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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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bNAber Resource Report Resource Website 1+ mentions |
bNAber (RRID:SCR_010510) | bNAber | data or information resource, database | bNAber is the Broadly Neutralizing Antibody E-Resource Database, analysis, visualization, and data discovery tool for broadly neutralizing HIV-1 antibodies (bNAbs). bNAber seeks to be a vital tool in the search for an AIDS vaccine. | sanford burnham medical research institute, hiv, aids | is related to: CHAVI-ID | HIV, AIDS | NIAID UM1AI100663; NIGMS R01GM101457 |
nlx_158732 | SCR_010510 | SciCrunch Registry | 2026-10-24 12:50:59 | 7 | |||||||
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VIOLIN: Vaccine Investigation and Online Information Network Resource Report Resource Website 10+ mentions |
VIOLIN: Vaccine Investigation and Online Information Network (RRID:SCR_012749) | VIOLIN | data or information resource, database | A web-based central resource that integrates vaccine literature data mining, vaccine research data curation and storage, and curated vaccine data analysis for vaccines and vaccine candidates developed against various pathogens of high priority in public health and biological safety. The vaccine data includes research data from vaccine studies using humans, natural and laboratory animals.VIOLIN extracts and stores vaccine-related, peer-reviewed papers from PubMed. Several powerful literature searching and data mining programs have been developed. These include an advanced keywords search program, a natural languagae processing (NLP) based literature retrieval program, a MeSH-based literature browser, and a literature alert program. Registered users can subscribe to our email alert service and will be notified of any newly published vaccine papers in the areas of interest. These literature mining programs are designed to help the user and VIOLIN database curators to find efficiently needed vaccine articles and sentences within full-text articles that contain searched keywords or categories.A web-based literature mining and curation system (Limix) is available for registered users/curators to search, curate, and submit structured vaccine data into the VIOLIN database. The curated vaccine-related information contains many categories such as general pathogenesis, protective immunity, vaccine preparation and characteristics, host responses including vaccination protocol and efficacy against virulent pathogen infections. All data within the database is edited manually and is derived primarily from peer-reviewed publications. The curated data is stored in a relational database and can be queried using various VIOLIN search programs. Vaccine-related pathogen and host genes are annotated and available for searchs based on a customized BLAST program. All VIOLIN data are available for download into an XML-based data exchange format.VIOLIN is designed to be a vital source of vaccine information and will provide researchers in basic and clinical sciences with curated data and bioinformatics tools to facilitate understanding and development of vaccines to fight infectious diseases. Category: Other Molecular Biology Databases Subcategory: Drugs and drug design | immunology, infectious diseases, molecular biology, pathogen, public health, vaccine | has parent organization: University of Michigan; Ann Arbor; USA | NIAID U24 AI125008 | nif-0000-03629 | SCR_012749 | SciCrunch Registry | Violin 2.0, Vaccine Investigation and Online Information Network | 2026-10-24 12:51:04 | 27 | |||||||
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ApiDB ToxoDB Resource Report Resource Website 100+ mentions |
ApiDB ToxoDB (RRID:SCR_013453) | ApiDB ToxoDB | data or information resource, database | A genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. Organisms * Toxoplasma gondii (ME49, RH, GT1, Veg strains) * Neospora caninum * environmental isolate sequences from numerous species Tools * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Toxoplasma, Neospora Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * Ancillary Genome Browse: Access Additional info like Probeset data and Toxoplasma Array info | end-sequencing, bac clone, data mining tool, microarray, proteomic sequencing, toxoplasma gondii, bac clone, 8x random shotgun, genomic sequencing project, snp, qtl, sequencing, genomic, non-vertebrate, unicellular, eukaryote, genome, pathogen, toxoplasmosis, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Eukaryotic Pathogen Database Resources |
NIAID contract HHSN266200400037C | PMID:18003657 PMID:12519989 |
r3d100012266, biotools:toxodb, nif-0000-03572 | https://bio.tools/toxodb | http://ToxoDB.org | SCR_013453 | SciCrunch Registry | Toxoplasma Genomics Resource, ToxoDB | 2026-10-24 12:51:07 | 153 | ||||
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Mouse Phylogeny Viewer Resource Report Resource Website 10+ mentions |
Mouse Phylogeny Viewer (RRID:SCR_014071) | data or information resource, database | A custom genome browser which provides detailed answers to questions on the haplotype diversity and phylogenetic origin of the genetic variation underlying any genomic region of most laboratory strains of mice (both classical and wild-derived). Users can select a region of the genome and a set of laboratory strains and/or wild caught mice. The region is selected by specifying the start (e.g. 31200000 or 31200K or 31.2M), and end of the interval and the chromosome (i.e, autosome number and X chromosome). Samples can be selected by name or by entire set. Data sets include information on subspecific origin, heterozygosity regions, and haplotype coloring, among others. | mouse, genetic, software, phylogeny, browser | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | NHGRI P50 HG 006582; NIAID U54 AI 081680; NSF ISS 0534580 |
PMID:22536897 | SCR_014071 | SciCrunch Registry | 2026-10-24 12:51:08 | 11 | |||||||||
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Xenopus laevis Research Resource for Immunobiology (XLRR) Resource Report Resource Website 1+ mentions |
Xenopus laevis Research Resource for Immunobiology (XLRR) (RRID:SCR_014354) | XLRR | biomaterial supply resource, material resource | A comprehensive resource specializing in the use of the amphibian Xenopus laevis (the African clawed frog) for biomedical and immunological research. Several genetically-defined inbred strains and clones are available for study. The facility also maintains and develops research tools such as transgenic animals, monoclonal antibodies, cell lines, DNA libraries, and molecular probes. XLRR includes a satellite facility devoted to study infectious diseases caused by iridovirus. Technical assistance, education, and training are also provided. | Immunology, cancer, inbred frog, cloned frog, monoclonal antibody, xenopus laevis, lymphoid tumor cell lines | NIAID | SCR_014354 | SciCrunch Registry | Xenopus laevis Research Resource, Xenopus laevis Research Resource for Immunobiology | 2026-10-24 12:51:46 | 4 | |||||||||
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Penn machine learning benchmark repository Resource Report Resource Website |
Penn machine learning benchmark repository (RRID:SCR_017138) | PMLB | data or information resource, data set | Python wrapper for Penn Machine Learning Benchmark data repository. Large, curated repository of benchmark datasets for evaluating supervised machine learning algorithms. Part of PyPI https://pypi.org/ | benchmark, suite, machine, learning, evaluation, comparison, repository, curated, dataset | NCATS TR001263; NEI EY022300; NHLBI HL134015; NIAID AI116794; NIDDK DK112217; NIEHS ES013508; NLM LM009012; NLM LM010098; NLM LM011360; Warren Center for Network and Data Science |
PMID:29238404 | Free, Restricted | https://github.com/EpistasisLab/penn-ml-benchmarks | SCR_017138 | SciCrunch Registry | Penn Machine Learning Benchmark | 2026-10-24 12:52:53 | 0 | ||||||
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HIV-1 Human Protein Interaction Database Resource Report Resource Website 10+ mentions |
HIV-1 Human Protein Interaction Database (RRID:SCR_006879) | HIV-1 Human Protein Interaction Database | data or information resource, database | A database of interactions between HIV-1 and human proteins published in the peer-reviewed literature. The goal is to provide a concise, yet detailed, summary of all known interactions of HIV-1 proteins with host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV/AIDS. For each HIV-1 human protein interaction the following information is provided: * NCBI Reference Sequence (RefSeq) protein accession numbers. * NCBI Entrez Gene ID numbers. * Amino acids from each protein that are known to be involved in the interaction. * Brief description of the protein-protein interaction. * Keywords to support searching for interactions. * PubMed identification numbers (PMIDs) for all journal articles describing the interaction. In addition, all protein-protein interactions documented in the database are integrated into Entrez Gene records and listed in the ''HIV-1 protein interactions'' section of Entrez Gene reports. The database is also tightly linked to other databases through Entrez Gene, enabling users to search for an abundance of information related to HIV pathogenesis and replication. | protein-protein interaction, protein, interaction, cellular protein |
is related to: VirHostNet: Virus-Host Network has parent organization: NCBI |
Human immunodeficiency virus, Type 1 | NIAID contract N01-AI-05415; NIAID N01-AI-70042 |
PMID:18927109 PMID:19025396 PMID:19262354 |
Acknowledgement requested | nif-0000-02964 | SCR_006879 | SciCrunch Registry | HIV-1: Human Protein Interaction Database, Human immunodeficiency virus type 1 human protein interaction database at NCBI | 2026-10-24 12:50:41 | 13 | ||||
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CuticleDB Resource Report Resource Website 10+ mentions |
CuticleDB (RRID:SCR_007045) | cuticleDB | data or information resource, database | A relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the five sequenced genomes where manual annotation has been applied to cuticular proteins: Anopheles gambiae, Apis mellifera, Bombyx mori, Drosophila melanogaster, and Nasonia vitripennis. Some sequences were confirmed as authentic cuticular proteins because protein sequencing revealed that they were present in cuticle; others were identified by sequence homology and other criteria. Entries provides information about whether sequences are putative or authentic cuticular proteins. CuticleDB was primarily designed to contain correct and full annotation of cuticular protein data. The database will be of help to future genome annotators. Users will be able to test hypotheses for the existence of known and also of yet unknown motifs in cuticular proteins. An analysis of motifs may contribute to understanding how proteins contribute to the physical properties of cuticle as well as to the precise nature of their interaction with chitin. | genome, cuticle, cuticle protein, cuticular protein, cdna, protein, insect, exoskeleton, annotation, chitin, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
University of Athens; Athens; Greece ; NIAID AI055624 |
PMID:15453918 | biotools:cuticledb, nif-0000-02708 | https://bio.tools/cuticledb | SCR_007045 | SciCrunch Registry | CuticleDB - A relational database of Arthropod cuticular proteins | 2026-10-24 12:50:42 | 14 | |||||
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ReBATE Resource Report Resource Website |
ReBATE (RRID:SCR_017139) | software resource, software toolkit | Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity . | compare, relief, feature, algorithm, data, mining, variable, heterogeneous, pattern, genetic | has parent organization: University of Pennsylvania; Philadelphia; USA | NCATS TR001263; NEI EY022300; NHLBI HL134015; NIAID AI116794; NIDDK DK112217; NIEHS ES013508; NLM LM009012; NLM LM010098; NLM LM011360; Warren Center for Network and Data Science |
PMID:30030120 | Free, Available for download, Freely available | https://epistasislab.github.io/ReBATE/ | SCR_017139 | SciCrunch Registry | Relief Based Algorithm Training Environment | 2026-10-24 12:51:48 | 0 | ||||||
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MaAsLin2 Resource Report Resource Website 100+ mentions |
MaAsLin2 (RRID:SCR_023241) | software resource, software toolkit | SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. | Microbiome Multivariable Associations with Linear Models, | NHGRI R01HG005220; NIAID U19AI110820; NIDDK R24DK110499; NIDDK U54DK102557; NSF DEB-2028280 |
DOI:10.1371/journal.pcbi.1009442 | Free, Available for download, Freely available | https://huttenhower.sph.harvard.edu/maaslin/ | SCR_023241 | SciCrunch Registry | 2026-10-24 12:51:56 | 212 | ||||||||
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New York University School of Medicine IonLab Core Facility Resource Report Resource Website 10+ mentions |
New York University School of Medicine IonLab Core Facility (RRID:SCR_021754) | access service resource, core facility, service resource | Electrophysiology core facility that is part of Ion Channels and Transporters in Immunity Research Program.Research area includes ion channel and transporter function and ionic signaling in immune cells.Users who are studying other cell types or organ systems are welcome.Provides assistance with experimental design, training, implementation, and data analysis. | USEDit, ABRF, ion channel, transporter function, ionic signaling, immune cells |
is listed by: ABRF CoreMarketplace has parent organization: New York University School of Medicine; New York; USA |
NIAID AI097302 | open | ABRF_1221 | https://coremarketplace.org/?FacilityID=1221 | SCR_021754 | SciCrunch Registry | IonLab | 2026-10-24 12:53:06 | 10 | ||||||
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ColabFold Resource Report Resource Website 100+ mentions |
ColabFold (RRID:SCR_025453) | software resource, source code | Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding. | prediction of protein structures and complexes, protein folding, protein structure prediction, | Max Planck Society ; National Research Foundation of Korea ; NIAID R21AI156595; NIH Office of the Director DP5OD026389; NSF ; Seoul National University ; University of Göttingen |
PMID:35637307 | Free, Available for download, Freely available | https://github.com/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb | SCR_025453 | SciCrunch Registry | 2026-10-24 12:53:40 | 493 | ||||||||
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ClipKIT Resource Report Resource Website 10+ mentions |
ClipKIT (RRID:SCR_026411) | software application, software resource, source code | Software fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others. Multiple sequence alignment-trimming algorithm for accurate phylogenomic inference. | multiple sequence, alignment trimming, accurate phylogenomic inference, | Burroughs Wellcome Fund ; Fundamental Research Funds for the Central Universities ; Guggenheim Foundation ; Howard Hughes Medical Institute ; National Science Foundation ; NIAID 1R56AI146096; Zhejiang University |
PMID:33264284 | Free, Available for download, Freely available | SCR_026411 | SciCrunch Registry | 2026-10-24 12:53:59 | 49 | |||||||||
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Pathogens Portal Node Toolbox Resource Report Resource Website |
Pathogens Portal Node Toolbox (RRID:SCR_027086) | software resource, software toolkit, source code | Software package and code for Pathogen Portal node (i.e. a local Pathogens Portal, such as the Swedish and Dutch Pathogens Portals). Allows users to create their own node quickly and easily. | Pathogen Portal node, Swedish Pathogens Portal, Dutch Pathogens Portal, SciLifeLab | NIAID U24AI183840 | Free, Available for download, Freely available | SCR_027086 | SciCrunch Registry | 2026-10-24 12:54:12 | 0 | ||||||||||
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InterProSurf Resource Report Resource Website |
InterProSurf (RRID:SCR_027791) | data access protocol, software resource, web application, web service | Web server for predicting interacting sites on protein surfaces. Analyzes solvent-accessible residues likely to participate in PPIs.Predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of protein complex. | Analyzes solvent-accessible residues, predicting interacting sites on protein surfaces, interacting amino acid residues in proteins, proteins that are most likely to interact with other proteins, | NIAID R01 AI064913; NIAID R21 AI055746 |
PMID:17933856 | Free, Freely available, | SCR_027791 | SciCrunch Registry | 2026-10-24 12:54:31 | 0 | |||||||||
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spaCR Resource Report Resource Website |
spaCR (RRID:SCR_029041) | spaCR | 1d time-series analysis software, data analysis software, data processing software, software application, software resource, time-series analysis software | Software Python framework that links pooled CRISPR-Cas9 perturbations to single-cell spatial phenotypes. It segments cells, nuclei, pathogens and organelles in high-content microscopy images with Cellpose, measures morphology, intensity, texture, spatial and colocalization features into a single SQLite project, supports keyboard-driven annotation and active learning, trains image and measurement-based classifiers with held-out performance recorded per checkpoint, maps sequencing reads to wells and gRNA barcodes, and estimates per-guide and per-gene effects by multiple linear regression to produce a ranked hit list. It runs as a Qt desktop application or headlessly on a workstation, server or cluster, on Linux, macOS and Windows, with CUDA, ROCm, Metal and Intel XPU acceleration. | CRISPR screen; pooled screen; image-based screening; high-content screening; spatial phenotype; single-cell; cell segmentation; Cellpose; deep learning; image classification; barcode mapping; regression; host-pathogen; Toxoplasma gondii; microscopy; Python; SQLite | NIAID AI007413; NIAID AI180278; NIGMS GM151129; NIH Office of the Director OD034245; Swedish Research Council 2021-06749 |
PMID:42465465 | Free, Available for download, Freely available | https://pypi.org/project/spacr/ | SCR_029041 | SciCrunch Registry | , spacr; spaCR: spatial phenotype analysis of CRISPR screens | 2026-10-24 12:54:55 | 0 | ||||||
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HCV Sequence Database Resource Report Resource Website 10+ mentions |
HCV Sequence Database (RRID:SCR_006019) | HCV Sequence Database | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | The HCV sequence database collects and annotates sequence data and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, based on the model of the highly regarded Los Alamos HIV database. The hepatitis C virus (HCV) is a significant threat to public health worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. At present, some 30 000 HCV sequences have been published. This central website provides annotated sequences and analysis tools that will be helpful to HCV scientists worldwide. Things you can do: * Find sequences in the database * Download sequences from the database * Retrieve data about the sequences * Analyze sequences * Work with the sequences using our tools * Download ready-made alignments The HCV sequence database was officially launched in September 2003. Since then, its usage has steadily increased and is now at an average of approximately 280 visits per day from distinct IP addresses. | hepatitis c virus, sequence, annotation | has parent organization: HCV Databases | Hepatitis C | NIAID | PMID:15377502 | Public | nlx_151411 | SCR_006019 | SciCrunch Registry | Hepatitis C Sequence Database, Hepatitis C Virus Sequence Database, Los Alamos hepatitis C sequence database | 2026-10-24 12:45:36 | 19 | ||||
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Ontobee Resource Report Resource Website 50+ mentions |
Ontobee (RRID:SCR_006321) | Ontobee | controlled vocabulary, data or information resource, database, ontology, service resource | Web-based linked data server and browser specifically designed for ontology terms, it supports ontology visualization, query, and development. Ontobee provides a web interface for displaying the details and hierarchy of a specific ontology term. Meanwhile, Ontobee provides a RDF source code for the particular web page, which supports remote query of the ontology term and the Semantic Web. Ontobee provides an efficient and publicly available method to promote ontology sharing, interoperability, and data integration. | visualization, query, development, ontology, ontology sharing, interoperability, data integration, sparql, FASEB list |
lists: Porifera Ontology lists: Chemical Methods Ontology is related to: eagle-i research resource ontology has parent organization: University of Michigan Medical School; Michigan; USA |
NIAID R01AI081062 | Public | nlx_152048 | SCR_006321 | SciCrunch Registry | 2026-10-24 12:45:41 | 76 | |||||||
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HIV Sequence Database Resource Report Resource Website 100+ mentions |
HIV Sequence Database (RRID:SCR_002906) | HIV Sequence Database | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. HIV Sequence Database is a database of annotated HIV sequences, plus a variety of tools and information for researchers studying HIV and SIV. The main aim of this website is to provide easy access to our sequence database, alignments, and the tools and interfaces we have produced. The HIV Sequence Database focuses on five primary goals: * Collecting HIV and SIV sequence data (all sequences since 1987) * Curating and annotating this data, and making it available to the scientific community * Computer analysis of HIV and related sequences * Production of software for the analysis of (sequence) data * The data and analyses on this site and published in a yearly printed publication, the HIV sequence Compendium, which is available free of charge. | drug resistance, genetics, mutation, vaccine, human immunodeficiency virus, siv, sequence, alignment, simian immunodeficiency virus, FASEB list | has parent organization: HIV Databases | Human immunodeficiency virus, Simian immunodeficiency virus | NIAID | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02967 | SCR_002906 | SciCrunch Registry | 2026-10-24 12:44:49 | 110 | ||||||
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Weighted Gene Co-expression Network Analysis Resource Report Resource Website 1000+ mentions |
Weighted Gene Co-expression Network Analysis (RRID:SCR_003302) | WGCNA | data analysis software, data processing software, software application, software resource | Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, co-expression, analysis, network, bio.tools, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of California at Los Angeles; California; USA |
NCI P50CA092131; NIDA 1R01DA030913-01; NIDCR R01DE019255; NIAID U19 AI063603-01 |
PMID:19114008 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31889, biotools:crosslinkwgcna | http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpackages/WGCNA/#citation, https://bio.tools/crosslinkwgcna | SCR_003302 | SciCrunch Registry | WGCNA: an R package for weighted correlation network analysis | 2026-10-24 12:44:55 | 1879 |
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