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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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CASHX Resource Report Resource Website 1+ mentions |
CASHX (RRID:SCR_005477) | CASHX | software resource | Software pipeline to parse, map, quantify and manage large quantities of sequence data. CASHX is a set of tools that can be used together, or as independent modules on their own. The reference genome alignment tools can be used with any reference sequence in fasta format. The pipeline was designed and tested using Arabidopsis thaliana small RNA reads generated using an Illumina 1G. |
is listed by: OMICtools has parent organization: Oregon State University; Oregon; USA |
NSF MCB-1231726; NIAI AI43288 |
PMID:19307293 | OMICS_00655 | SCR_005477 | Cache ASsisted Hash Search with Xor logic Pipeline, CASHX Pipeline, Cache ASsisted Hash Search with Xor logic | 2026-09-12 12:56:26 | 4 | |||||||
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Latin American Brain Mapping Network (LABMAN) Resource Report Resource Website |
Latin American Brain Mapping Network (LABMAN) (RRID:SCR_005509) | LABMAN | community building portal, data or information resource, portal, service resource, training service resource | On March 8, 2008 in Havana, the Latin American Network for Brain Mapping (LABMAN) was created with participants from Argentina, Brazil, Colombia, Cuba and Mexico. The focus of LABMAN is to promote neuroimaging and systems neuroscience in the region through the implementation of training and exchange programs, and to increase public awareness of the Latin American potential to contribute both to basic and applied research in human brain mapping. The immediate LABMAN goals are to: * Train specialists in all major imaging techniques. * Expedite the transfer of new scientific and technical knowledge from abroad. * Increase the scientific productivity of the region. * Drastically increase the awareness of local governments, international organizations and of the general public of brain mapping results on potential. * Organize multinational projects in areas of special relevance to the region, e.g. nutrition, pediatric development, neurodegeneration. Latin American Brain Mapping Network (LABMAN) participants : * Cuban Neuroscience Center * University of Buenos Aires * University of Sao Paulo * Universidad del Valle, Cal��, Colombia * UAM Iztapalapa, Mexico City, Mexico | neuroimaging, systems neuroscience, human, neuroscience, brain mapping |
has parent organization: Max Planck Institute for Biological Cybernetics; Tubingen; Germany has parent organization: CBRAIN |
PMID:19324094 | nlx_144610 | http://ijbem.k.hosei.ac.jp/2006-/volume10/number4/100407.pdf | SCR_005509 | Latin American Brain Mapping Network | 2026-09-12 12:56:27 | 0 | ||||||
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TreQ Resource Report Resource Website |
TreQ (RRID:SCR_005505) | TreQ | software resource | A software read mapper for high-throughput DNA sequencing reads, in particular one to several hundred nucleotides in length, and for large edit distance between sequencing read and match in the reference genome. It can cope particularly well with indels for single-best hit recall of 200nt reads simulated from the human reference genome. TreQ performs best at a running time comparable to BWA at large edit distance settings. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Rutgers University; New Jersey; USA |
PMID:22962448 | GNU General Public License | OMICS_00695, biotools:treq | https://bio.tools/treq | SCR_005505 | TreQ: Indel-tolerant Read Mapper | 2026-09-12 12:56:27 | 0 | |||||
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MicrobesOnline Resource Report Resource Website 100+ mentions |
MicrobesOnline (RRID:SCR_005507) | MicrobesOnline | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource, source code | MicrobesOnline is designed specifically to facilitate comparative studies on prokaryotic genomes. It is an entry point for operon, regulons, cis-regulatory and network predictions based on comparative analysis of genomes. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html. | microbe, genome, bacteria, archaea, fungi, prokaryote, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
DOE DE-AC02-05CH11231 | PMID:19906701 | nlx_144607, biotools:microbesonline | https://bio.tools/microbesonline | SCR_005507 | Microbial Genomics Database, Microbes Online | 2026-09-12 12:56:27 | 166 | |||||
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University of Lleida; Lleida; Spain Resource Report Resource Website |
University of Lleida; Lleida; Spain (RRID:SCR_005500) | UdL | university | University based in Lleida, Spain. It was the first university in Catalonia and the whole Crown of Aragon. It was founded in 1300, using the name of Estudi General de Lleida.Leading institution in Spain for research and education in the fields of Agronomy, Food Technology and Forestry. | is related to: Pharma-Planta Consortium | nlx_158307 | http://www.udl.cat/en/udl.html | SCR_005500 | University of Lleida, Universitat de Lleida | 2026-09-12 12:56:27 | 0 | ||||||||
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HeadIT Resource Report Resource Website 1+ mentions |
HeadIT (RRID:SCR_005657) | HeadIT | data or information resource, data repository, data set, service resource, storage service resource | Platform for sharing, download, and re-analysis or meta-analysis of sophisticated, fully annotated, human electrophysiological data sets. It uses EEG Study Schema (ESS) files to provide task, data collection, and subject metadata, including Hierarchical Event Descriptor (HED) tag descriptions of all identified experimental events. Visospatial task data also available from, http://sccn.ucsd.edu/eeglab/data/headit.html: A 238-channel, single-subject EEG data set recorded at the Swartz Center, UCSD, by Arnaud Delorme, Julie Onton, and Scott Makeig is al. | electrophysiology, data sharing, eeg, visual-auditory cued attention shift paradigm, adult, early adult human, late adult human, memory task, modified sternberg working memory task, visual, auditory, auditory oddball, memory, task |
uses: HED Tags is related to: EEGLAB has parent organization: University of California at San Diego; California; USA |
Normal, Healthy, Others possible | NIMH R01-MH084819; NINDS R01-NS047293 |
Public, Must agree to Data Use Agreement and Terms of Use., Account required for collaboration and to upload data. | nlx_149081 | http://headit-beta.ucsd.edu/, http://sccn.ucsd.edu/eeglab/data/headit.html | http://HeadIT.org | SCR_005657 | Human Electrophysiology Anatomic Data & Integrated Tools (HeadIT) Resource, Human Electrophysiology Anatomic Data & Integrated Tools Resource, Human Electrophysiology Anatomic Data & Integrated Tools, Human Electrophysiology Anatomic Data and Integrated Tools (HeadIT) Resource | 2026-09-12 12:56:29 | 5 | |||
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DiProGB Resource Report Resource Website 1+ mentions |
DiProGB (RRID:SCR_005651) | DiProGB | software resource | Genome browser that encodes the genome sequence by physico-chemical dinucleotide properties such as stacking energy, melting temperature or twist angle. Analyses can be performed for the + and ?, as well as for the double strand. | genome, browser, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Dinucleotide Property Database |
PMID:19605418 | Free, Freely available | biotools:diprogb, OMICS_00880 | https://bio.tools/diprogb | SCR_005651 | DiProGB - The Dinucleotide Properties Genome Browser, Dinucleotide Properties Genome Browser | 2026-09-12 12:56:29 | 4 | |||||
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MagicViewer Resource Report Resource Website 10+ mentions |
MagicViewer (RRID:SCR_005648) | MagicViewer | software resource | Software to easily visualize the short reads alignment, identify the genetic variation and associate with the annotation information of reference genome. MagicViewer provides a user-friendly interface in which large-scale short reads and sequencing depth can be easily visualized in zoomable images under user definable color scheme through an operating system-independent manner with the implement of Java language. Meanwhile, it holds a versatile genetic variation annotation and visualization interface, providing details of the query options, functional classifications, subset selection, sequence association and primer design. | dna methylation, bisulfite sequencing |
is listed by: OMICtools has parent organization: Wenzhou Medical University; Zhejiang; China |
PMID:20444865 | Free, Public | OMICS_00887 | SCR_005648 | MagicViewer: Integrated Solution for Next-generation Sequencing Data Visualization and Genetic Variation Detection and Annotation | 2026-09-12 12:56:29 | 16 | ||||||
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Bambino Resource Report Resource Website 1+ mentions |
Bambino (RRID:SCR_005649) | Bambino | analysis service resource, data analysis service, production service resource, service resource, software resource | A variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. Bambino may be launched online via Java Web Start or downloaded and run locally. | java, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: National Cancer Institute |
PMID:21278191 | Https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/Bambino_Click-thru-agreement-for-executable_final.txt | OMICS_00876, biotools:bambino | https://bio.tools/bambino | SCR_005649 | Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format | 2026-09-12 12:56:29 | 5 | |||||
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MATRICS - Measurement And Treatment Research to Improve Cognition in Schizophrenia Resource Report Resource Website 1+ mentions |
MATRICS - Measurement And Treatment Research to Improve Cognition in Schizophrenia (RRID:SCR_005644) | MATRICS | knowledge environment | Cognitive deficits -- including impairments in areas such as memory, attention, and executive function -- are a major determinant and predictor of long-term disability in schizophrenia. Unfortunately, available antipsychotic medications are relatively ineffective in improving cognition. Scientific discoveries during the past decade suggest that there may be opportunities for developing medications that will be effective for improving cognition in schizophrenia. The NIMH has identified obstacles that are likely to interfere with the development of pharmacological agents for treating cognition in schizophrenia. These include: (1) a lack of a consensus as to how cognition in schizophrenia should be measured; (2) differing opinions as to the pharmacological approaches that are most promising; (3) challenges in clinical trial design; (4) concerns in the pharmaceutical industry regarding the US Food and Drug Administration''s (FDA) approaches to drug approval for this indication; and (5) issues in developing a research infrastructure that can carry out clinical trials of promising drugs. The MATRICS program will bring together representatives of academia, industry, and government in a consensus process for addressing all of these obstacles. Specific goals of the NIMH MATRICS are: * To catalyze regulatory acceptance of cognition in schizophrenia as a target for drug registration. * To promote development of novel compounds to enhance cognition in schizophrenia. * Leverage economic research power of industry to focus on important but neglected clinical targets. * Identify lead compounds and if deemed feasible, support human proof of concept trials for cognition in schizophrenia. | schizophrenia, cognitive deficit, memory, attention, executive function, disability, cognition, clinical | has parent organization: University of California at Los Angeles; California; USA | Schizophrenia | NIMH | nlx_146271 | SCR_005644 | Measurement And Treatment Research to Improve Cognition in Schizophrenia, Measurement Treatment Research to Improve Cognition in Schizophrenia | 2026-09-12 12:56:29 | 6 | ||||||
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WISECONDOR Resource Report Resource Website 10+ mentions |
WISECONDOR (RRID:SCR_005646) | WISECONDOR | software resource | A set of python scripts that detects fetal chromosomal and subchromosomal duplications and deletions in maternal blood samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: Netherlands Bioinformatics Centre |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00354 | SCR_005646 | WIthin-SamplE COpy Number aberration DetectOR | 2026-09-12 12:56:29 | 12 | ||||||||
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TRANSPATH Resource Report Resource Website 1+ mentions |
TRANSPATH (RRID:SCR_005640) | TRANSPATH | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. It can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyzer. Cross-references to important sequence and signature databases such as EMBL/GenBank UniProt/Swiss-Prot InterPro or Ensembl EntrezGene RefSeq are provided. The database is equipped with the tools for data visualization and analysis. It has three modules: the first one is the data, which have been manually extracted, mostly from the primary literature; the second is PathwayBuilder, which provides several different types of network visualization and hence facilitates understanding; the third is ArrayAnalyzer, which is particularly suited to gene expression array interpretation, and is able to identify key molecules within signalling networks (potential drug targets). These key molecules could be responsible for the coordinated regulation of downstream events. Manual data extraction focuses on direct reactions between signalling molecules and the experimental evidence for them, including species of genes/proteins used in individual experiments, experimental systems, materials and methods. This combination of materials and methods is used in TRANSPATH to assign a quality value to each experimentally proven reaction, which reflects the probability that this reaction would happen under physiological conditions. Another important feature in TRANSPATH is the inclusion of transcription factor-gene relations, which are transferred from TRANSFAC, a database focused on transcription regulation and transcription factors. Since interactions between molecules are mainly direct, this allows a complete and stepwise pathway reconstruction from ligands to regulated genes. | signal transduction, network analyzer, transcriptional regulator, transcription factor, metabolic pathway, signaling pathway, protein-protein interaction, gene-regulatory pathway, signal transduction pathway, complex, signaling molecule, reaction, molecule, gene, pathway, gene expression |
is related to: TRANSFAC is related to: GeneTrail has parent organization: BIOBASE Corporation |
BMBF 031U210B; BMBF 0313092; European Union FP6 contract LSHG-CT-2004-503568; European Union MRTN-CT-2004-512285 |
PMID:18629064 PMID:16381929 PMID:12519957 PMID:11724734 |
Free for academic use, Free for non-profit use, Account required | nif-0000-03580 | http://transpath.gbf.de, http://www.gene-regulation.com/pub/databases.html, http://www.biobase.de/pages/products/databases.html | SCR_005640 | 2026-09-12 12:56:29 | 3 | |||||
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BS Seeker Resource Report Resource Website 1+ mentions |
BS Seeker (RRID:SCR_005641) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software which performs accurate and fast mapping of bisulfite-treated short reads. Supplementary information and examples are provided on the site. | bisulfite sequencing, sequence analysis software, short read, sequence mapping, bio.tools |
uses: Bowtie is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Bs-Seeker2 has parent organization: University of California at Los Angeles; California; USA |
PMID:20416082 | Free, Available for download, Freely available | OMICS_00578, biotools:bs_seeker | https://bio.tools/bs_seeker | SCR_005641 | Bisulfite Sequence Seeker | 2026-09-12 12:56:29 | 3 | ||||||
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MRI Research Safety and Ethics Resource Report Resource Website |
MRI Research Safety and Ethics (RRID:SCR_005642) | MRI Research Safety and Ethics | data or information resource, narrative resource, standard specification | NIMH recognizes the need to consider safety and ethical issues related to both the administration of MR (magnetic resonance) facilities and the use of these facilities for research. This document summarizes the points to consider discussed by the National Advisory Mental Health Council (NAMHC) Workgroup. Examples of safe and ethical practices are discussed in relation to several issues. These examples are intended to be illustrative and should not be interpreted as an exhaustive or exclusive list. This document was presented to the full NIMH Council on September 15, 2006 and approved unanimously. By making the points to consider document available publicly, NIMH intends to provide a resource for researchers and institutions that use MRI in research. The agenda was organized into six topics, which provide the organization for the points to consider that follow: A. MRI screening B. Training, operating, and emergency procedures C. Physical facilities D. Scanning/participant health variables E. Context- Specific Considerations: University vs. medical settings F. Additional data needs and updating The NIMH believes that investigators, institutions and facilities can use this document as a resource for the development, administration, evaluation, and use of MRI research facilities. | mri, research, neuroscience, imaging | has parent organization: National Institute of Mental Health | NIMH | nlx_146267 | SCR_005642 | MRI Research Safety and Ethics: Points to Consider, MRI Research Safety Ethics | 2026-09-12 12:56:29 | 0 | |||||||
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Internet Analysis Tools Registry Resource Report Resource Website 1+ mentions |
Internet Analysis Tools Registry (RRID:SCR_005638) | IATR | data processing software, image analysis software, software application, software repository, software resource | A centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools. It is hoped that this helps the tool developers to get their tools to a larger user community and to reduce redundancy (or at least utilize tool redundancy to facilitate optimal tool design) in tool development. This also helps tool users in identification of the existing tools for specific problems as they arise. The registry is designed to be self-moderated. This means that all tool entries are owned by some responsible party who enters the tool information, and keeps it up to date via the Web. | database, tool, neuroimaging, image, analysis |
lists: Extensible MATLAB Medical image Analysis is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Harvard Medical School; Massachusetts; USA |
Human Brain Project | Public Domain | nlx_146252 | SCR_005638 | IATR - Internet Analysis Tools Registry | 2026-09-12 12:56:29 | 1 | ||||||
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Hunan Normal University; Changsha; China Resource Report Resource Website |
Hunan Normal University; Changsha; China (RRID:SCR_005639) | university | University founded in 1938, is a higher education institution in Changsha, Hunan Province. The university is a national 211 Project university, one of 100 key universities in the 21st century that enjoy priority in obtaining national funds. | is parent organization of: Animal Toxin Database | nlx_79811 | http://www.hunnu.edu.cn/english/ | SCR_005639 | Hunan Normal University | 2026-09-12 12:56:29 | 0 | |||||||||
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COBrA Resource Report Resource Website 1000+ mentions |
COBrA (RRID:SCR_005677) | COBrA | software resource | COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Semantic Web formats RDF, RDFS and OWL. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | ontology, anatomy, browser, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: OBO has parent organization: University of Edinburgh; Scotland; United Kingdom |
BBSRC 15/BEP 17046 | PMID:15513995 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149117 | SCR_005677 | COBrA - An Ontology Browser for Anatomy, COBrA: a bio-ontology editor | 2026-09-12 12:56:29 | 1396 | |||||
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Roth Laboratory Resource Report Resource Website 1+ mentions |
Roth Laboratory (RRID:SCR_005711) | Roth Lab | data or information resource, laboratory portal, organization portal, portal, software resource | The Roth Laboratory is designing and interpreting large-scale experiments to understand pathway structure and its relationship to phenotype and human disease. Software for research focused on a specific research goal is available. Current experimental interests: * Exploiting parallel sequencing technology to phenotype all pairwise gene deletion combinations in S. cerevisiae, with initial application to genes involved in transcription. * Generation of S. cerevisiae strains carrying dozens of chosen targeted deletions, with initial application to delete all ABC transporters imparting multidrug resistance. * Targeted insertion of gene sets encoding entire human pathways into S. cerevisiae, with initial application to genes involved in drug metabolism. Current computational interests: * Systematic analysis of genetic interaction to reveal redundant systems and order of action in genetic pathways * Integrating large-scale studies - including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns - to quantitatively assign function to genes and guide experimentation and disease association studies. * Alternative splicing and its relationship to protein interaction networks. | gene, pathway, phenotype, disease, transcription, drug metabolism, drug, metabolism, protein-protein interaction, transcription-regulatory interaction, protein interaction, protein |
has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard Medical School; Massachusetts; USA is parent organization of: FuncAssociate: The Gene Set Functionator |
nlx_149163 | http://llama.med.harvard.edu | SCR_005711 | 2026-09-12 12:56:30 | 5 | ||||||||
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netClass Resource Report Resource Website |
netClass (RRID:SCR_005672) | netClass | software resource | An R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. The package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: # average gene expression of pathway (aep); # pathway activities classification (PAC); # Hub network classification (hubc); # filter via top ranked genes (FrSVM); # network smoothed t-statistic (stSVM). | protein-protein interaction network, biomarker discovery, classification, micoarray, gene expression profile, protein-protein interaction, gene expression, gene, biomarker |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24443376 | Free, Public | OMICS_02241 | SCR_005672 | 2026-09-12 12:56:29 | 0 | |||||||
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University of Pacific; California; USA Resource Report Resource Website |
University of Pacific; California; USA (RRID:SCR_005706) | university | Private Methodist affiliated university with its main campus in Stockton, California, and graduate campuses in San Francisco and Sacramento. | is parent organization of: University of the Pacific School of Pharmacy and Health Sciences | nlx_70007 | SCR_005706 | 2026-09-12 12:56:30 | 0 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
