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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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TWiP - This Week in Parasitism Resource Report Resource Website |
TWiP - This Week in Parasitism (RRID:SCR_006788) | TWiP | data or information resource, narrative resource, podcast | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. This Week in Parasitism (TWiP) is a podcast about eukaryotic parasites hosted by Vincent Racaniello and Dick Despommier. Following in the path of their successful podcast ''This Week in Virology'' (TWiV), they strive for an informal yet informative conversation about parasites which is accessible to everyone, no matter what their science background. As science Professors at Columbia University, they have spent their entire academic careers directing research laboratories focused on parasites (Dick) and viruses (Vincent). Their enthusiasm for teaching inspired them to reach beyond the classroom with new media. TWiP is for everyone who wants to learn about parasites in a relaxing way. Music used on TWiP is composed and performed by Ronald Jenkees and used with permission. | parasite | has parent organization: MicrobeWorld | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151571 | SCR_006788 | This Week in Parasitism (TWiP), This Week in Parasitism | 2026-09-12 12:56:45 | 0 | |||||||
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MatOFF Resource Report Resource Website 1+ mentions |
MatOFF (RRID:SCR_006821) | MatOFF | data analysis software, data processing software, software application, software resource, source code | An interactive analysis program that searches neurophysiological data and plots the results. MatOFF was developed especially for dealing with the complexities common to behavioral neurophysiological experiments. It runs under Windows 2000 or XP and relies on MATLAB version R11.1 (or above) for all operations. MatOFF searches a data file to locate and plot epochs (trials) of special interest to the investigator. Appropriate input data files have time-stamped event codes, usually including neuron action potential firing events (spikes), and digitized analog data. The user specifies a list of event code numbers that uniquely identify a sequence of events. MatOFF uses this sequence to search the raw data file, select the epochs that meet the criteria, time-shift the trials to align them on a common event, order the epochs based on user-selected criteria, and plot the results based on a collection of page formatting specifications. MatOFF will also save extracted data and some statistics to disk. Features: * Powerful, interactive searching tools for locating relevant experimental events * Compatible with Cortex data acquisition program * Compatible with Plexon data acquisition system * Flexible, publication-quality graphical display and printing * Comprehensive scripting language * Supports learning and other dynamic behavior * Integrated interface to MATLAB functions * Automatic alignment of trial data and generation of histograms * Large variety of options for selecting and ordering trial data * Descriptive and non-parametric statistics * XY analog displays * Data export with flexible format control * Up to 72 plots per page * Display templates can be saved and reloaded * Free for public or private use * Adaptable to almost any data file format | neurophysiology, behavioral neurophysiology, behavior, electrophysiology, matlab | has parent organization: NIMH CORTEX | NIMH | nlx_143876 | SCR_006821 | NIMH MatOFF | 2026-09-12 12:56:46 | 3 | |||||||
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BMDExpress Resource Report Resource Website 10+ mentions |
BMDExpress (RRID:SCR_006823) | BMDExpress | data analysis software, data processing software, software application, software resource | Bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments. | bioinformatics, microarray, software, toxicogenomics |
is related to: The Hamner Institute for Health Sciences: BMDExpress and The multiple-path particle dosimetry has parent organization: SourceForge |
MIT License | nlx_152743 | SCR_006823 | 2026-09-12 12:56:46 | 38 | ||||||||
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PeptideAtlas Resource Report Resource Website 500+ mentions |
PeptideAtlas (RRID:SCR_006783) | PeptideAtlas | data or information resource, data repository, database, service resource, storage service resource | Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. The raw data, search results, and full builds can be downloaded for other uses. All results of sequence searching are processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner ensuring a high quality database. All peptides are mapped to Ensembl and can be viewed as custom tracks on the Ensembl genome browser. The long term goal of the project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins. The PeptideAtlas provides a method and a framework to accommodate proteome information coming from high-throughput proteomics technologies. The online database administers experimental data in the public domain. You are encouraged to contribute to the database. | proteomics, peptide, mass spectrometry, annotation, eukaryotic, genome, peptide sequence, high-throughput mass spectrometry, ensembl, peptideprophet, protein sequence, blood plasma, protein, eukaryotic cell, dna, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: ProteomeXchange is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Biositemaps is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: ProteomeXchange is related to: NIH Data Sharing Repositories is related to: Integrated Manually Extracted Annotation has parent organization: Institute for Systems Biology; Washington; USA |
NCI ; NHGRI ; NIGMS |
PMID:20013378 PMID:23215161 PMID:16381952 PMID:15642101 |
Public, The community can contribute to this resource, Acknowledgement requested | nif-0000-03266, r3d100010889, biotools:peptideatlas | https://bio.tools/peptideatlas, https://doi.org/10.17616/R3BK61 | SCR_006783 | Peptide Atlas, PeptideAtlas | 2026-09-12 12:56:45 | 511 | ||||
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mubiomics Resource Report Resource Website 1+ mentions |
mubiomics (RRID:SCR_006785) | mubiomics | software resource | A set of scripts (mostly python) for processing reads generated by the Roche 454 or Illumina next-gen sequencing platforms. Included are quality control, read demultiplexing and microbiome characterisation scripts for use with usearch, pplacer and RDP classifier. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01059 | SCR_006785 | mubiomics - Scripts for processing next-gen sequencing data | 2026-09-12 12:56:45 | 4 | |||||||||
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ShortRead Resource Report Resource Website 100+ mentions |
ShortRead (RRID:SCR_006813) | ShortRead | software resource | Software package for input, quality assessment and exploration of high-throughput sequence data. Used for input, quality assurance, and basic manipulation of `short read'' DNA sequences such as those produced by Solexa, 454, and related technologies, including exible import of common short read data formats. | high throughput sequence data, short read, DNA sequences, short read data |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: Bioconductor |
PMID:19654119 | Free, Available for download, Freely available | OMICS_01076 | https://sources.debian.org/src/r-bioc-shortread/ | SCR_006813 | ShortRead - Classes and methods for high-throughput short-read sequencing data. | 2026-09-12 12:56:46 | 235 | |||||
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mutationSeq Resource Report Resource Website 10+ mentions |
mutationSeq (RRID:SCR_006815) | mutationSeq | software resource | A software suite using feature-based classifiers for somatic mutation prediction from paired tumour/normal next-generation sequencing data. mutationSeq has the advantages of integrating different features (e.g., base qualities, mapping qualities, strand bias, and tailed distance features), and validated somatic mutations to make predictions. Given paired normal/tumour bam files, mutationSeq will output the probability of each candidate site being somatic. | next-generation sequencing, somatic mutation, tumor, normal |
is listed by: OMICtools is related to: JointSNVMix has parent organization: BC Cancer Agency |
Tumor, Normal | PMID:22084253 | OMICS_00086 | SCR_006815 | 2026-09-12 12:56:46 | 24 | |||||||
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University of Rostock; Mecklenburg-Vorpommern; Germany Resource Report Resource Website 1+ mentions |
University of Rostock; Mecklenburg-Vorpommern; Germany (RRID:SCR_006816) | university | Public university located in Rostock, Mecklenburg-Vorpommern, Germany. Founded in 1419. |
is parent organization of: neuroVIISAS is parent organization of: SysZNF - C2H2 Zinc Finger genes |
nlx_151399, grid.10493.3f, Wikidata:Q159895, ISNI:121858338 | https://ror.org/03zdwsf69 | SCR_006816 | Universit�t Rostock, University of Rostock, Universitat Rostock | 2026-09-12 12:56:46 | 1 | |||||||||
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Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology Resource Report Resource Website |
Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology (RRID:SCR_006776) | RPO | controlled vocabulary, data or information resource, ontology | A controlled vocabulary of ontology class structures and entities of observed phenotypic terms for primary immunodeficiency diseases (PIDs) that facilitate global sharing and free exchange of PID data with users'' communities | owl | is listed by: BioPortal | Primary Immunodeficiency Disease | nlx_157576 | SCR_006776 | Resource of Asian Primary Immunodeficiency Diseases (RAPID) Phenotype Ontology, RAPID phenotype ontology | 2026-09-12 12:56:45 | 0 | |||||||
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RIPSeeker Resource Report Resource Website 10+ mentions |
RIPSeeker (RRID:SCR_006810) | RIPSeeker | software resource | A statistical software package for identifying protein-associated transcripts from RIP-seq experiments. Infer and discriminate RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation. | rip-seq |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 | OMICS_00569 | SCR_006810 | RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments | 2026-09-12 12:56:46 | 12 | |||||||
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Chemical Effects in Biological Systems (CEBS) Resource Report Resource Website 10+ mentions |
Chemical Effects in Biological Systems (CEBS) (RRID:SCR_006778) | CEBS | data or information resource, data repository, database, service resource, storage service resource | Repository for toxicogenomics data, including study design and timeline, clinical chemistry and histopathology findings and microarray and proteomics data. Data derived from studies of chemicals and of genetic alterations, and is compatible with clinical and environmental studies. Data relating to environmental health, pharmacology, and toxicology. It is not necessary to have microarray data, but study design and phenotypic anchoring data are required.CEBS contains raw microarray data collected in accordance with MIAME guidelines and provides tools for data selection, pre-processing and analysis resulting in annotated lists of genes of interest. Biomedical Investigation Database is another component of CEBS system. used to load and curate study data prior to export to CEBS, in addition to capturing and displaying novel data types such as PCR data, or additional fields of interest, including those defined by the HESI Toxicogenomics Committee. BID has been shared with Health Canada and the US Environmental Protection Agency. | caenorhabditis elegans, chemical study, microarray, genetic alteration, toxicogenomics, environmental health, study design, timeline, clinical chemistry, histopathology, proteomics, chemical, clinical, microarray hybridization, gel image, phenotype, pharmacology, toxicology |
is recommended by: National Library of Medicine has parent organization: National Institute of Environmental Health Sciences |
NIEHS ; NIGMS |
PMID:17962311 | Free, Freely available | nif-0000-02649, r3d100010314 | https://doi.org/10.17616/R3W02M | SCR_006778 | CEBS, Chemical Effects in Biological Systems (CEBS), Chemical Effects in Biological Systems | 2026-09-12 12:56:45 | 19 | ||||
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C. elegans Development Vocabulary Resource Report Resource Website |
C. elegans Development Vocabulary (RRID:SCR_006811) | WB-LS | controlled vocabulary, data or information resource, ontology | A structured controlled vocabulary of the development of Caenorhabditis elegans. | obo |
is listed by: BioPortal has parent organization: WormBase |
nlx_157346 | SCR_006811 | 2026-09-12 12:56:46 | 0 | |||||||||
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BioBricks Foundation Resource Report Resource Website 10+ mentions |
BioBricks Foundation (RRID:SCR_006779) | BBF | institution | The BioBricks Foundation (BBF) is dedicated to advancing synthetic biology to benefit all people and the planet. To achieve this, we must make engineering biology easier, safer, equitable, and more open. We do this in the following ways: by ensuring that the fundamental building blocks of synthetic biology are freely available for open innovation; by creating community, common values and shared standards; and by promoting biotechnology for all constructive interests. We envision a world in which scientists and engineers work together using BioBric parts freely available standardized biological parts to create safe, ethical solutions to the problems facing humanity. We envision synthetic biology as a force for good in the world. We see a future in which architecture, medicine, environmental remediation, agriculture, and many other fields are using the technology of synthetic biology. Our supporters are many and include corporations, individuals, institutions, foundations, government, corporations, and others. Currently, the BBF''s key programs include: * BIOFAB * BioBrick Public Agreement * Technical Standards Framework * Conferences and Workshops * BBF Global Network * OpenWetWare | is parent organization of: OpenWetWare | grid.487833.3, nlx_19572 | https://ror.org/03kqtp318 | SCR_006779 | 2026-09-12 12:56:45 | 36 | |||||||||
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Thompson Center for Autism and Neurodevelopmental Disorders Resource Report Resource Website |
Thompson Center for Autism and Neurodevelopmental Disorders (RRID:SCR_006812) | Thompson Center | data or information resource, disease-related portal, portal, topical portal, training resource | The mission of the Thompson Center is to improve the lives of individuals and families affected by autism and neurodevelopmental disorders through world class programs that integrate research, clinical service delivery, education and public policy. The Thompson Center''s vision is to become a recognized national center of excellence that serves as a model of interdisciplinary practice, research and training in the field of autism and neurodevelopmental disorders. At the MU Thompson Center, education and training activities are a key part of our mission. Our goal is to teach others about the needs of persons with autism and other neurodevelopmental disorders and their families. In addition, we strive to help learners acquire skills needed to improve the outcomes of individuals with developmental differences. These skills include evidence-based assessment and intervention strategies, interdisciplinary approaches to service delivery, research methods, and policy development. The Thompson Center offers a range of health, educational and behavioral services in one location for individuals with autism and other developmental concerns. Professionals from different disciplines strive to deliver family-centered care that is comprehensive and coordinated. Autism recently has been recognized as a national public health concern, and federal research funding in this area has increased substantially. Faculty members engage in research that will lead to early identification, treatment and ultimately prevention of autism spectrum disorders (ASD). How findings may eventually translate into improved outcomes in clinical and community settings is a primary goal of our research. | research, training, service, resource | has parent organization: University of Missouri; Missouri; USA | Autism, Neurodevelopmental disease, Autism spectrum disorder | nlx_151589 | SCR_006812 | MU Thompson Center, Thompson Center for Autism Neurodevelopmental Disorders, MU Thompson Center for Autism and Neurodevelopmental Disorders | 2026-09-12 12:56:46 | 0 | |||||||
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Ensembl Genomes Resource Report Resource Website 100+ mentions |
Ensembl Genomes (RRID:SCR_006773) | data access protocol, data or information resource, database, software resource, web service | Database portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualization platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community - essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimized data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualized in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site. | genome, gold standard, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: Ensembl is related to: g:Profiler has parent organization: European Bioinformatics Institute |
European Molecular Biology Laboratory ; European Union FELICS 021902 (RII3); BBSRC BB/F019793/1 |
PMID:24163254 PMID:19884133 |
r3d100011197, OMICS_01648, biotools:ensembl_genomes, nlx_65207 | https://bio.tools/ensembl_genomes, https://doi.org/10.17616/R3MW6M | SCR_006773 | Ensembl Genomes: Extending Ensembl across the taxonomic space, EnsemblGenomes, Ensembl Genome | 2026-09-12 12:56:45 | 320 | ||||||
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Canadian Bioinformatics Workshops Resource Report Resource Website 1+ mentions |
Canadian Bioinformatics Workshops (RRID:SCR_006774) | CBW | data or information resource, narrative resource, short course, training material, training resource, workshop | Offers one and two week short courses in bioinformatics, genomics and proteomics in response to an identified need for a skilled bioinformatics workforce in Canada. For eight years, the series offered short courses in bioinformatics, genomics and proteomics in various cities across Canada. Taught by top faculty from Canada and the US, the courses offered small classes and hands-on instruction. The CBW initiated development of a new format and series of exciting workshops focusing on training the researchers of these advanced technologies on the latest approaches being used in computational biology to deal with the new data. Past workshop content is available under a Creative Commons License. | education, bioinformatics, course, genomics, proteomics |
is related to: Bioinformatics Jobs Board has parent organization: Ontario Institute for Cancer Research |
Canadian Institutes of Health Research ; Ontario Institute for Cancer Research ; Institute of Genetics ; Genome British Columbia ; PrioNet Canada ; MathWorks ; ActiveState |
Creative Commons License | nif-0000-10185 | SCR_006774 | bioinformatics.ca | 2026-09-12 12:56:45 | 3 | ||||||
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Qudaich Resource Report Resource Website |
Qudaich (RRID:SCR_006775) | Qudaich | software resource | A software package for local sequence alignment for next-generation sequencing (NGS) data. It generates the pairwise local alignments between a query dataset against a database. The main design purpose of qudaich is to focus on datasets from next generation sequencing. These the datasets generally have hundreds of thousand sequences or more, and so, the input database should contain large number of sequences. Qudaich is flexible and its algorithmic structure imposes no restriction on the absolute limit of the acceptable read length, but the current version of qudaich allow read length <2000 bp. Qudaich can be used to align DNA, translated DNA and protein sequences. | next-generation sequencing, alignment |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00678 | SCR_006775 | Queries and unique database alignment inferred by clustering homologs | 2026-09-12 12:56:45 | 0 | ||||||||
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Adverse Event Ontology Resource Report Resource Website |
Adverse Event Ontology (RRID:SCR_006807) | AEO | controlled vocabulary, data or information resource, ontology | AEO represents the Adverse Event Ontology, a community-driven ontology developed to standardize and integrate data on biomedical adverse events (e.g., vaccine adverse events) and support computer-assisted reasoning. The AEO also can be found in BioPortal, http://bioportal.bioontology.org/ontologies/45534?p=terms | has parent organization: SourceForge | nlx_44108 | SCR_006807 | 2026-09-12 12:56:46 | 0 | ||||||||||
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ADAPT Resource Report Resource Website 500+ mentions |
ADAPT (RRID:SCR_006769) | ADAPT | data analysis software, data processing software, software application, software resource | Software tool as plug-in developed for ImageJ/FIJI platform to automatically detect and analyse cell migration and morphodynamics. Provides whole cell analysis of multiple cells, while also returning data on individual membrane protrusion events. | Cell migration analysis, morphodynamics analysis, whole cell analysis |
has parent organization: Biomedical Simulations Resource is a plug in for: ImageJ |
NIBIB P41-EB001978; NCRR P41-RR01861 |
DOI:10.1083/jcb.201501081 | Acknowledgement requested, Registration required | nlx_152570 | https://github.com/djpbarry/Adapt | SCR_006769 | Automated Detection and Analysis of ProTrusions | 2026-09-12 12:56:45 | 603 | ||||
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PeproTech Resource Report Resource Website 10000+ mentions |
PeproTech (RRID:SCR_006802) | commercial organization | An Antibody supplier | nlx_152428 | SCR_006802 | 2026-09-12 12:56:45 | 27849 |
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