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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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 | 2026-09-05 06:25:33 | 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 | 2026-09-05 06:25:33 | 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 | SINOMO (SIngular NOde MOtifs), Singular Node Motifs, SIngular NOde MOtifs | 2026-09-05 06:25:33 | 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 | MINC / Atlases | 2026-09-05 06:25:32 | 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 | 2026-09-05 06:25:33 | 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, data set, disease-related portal, portal, topical 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 | 2026-09-05 06:25:34 | 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, department portal, graduate program resource, organization portal, 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 | 2026-09-05 06:25:34 | 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 | 2026-09-05 06:25:34 | 120 | |||||||
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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 | 2026-09-05 06:25:34 | 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 | 2026-09-05 06:25:34 | 39 | |||||||
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Anne O'Tate Resource Report Resource Website 1+ mentions |
Anne O'Tate (RRID:SCR_005340) | Anne O'Tate | service resource | A web based search tool to help you gain an overview of the set of articles (up to 25,000 most recent articles) retrieved by a PubMed query. Once you enter a query, you can select different types of summary information to view: Important words, Topics, Authors, Affiliations, Journals, Year, Clustered by topic. | database |
is listed by: OMICtools is related to: PubMed has parent organization: University of Illinois at Chicago; Illinois; USA |
PMID:18279519 | OMICS_01171 | SCR_005340 | 2026-09-05 06:25:34 | 2 | ||||||||
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GEM Resource Report Resource Website 10+ mentions |
GEM (RRID:SCR_005339) | GEM | software resource | Java software for studying protein-DNA interaction using ChIP-seq / ChIP-exo data. It links binding event discovery and motif discovery with positional priors in the context of a generative probabilistic model of ChIP data and genome sequence, resolves ChIP data into explanatory motifs and binding events at unsurpassed spatial resolution. GEM reciprocally improves motif discovery using binding event locations, and binding event predictions using discovered motifs. | chip-seq, chip-exo, genome, event, motif, protein-dna interaction, java, transcription factor, genome sequence, motif discovery, binding event calling |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
PMID:22912568 | OMICS_00441 | SCR_005339 | Genome wide Event finding and Motif discovery, GEM: ChIP-Seq and ChIP-exo analysis tool | 2026-09-05 06:25:33 | 12 | |||||||
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Hiclib Resource Report Resource Website 10+ mentions |
Hiclib (RRID:SCR_005535) | Hiclib | software resource | An Software resource | is listed by: OMICtools | OMICS_00521 | SCR_005535 | 2026-09-05 06:25:37 | 22 | ||||||||||
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SHRiMP Resource Report Resource Website 100+ mentions |
SHRiMP (RRID:SCR_005496) | SHRiMP | software resource | A software package for aligning genomic reads against a target genome. | next generation sequencing, alignment |
is used by: Jambalaya is listed by: OMICtools is related to: Jambalaya is related to: Proovread has parent organization: University of Toronto; Ontario; Canada |
PMID:21278192 | OMICS_00685 | SCR_005496 | SHRiMP - SHort Read Mapping Package | 2026-09-05 06:25:36 | 208 | |||||||
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BrainEthics Resource Report Resource Website |
BrainEthics (RRID:SCR_005530) | BrainEthics | blog, book, data or information resource, narrative resource | There are a lot of fine blogs out there covering the avalance of current neuroscience research. With this blog Thomas Rams��y & Martin Skov want to highlight the many consequences of this growing understanding of the human brain. We are especially interested in two types of consequences: Tinkering with the brain and What is it like to be a human being? * Tinkering with the brain: First and foremost, with an understanding of how the brain works comes the possibility of tinkering with it. We already use billions of dollars every year on psychopharmocologia trying to treat depression, schizophrenia, obsessive-compulsive disorder and other mental diseases. But should we also use our knowledge of the brain to treat undesirable mental traits such as pedophilia or sociopathy? And what about enhancing normal brains? Clearly, evolution hasn''t endowed us with the most efficient brain imaginable. Shouldn''t we do something about its many shortcomings? * What is it like to be a human being?: Secondly, our view of human behavior is sure to change with our improved understanding of the human brain. Our knowledge of core human faculties such as language, social reasoning, aesthetics, and economics is already being challenged by modern neuroscience, yielding multiple hard questions. Do we have a free will? Is the mind innate or plastic? If people are not responsible for their actions (since all actions are caused by blind molecular processes) does our legal system still make sense? In short, will modern neuroscience come to completely redefine human nature? We try to discuss contemporary research literature, not just news reports. Although we will occasionally also target popular science reports, since we believe they play an important role in dissemining lessons from the lab. And in the future we plan to also post interviews with interesting researchers, as well as link to our own publications in journals and books. Additionally, the latest and most important books in the multidisciplinary field of neuroscience, cognition, psychology, ethics and economics are presented. | brain, science, ethics, neuroethics, human, behavior | is parent organization of: BrainEthics Podcast | nlx_144626 | SCR_005530 | Brain Ethics, BrainEthics - Consequences of Brain Science | 2026-09-05 06:25:37 | 0 | ||||||||
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SMALT Resource Report Resource Website 500+ mentions |
SMALT (RRID:SCR_005498) | SMALT | software resource | Software that aligns DNA sequencing reads with a reference genome. Reads from a wide range of sequencing platforms, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including paired reads. |
is listed by: OMICtools is related to: Sequence Search and Alignment by Hashing Algorithm has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
OMICS_00686 | SCR_005498 | 2026-09-05 06:25:36 | 516 | ||||||||||
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French Ministry of Higher Education and Research Resource Report Resource Website 10+ mentions |
French Ministry of Higher Education and Research (RRID:SCR_005532) | MESR | institution | Ministry of Higher Education, Research and Innovation, France is one of the 900 Higher Education-related Organizations and Associations. |
is parent organization of: CIRAD is parent organization of: French National Center for Scientific Research |
ISNI: 0000 0001 2369 5464, Wikidata: Q2726949, grid.425729.f, Crossref funder ID: 501100004792, nlx_143604 | https://ror.org/03sjk9a61 | SCR_005532 | Ministere de i''Enseignement Supereur et de la Recherche, Ministere de l''Enseignement Supérieur et de la Recherche, French Ministry of Research, The Ministry, Le ministre | 2026-09-05 06:25:37 | 38 | ||||||||
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TIGRFAMS Resource Report Resource Website 100+ mentions |
TIGRFAMS (RRID:SCR_005493) | JCVI TIGRFAMS, TIGRFAM | data or information resource, data set, database | Consists curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. Starting with release 10.0, TIGRFAMs models use HMMER3, which provides excellent search speed as well as exquisite search sensitivity. See the "TIGRFAMs Complete Listing" page to review the accession, protein name, model type, and EC number (if assigned) of all models. TIGRFAMs is a member database in InterPro. The HMM libraries and supporting files are available to download and use for free from our FTP site. | sequence alignment, hidden markov model, protein sequence, classification, protein, protein family, sequence homology, sequence, homology, function, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: InterPro is related to: InterPro has parent organization: J. Craig Venter Institute |
PMID:23197656 | Free | nif-0000-03560, OMICS_01700, biotools:tigrfams | https://bio.tools/tigrfams | http://www.tigr.org/TIGRFAMs | SCR_005493 | TIGRFAMs | 2026-09-05 06:25:36 | 142 | ||||
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Segemehl Resource Report Resource Website 10+ mentions |
Segemehl (RRID:SCR_005494) | Segemehl | software resource | A software to map short sequencer reads to reference genomes. It is able to detect not only mismatches but also insertions and deletions. Furthermore, it is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ANNOgesic has parent organization: University of Leipzig; Saxony; Germany |
PMID:24512684 PMID:22581174 PMID:19750212 DOI:10.1371/journal.pcbi.1000502 |
Acknowledgement requested, Free, Public | biotools:segemehl, OMICS_00683 | https://bio.tools/segemehl, https://sources.debian.org/src/segemehl/ | SCR_005494 | segemehl - short read mapping with gaps | 2026-09-05 06:25:36 | 48 | |||||
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PASS Resource Report Resource Website 1000+ mentions |
PASS (RRID:SCR_005490) | PASS | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 19, 2020.A program to align short sequences that has been developed with an innovative strategy to perform fast gapped and ungapped alignment onto a reference sequence. It supports several data formats and allows the user to modulate very finely the sensitivity of the alignments. The program is designed to handle huge amounts of short reads generated by ILLUMINA, SOLiD and Roche-454 technology. The optimization of the internal data structure and a filter based on precomputed short-word alignments allow the program to skip false positives in the extension phase, thus reducing the execution time without loss of sensitivity. The final alignment is performed by dynamic programming., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: PASS-bis has parent organization: University of Padua; Padua; Italy |
PMID:19218350 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pass, OMICS_00673 | https://bio.tools/pass | SCR_005490 | PASS: a program to align short sequences | 2026-09-05 06:25:36 | 2085 |
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