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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Ontogenesis Resource Report Resource Website 1+ mentions |
Ontogenesis (RRID:SCR_005380) | Ontogenesis | training material, narrative resource, data or information resource, blog | 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 | 2026-08-01 12:02:51 | 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 | hydra-sv | 2026-08-01 12:02:58 | 115 | ||||||||
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Taverna Knowledge Blog Resource Report Resource Website |
Taverna Knowledge Blog (RRID:SCR_005381) | Taverna Knowledge Blog | training material, narrative resource, data or information resource, blog | 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 | 2026-08-01 12:02:53 | 0 | |||||||
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becas Resource Report Resource Website 10+ mentions |
becas (RRID:SCR_005337) | software resource, data access protocol, service 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 | 2026-08-01 12:02:52 | 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 | 2026-08-01 12:02:52 | 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 | 2026-08-01 12:02:58 | 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 | 2026-08-01 12:02:50 | 12 | |||||||||
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NCBO Annotator Resource Report Resource Website 1+ mentions |
NCBO Annotator (RRID:SCR_005329) | NCBO Annotator | data access protocol, service resource, production 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 | 2026-08-01 12:02:58 | 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 | 2026-08-01 12:02:58 | 0 | |||||
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CoPub Resource Report Resource Website 1+ mentions |
CoPub (RRID:SCR_005327) | CoPub | software resource, data access protocol, service 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 | 2026-08-01 12:02:50 | 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 | German Institute for Economic Research, Deutsches Institut fur Wirtschaftsforschung, Deutsches Institut f�r Wirtschaftsforschung Berlin, Deutsches Institut f�r Wirtschaftsforschung | 2026-08-01 12:02:58 | 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 | ontology, controlled vocabulary, data or information resource | 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 | 2026-08-01 12:02:52 | 0 | ||||||||
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SINOMO Resource Report Resource Website |
SINOMO (RRID:SCR_005286) | SINOMO | data processing software, data analysis 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 | SINOMO (SIngular NOde MOtifs), Singular Node Motifs, SIngular NOde MOtifs | 2026-08-01 12:02:58 | 0 | ||||
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MINC/Atlases Resource Report Resource Website 1+ mentions |
MINC/Atlases (RRID:SCR_005281) | MINC/Atlases | data or information resource, narrative resource, atlas, 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 | MINC / Atlases | 2026-08-01 12:02:58 | 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, service resource, production 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 | 2026-08-01 12:02:52 | 7 | |||||||||
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ADHD-200 Sample Resource Report Resource Website 10+ mentions |
ADHD-200 Sample (RRID:SCR_005358) | ADHD-200, | data or information resource, portal, topical portal, data set, disease-related portal | A grassroots initiative dedicated to accelerating the scientific community''''s understanding of the neural basis of ADHD through the implementation of open data-sharing and discovery-based science. They believe that a community-wide effort focused on advancing functional and structural imaging examinations of the developing brain will accelerate the rate at which neuroscience can inform clinical practice. The ADHD-200 Global Competition invited participants to develop diagnostic classification tools for ADHD diagnosis based on functional and structural magnetic resonance imaging (MRI) of the brain. Applying their tools, participants provided diagnostic labels for previously unlabeled datasets. The competition assessed diagnostic accuracy of each submission and invited research papers describing novel, neuroscientific ideas related to ADHD diagnosis. Twenty-one international teams, from a mix of disciplines, including statistics, mathematics, and computer science, submitted diagnostic labels, with some trying their hand at imaging analysis and psychiatric diagnosis for the first time. The data for the competition was provided by the ADHD-200 Consortium. Consortium members from institutions around the world provided de-identified, HIPAA compliant imaging datasets from almost 800 children with and without ADHD. A phenotypic file including all of the test set subjects and their diagnostic codes can be downloaded. Winner is presented. The ADHD-200 consortium included: * Brown University, Providence, RI, USA (Brown) * The Kennedy Krieger Institute, Baltimore, MD, USA (KKI) * The Donders Institute, Nijmegen, The Netherlands (NeuroImage) * New York University Medical Center, New York, NY, USA (NYU) * Oregon Health and Science University, Portland, OR, USA (OHSU) * Peking University, Beijing, P.R.China (Peking 1-3) * The University of Pittsburgh, Pittsburgh, PA, USA (Pittsburgh) * Washington University in St. Louis, St. Louis, MO, USA (WashU) | mri, fmri, brain, neuroimaging, attention deficit-hyperactivity disorder, anatomical, resting state functional mri, child, adolescent, human, young, early adult human, functional imaging, structural imaging, normal, normal control |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Neuro Bureau has parent organization: 1000 Functional Connectomes Project is parent organization of: ADHD-200 Preprocessed Data |
Attention deficit-hyperactivity disorder | Account required, Acknowledgement requested, Non-commercial | nlx_144426 | SCR_005358 | ADHD-200 Consortium | 2026-08-01 12:02:50 | 20 | ||||||
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University of Delaware Behavioral Neuroscience Graduate Program Resource Report Resource Website |
University of Delaware Behavioral Neuroscience Graduate Program (RRID:SCR_005353) | UD Behavioral Neuroscience Program, UD Behavioral Neuroscience Graduate Program | data or information resource, portal, organization portal, graduate program resource, department portal | Ph.D. program in Behavioral Neuroscience is committed to training exceptional students for independent neuroscience research careers in academic, governmental, or industrial settings. Our program provides training in biological foundations of behavior, with particular focus on sensation, learning and memory, affect, development, and neural plasticity. | has parent organization: University of Delaware; Delaware; USA | nif-0000-02169 | http://w3.psych.udel.edu/graduate/behavneuro/index.asp, http://www.psych.udel.edu/graduate/detail/category/behavioral_neuroscience/ | SCR_005353 | University of Delaware Behavioral Neuroscience Graduate Program | 2026-08-01 12:02:58 | 0 | ||||||||
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FaBox Resource Report Resource Website 100+ mentions |
FaBox (RRID:SCR_005350) | FaBox | software resource | Tools for splitting, joining and otherwise manipulating FASTA format sequence files. The first tools in the toolbox is for manipulating fasta headers, cropping alignments and doing some sequence comparison allowing users to combine the description of data (often in excel spreadsheets) with the actual data (often DNA sequences). Also, producing correct input files for a range of programs seems to be problematic for the average user. Hence, some converters in some of the services have been included as well as some stand-alone converters. The converters are not necessarily meant to provide the final input file, but you''ll get a valid input file for Arlequin, MrBayes etc. - that you may further edit so it suit your needs. This means that you may need to combine several of the tools to finish your handling - but it keeps it relatively simple to use. Please note that FaBox is written in PHP and ONLY RUNS ON A WEBSERVER. | fasta, dna, protein sequence, dna sequence, protein, sequence, php |
is listed by: OMICtools has parent organization: Aarhus University; Aarhus; Denmark |
Acknowledgement requested | OMICS_01165 | SCR_005350 | FaBox - an online fasta sequence toolbox | 2026-08-01 12:02:50 | 116 | |||||||
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Charles R. Drew University of Medicine and Science; California; USA Resource Report Resource Website |
Charles R. Drew University of Medicine and Science; California; USA (RRID:SCR_005346) | CDU | university | A private, nonprofit, nonsectarian, Historically Black College and University and a Minority Serving Institution located in Willowbrook, unincorporated Los Angeles County, California, United States. |
is parent organization of: CDU Cancer Research and Training Core Facility is parent organization of: CDU AXIS Biomedical Informatics function is parent organization of: CDU Exercise Physiology Laboratory is parent organization of: CDU Metabolic and Oxidative Stress Core Laboratory is parent organization of: CDU Morphometry and Stereology Laboratory is parent organization of: CDU Vivarium |
nlx_156105, Crossref funder ID:100006453, ISNI:0000 0001 2323 2312, grid.254041.6, Wikidata:Q5081831 | https://ror.org/038x2fh14 | SCR_005346 | Charles R. Drew University of Medicine and Science | 2026-08-01 12:02:50 | 0 | ||||||||
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PeakSeq Resource Report Resource Website 10+ mentions |
PeakSeq (RRID:SCR_005349) | PeakSeq | software resource | A software program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:19122651 | biotools:peakseq, OMICS_00453 | https://bio.tools/peakseq | SCR_005349 | 2026-08-01 12:02:58 | 39 |
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