from discovery to cure, Hallervorden-Spatz Syndrome Association, HSSA | 2026-09-05 06:25:34 | 5 | ||||||||
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Integrated Jobs Resource Report Resource Website |
Integrated Jobs (RRID:SCR_005384) | data or information resource, database, job resource | A virtual database currently indexing the following scientific Job resources: Naturejobs, Monster, Indeed, Hays, jobs.ac.uk, New Scientist Jobs, Science Careers, Access-ScienceJobs.co.uk, TheScienceJobs.com, ScienceBlogs: Jobs, and It Takes 30. | employment, job opportunity, scientific job, science, job, database |
is used by: NIF Data Federation is related to: Naturejobs is related to: Monster is related to: Indeed is related to: Hays is related to: jobs.ac.uk is related to: New Scientist Jobs is related to: Science Careers is related to: Access-ScienceJobs.co.uk is related to: TheScienceJobs.com is related to: ScienceBlogs: Jobs is related to: It Takes 30 has parent organization: Integrated |
Data are licensed by their respective owners, Use and distribution is subject to the Terms of Use by the original resource | nlx_144460 | https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-14 http://neuinfo.org/nif/nifgwt.html?query=nlx_144460, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_144460-1, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-14 | SCR_005384 | Integrated Job, Neuroscience Information Framework Integrated Jobs, NIF Integrated Jobs View, Integrated Job View, NIF Jobs, Integrated Jobs View, NIF Jobs View, NIF Integrated Jobs | 2026-09-05 06:25:34 | 0 | |||||||
|
SPLITREAD Resource Report Resource Website 1+ mentions |
SPLITREAD (RRID:SCR_005264) | SPLITREAD | software resource | Software for detecting INDELs (small insertions and deletion with size less than 50bp) as well as large deletions that are within the coding regions from the exome sequencing data. It also can be applied to the whole genome sequencing data. | deletion, insertion, indel, genome, exome |
is listed by: OMICtools is related to: drFAST is related to: mrFAST is related to: mrsFAST is related to: VariationHunter is related to: NovelSeq is related to: mrCaNaVaR has parent organization: SourceForge |
OMICS_00323 | SCR_005264 | SPLITREAD - Split read based INDEL/SV Caller | 2026-09-05 06:25:32 | 3 | ||||||||
|
bioKepler Resource Report Resource Website 1+ mentions |
bioKepler (RRID:SCR_005385) | bioKepler | software resource | A Comprehensive Bioinformatics Scientific Workflow Module for Distributed Analysis of Large-Scale Biological Data that is distributed on top of the core Kepler scientific workflow system. | module, bioinformatics, workflow, next-generation sequencing |
is listed by: OMICtools is related to: Kepler is related to: Molecular Dynamics Workflow (BioKepler) |
NSF DBI-1062565 | Acknowledgement requested | OMICS_01139 | SCR_005385 | 2026-09-05 06:25:34 | 2 | |||||||
|
Ontogenesis Resource Report Resource Website 1+ mentions |
Ontogenesis (RRID:SCR_005380) | Ontogenesis | blog, data or information resource, narrative resource, training material | Knowledge Blog for descriptive, tutorial and explanatory material about building, using and maintaining ontologies, as well as the social processes and technology that support this. Ontogenesis features over 20 articles written by leading academics, and has attracted over 17,000 page reads. Articles are peer-reviewed. Following publication as reviewed, articles are stable and can be cited by stable URL or DOI. Ontogenesis is now archived by the British Library as part of the UK Web Archive and is indexed by Google Scholar. The initial idea for Ontogenesis came from Phillip Lord. You can read the original manifesto that they wrote, describing the purpose of this blog. Ontogenesis is the first and main example of a Knowledgeblog, a flexible and light-weight process for scientific publication. It has received funding from JISC. They are currently open to submissions. Please contact them if you want further information, or would like to offer articles for publication., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | ontology, scientific publication |
is related to: Knowledge Blog has parent organization: Knowledge Blog |
JISC | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144451 | SCR_005380 | 2026-09-05 06:25:34 | 3 | |||||||
|
Hydra Resource Report Resource Website 100+ mentions |
Hydra (RRID:SCR_005260) | Hydra | software resource | Software that detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose signatures corroborate the same putative breakpoint. Hydra can detect breakpoints caused by all classes of structural variation. Moreover, it was designed to detect variation in both unique and duplicated genomic regions; therefore, it will examine paired-end reads having multiple discordant alignments. Hydra does not attempt to classify SV breakpoints based on the mapping distances and orientations of each breakpoint cluster, it merely detects and reports breakpoints. This is an intentional decision, as it was observed that in loci affected by complex rearrangements, the type of variant suggested by the breakpoint signature is not always correct. Hydra does report the orientations, distances, number of supporting read-pairs, etc., for each breakpoint. It is suggested that downstream methods be used to classify variants based on the genomic features that they overlap and the co-occurrence of other breakpoints. For example, they developed BEDTools for exactly this purpose and the breakpoints reported by Hydra are in the BEDPE format used by BEDTools. Future releases of Hydra will include scripts that assist in the classification process. | structural variation, genome, genomic, breakpoint, c++, cnv, pem, paired-end, segmental duplication, rearrangement |
is listed by: OMICtools is listed by: SoftCite is related to: BEDTools has parent organization: Google Code has parent organization: University of Virginia; Virginia; USA |
OMICS_00318 | SCR_005260 | hydra-sv | 2026-09-05 06:25:32 | 119 | ||||||||
|
Taverna Knowledge Blog Resource Report Resource Website |
Taverna Knowledge Blog (RRID:SCR_005381) | Taverna Knowledge Blog | blog, data or information resource, narrative resource, training material | Taverna Knowledge Blog: Designing, Executing and Sharing Scientific workflows | scientific workflow, science, workflow |
is related to: Taverna has parent organization: Knowledge Blog |
The community can contribute to this resource | nlx_144452 | SCR_005381 | Taverna Knowledgeblog | 2026-09-05 06:25:34 | 0 | |||||||
|
becas Resource Report Resource Website 10+ mentions |
becas (RRID:SCR_005337) | data access protocol, service resource, software resource, web service | Web application, API and widget able to recognize and annotate biomedical concepts in text.Provides annotations for isolated, nested and intersected entities.Identifies concepts from multiple semantic groups, providing preferred names and enriching them with references to public knowledge resources. | Annotation, biomedical concept recognition, annotate biomedical concepts, text, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Aveiro; Aveiro; Portugal |
Free, Freely available | biotools:becas, OMICS_01173 | https://bioinformatics.ua.pt/software/becas/, https://bio.tools/becas | SCR_005337 | 2026-09-05 06:25:33 | 12 | ||||||||
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MiRPara Resource Report Resource Website 10+ mentions |
MiRPara (RRID:SCR_005294) | miRPara | software resource | A SVM (support vector machine-based software tool for prediction of most probable microRNA coding regions in genome scale sequences. | microrna, prediction, mirbase, novel, support vector machine, mirna, dicer, ago, coding region, genome sequence, high throughputut sequencing |
is listed by: OMICtools has parent organization: Google Code |
PMID:21504621 | GNU General Public License, v3, Acknowledgement requested | OMICS_00380 | SCR_005294 | mirpara - know and novel miRNA prediction software | 2026-09-05 06:25:33 | 25 | ||||||
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Zyagen Resource Report Resource Website 50+ mentions |
Zyagen (RRID:SCR_005295) | Zyagen | commercial organization | A commercial service organization from Zyagen. | is listed by: ScienceExchange | SciEx_13206 | SCR_005295 | 2026-09-05 06:25:33 | 98 | ||||||||||
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CHANCE Resource Report Resource Website 10+ mentions |
CHANCE (RRID:SCR_005330) | CHANCE | software resource | A standalone software package for ChIP-seq quality control and protocol optimization. | is listed by: OMICtools | OMICS_00429 | SCR_005330 | CHiP-seq ANalytics and Confidence Estimation | 2026-09-05 06:25:33 | 13 | |||||||||
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NCBO Annotator Resource Report Resource Website 1+ mentions |
NCBO Annotator (RRID:SCR_005329) | NCBO Annotator | data access protocol, production service resource, service resource, software resource, web service | A Web service that annotates textual metadata (e.g. journal abstract) with relevant ontology concepts. NCBO uses this Web service to annotate resources in the NCBO Resource Index. They also provide this Web service as a stand-alone service for users. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Their service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards. | ontology, annotation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: STOP has parent organization: BioPortal has parent organization: National Centers for Biomedical Computing has parent organization: Stanford University; Stanford; California |
NHGRI U54 HG004028 | PMID:19483092 | biotools:bioportal, nlx_144389, OMICS_01172 | https://bio.tools/bioportal | SCR_005329 | Open Biomedical Annotator, NCBO BioPortal Annotator | 2026-09-05 06:25:33 | 6 | |||||
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Assembly Likelihood Estimator Resource Report Resource Website |
Assembly Likelihood Estimator (RRID:SCR_005326) | ALE | software resource | Software using a probabalistic framework for determining the likelihood of an assembly given the data (raw reads) used to assemble it. It allows for the rapid discovery of errors and comparisons between similar assemblies. | standalone software, c, python |
is listed by: OMICtools has parent organization: DOE Joint Genome Institute has parent organization: Cornell University; New York; USA |
PMID:23303509 | Open-source license | OMICS_04067 | https://github.com/sc932/ALE | SCR_005326 | ALE: Assembly Likelihood Estimator | 2026-09-05 06:25:33 | 0 | |||||
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CoPub Resource Report Resource Website 1+ mentions |
CoPub (RRID:SCR_005327) | CoPub | data access protocol, service resource, software resource, web service | Text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database. It allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. | microarray, gene, literature, enrich, annotate, network, database, differential expression, bio.tools |
uses: MEDLINE uses: Gene Ontology is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Netherlands Bioinformatics Centre |
Netherlands Bioinformatics Centre | PMID:18442992 | Free, Public, Acknowledgement requested | OMICS_01178, biotools:copub | https://bio.tools/copub | http://services.nbic.nl/cgi-bin/copub/CoPub.pl | SCR_005327 | 2026-09-05 06:25:33 | 5 |
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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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