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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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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 | SciCrunch Registry | 2026-10-17 01:26:15 | 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 | SciCrunch Registry | NBIA Disorders Association: from discovery to cure, Hallervorden-Spatz Syndrome Association, HSSA | 2026-10-17 01:26:22 | 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 | SciCrunch Registry | 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 | 2026-10-17 01:26:17 | 0 | |||||||
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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 | SciCrunch Registry | SPLITREAD - Split read based INDEL/SV Caller | 2026-10-17 01:26:20 | 3 | ||||||||
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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 | SciCrunch Registry | 2026-10-17 01:26:17 | 2 | |||||||
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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 | SciCrunch Registry | 2026-10-17 01:26:17 | 3 | |||||||
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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 | SciCrunch Registry | hydra-sv | 2026-10-17 01:26:15 | 119 | ||||||||
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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 | SciCrunch Registry | Taverna Knowledgeblog | 2026-10-17 01:26:11 | 0 | |||||||
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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 | SciCrunch Registry | 2026-10-17 01:26:16 | 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 | SciCrunch Registry | mirpara - know and novel miRNA prediction software | 2026-10-17 01:26:16 | 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 | SciCrunch Registry | 2026-10-17 01:26:14 | 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 | SciCrunch Registry | CHiP-seq ANalytics and Confidence Estimation | 2026-10-17 01:26:16 | 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 | SciCrunch Registry | Open Biomedical Annotator, NCBO BioPortal Annotator | 2026-10-17 01:26:21 | 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 | SciCrunch Registry | ALE: Assembly Likelihood Estimator | 2026-10-17 01:26:16 | 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 | SciCrunch Registry | 2026-10-17 01:26:15 | 5 | ||||
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German Institute of Economic Research; Berlin; Germany Resource Report Resource Website |
German Institute of Economic Research; Berlin; Germany (RRID:SCR_005320) | DIW Berlin | institution | The German Institute for Economic Research or more commonly DIW Berlin is a economic research institute in Germany, involved in basic research and policy advice. | is parent organization of: German Socio-Economic Panel | Wikidata: Q155228, grid.8465.f, ISNI: 0000 0001 1931 3152, nlx_151828 | https://ror.org/0050vmv35 | SCR_005320 | SciCrunch Registry | German Institute for Economic Research, Deutsches Institut fur Wirtschaftsforschung, Deutsches Institut f�r Wirtschaftsforschung Berlin, Deutsches Institut f�r Wirtschaftsforschung | 2026-10-17 01:26:15 | 0 | ||||||||
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Computer Assisted Brain Injury Rehabilitation Ontology Resource Report Resource Website |
Computer Assisted Brain Injury Rehabilitation Ontology (RRID:SCR_005288) | CABRO | controlled vocabulary, data or information resource, ontology | A web ontology for the semantic representation of the computer assisted brain trauma rehabilitation domain. This is a novel and emerging domain, since it employs the use of robotic devices, adaptation software and machine learning to facilitate interactive, adaptive and personalized rehabilitation care, patient monitoring and assisted living. | owl | is listed by: BioPortal | Brain trauma | nlx_157373 | SCR_005288 | SciCrunch Registry | 2026-10-17 01:26:14 | 0 | ||||||||
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SINOMO Resource Report Resource Website |
SINOMO (RRID:SCR_005286) | SINOMO | data analysis software, data processing software, software application, software resource | Analysis-tool which identifies singular node motifs in a network. Network nodes can be described by node-motifs. It is an improvement to the method described in Costa et al. (2009). | network, network analysis, network motif, computational neuroscience, eeg, meg, electrocorticography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom |
EPSRC EP/G03950X/1; EPSRC EP/E002331/1; Korea Ministry of Education Science and Technology R32-10142; CNPq 301303/06-1; FAPESP 05/00587-5; FAPESP 2007/50633-9 |
PMID:21297963 | Creative Commons Attribution-NonCommercial License | nlx_144325 | http://www.nitrc.org/projects/sinomo | SCR_005286 | SciCrunch Registry | SINOMO (SIngular NOde MOtifs), Singular Node Motifs, SIngular NOde MOtifs | 2026-10-17 01:26:20 | 0 | ||||
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MINC/Atlases Resource Report Resource Website 1+ mentions |
MINC/Atlases (RRID:SCR_005281) | MINC/Atlases | atlas, data or information resource, narrative resource, reference atlas, wiki | A linear average model atlas produced by the International Consortium for Brain Mapping (ICBM) project. A set of full- brain volumetric images from a normative population specifically for the purposes of generating a model were collected by the Montreal Neurological Institute (MNI), UCLA, and University of Texas Health Science Center at San Antonio Research Imaging Center (RIC). 152 new subjects were scanned using T1, T2 and PD sequences using a specific protocol. These images were acquired at a higher resolution than the original average 305 data and exhibit improved contrast due predominately to advances in imaging technology. Each individual was linearly registered to the average 305 and a new model was formed. In total, three models were created at the MNI, the ICBM152_T1, ICBM152_T2 and ICBM152_PD from 152 normal subjects. This resulting model is now known as the ICBM152 (although the model itself has not been published). One advantage of this model is that it exhibits better contrast and better definition of the top of the brain and the bottom of the cerebellum due to the increased coverage during acquisition. The entirely automatic analysis pipeline of this data also included grey/white matter segmentation via spatial priors. The averaged results of these segmentations formed the first MNI parametric maps of grey and white matter. The maps were never made publicly available in isolation but have formed parts of other packages for some time including SPM, FSL AIR and as models of grey matter for EEG source location in VARETTA and BRAINWAVE. Again, as these models are an approximation of Talairach space, there are differences in varying areas, to continue our use of origin shift as an example, the ICBM models are approximately 152: +3.5mm in Z and +-co-ordinate -3.5mm and 2.0mm in Y as compared to the original Talairach origin. In addition to the standard analysis performed on the ICBM data, 64 of the subjects data were segmented using model based segmentation. 64 of the original 305 were manually outlined and a resulting parametric VOI atlas built. The native data from these acquisitions was 256x256 with 1mm slices. The final image resolution of this data was 181x217x181 with 1mm isotropic voxels. Refer to the ICBM152 NonLinear if you are fitting an individual to model and do not care about left/right comparisons. A short history of the various atlases that have been produced at the BIC (McConnell Brain Imaging Center, Montreal Neurological Institute) is provided. | atlas, brain, template, human, magnetic resonance imaging |
is related to: ICBM 152 Nonlinear atlases version 2009 is related to: McConnell Brain Imaging Center is related to: International Consortium for Brain Mapping is related to: Laboratory of Neuro Imaging is related to: International Consortium for Brain Mapping has parent organization: Wikibooks |
Normal | nlx_144315 | SCR_005281 | SciCrunch Registry | MINC / Atlases | 2026-10-17 01:26:15 | 3 | |||||||
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MAKER Web Annotation Service Resource Report Resource Website 1+ mentions |
MAKER Web Annotation Service (RRID:SCR_005318) | MWAS | data access protocol, production service resource, service resource, software resource, web service | The MAKER Web Annotation Service (MWAS) is an easily configurable web-accessible genome annotation pipeline. It''''s purpose is to allow research groups with small to intermediate amounts of eukaryotic and prokaryotic genome sequence (i.e. BAC clones, small whole genomes, preliminary sequencing data, etc.) to independently annotate and analyze their data and produce output that can be loaded into a genome database. MWAS is build on the stand alone genome annotation pipeline MAKER, and users who wish to annotate larger datasets and whole genomes are free to download MAKER for use on their own systems. MWAS 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. MWAS can also automatically train popular gene prediction algorithms for use on new genomes for which pre-existing information is limited. MAKER is a member of the Generic Model Organism Database (GMOD) project and output produced by this site can be directly used with other GMOD tools. Annotations can be directly viewed online by the user via GBrowse, JBrowse, and Apollo, or they can be downloaded for local analysis and integration into a genome database. MWAS also supplies summary statistics on sequence features via the Sequence Ontology tool SOBA. MWAS should prove especially useful for emerging model organism genome projects with minimal bioinformatics expertise and computer resources, since a user can produce final genome annotations without having to install and configure any software locally. | data management, human genome map, genome annotation, annotation, curation, genome, sequence |
is related to: MAKER has parent organization: University of Utah; Utah; USA |
nlx_144374 | SCR_005318 | SciCrunch Registry | 2026-10-17 01:26:16 | 7 |
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