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http://clonesearch.jdrfnpod.org/
Database of sequence data generated from high-throughput immunosequencing of the TCR beta chain (TRB) and B cell receptor (BCR) immunoglobulin heavy chain (IGH). This data comes from cells from NPOD donors.
Proper citation: nPOD TCR/BCR Search (RRID:SCR_015851) Copy
Collection of chemical compounds and associated information that were automatically extracted by text mining content of PubMed and PubChem databases. Unifies chemical lists from metabolomics, systems biology, environmental epidemiology, occupational expossure, toxiology and nutrition fields.
Proper citation: Blood Exposome Database (RRID:SCR_017610) Copy
Collection of reference datasets for human immunology, derived from control subjects in the NIAID ImmPort database . Available data include flow cytometry, CyTOF, multiplex ELISA, gene expression, HAI titers, clinical lab tests, HLA type, and others.
Proper citation: The 10000 Immunomes (RRID:SCR_016624) Copy
Open source adaptive immune receptor genotype and haplotype database. Core collection is inferred from immune receptor repertoire sequences and genomically derived material. Provides customisable reports, which allow users to study gene and allele usage in various ways.
Proper citation: VDJbase (RRID:SCR_022599) Copy
https://pypi.org/project/pmlb/
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/
Proper citation: Penn machine learning benchmark repository (RRID:SCR_017138) Copy
https://med.nyu.edu/research/scientific-cores-shared-resources/ion-laboratory
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.
Proper citation: New York University School of Medicine IonLab Core Facility (RRID:SCR_021754) Copy
https://immunedb.readthedocs.io/en/latest/
Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features.
Proper citation: ImmuneDB (RRID:SCR_017125) Copy
Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions.
Proper citation: immuneXpresso (RRID:SCR_017578) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 22, 2023. A database containing genomic/biological information on anopheline mosquitoes, with an emphasis on Anopheles gambiae, the world''''s most important malaria vector. AnoBase is an integrated, relational database of basic biological and genetic data on anopheline species, with a particular emphasis on Anopheles gambiae. It has been designed as an information source and research support tool for the broad vector biology community. Although AnoBase is not a primary genomic database that develops and provides tools to access the genome of the malaria mosquito, it nevertheless contains several sections that offer data of genomic interest such as in situ hybridization images, an integrated gene tool and direct online access to AnoXcel, the proteomic database of An. gambiae. Moreover, AnoBase also contains information on non-gambiae mosquito species and a novel section on studies related to insecticide resistance.
Proper citation: AnoBase: An Anopheles database (RRID:SCR_008166) Copy
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.
Proper citation: bNAber (RRID:SCR_010510) Copy
http://www.broad.mit.edu/annotation/fungi/fgi/
Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics.
Proper citation: Fungal Genome Initiative (RRID:SCR_003169) Copy
https://github.com/sokrypton/ColabFold
Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding.
Proper citation: ColabFold (RRID:SCR_025453) Copy
https://github.com/JLSteenwyk/ClipKIT
Software fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others. Multiple sequence alignment-trimming algorithm for accurate phylogenomic inference.
Proper citation: ClipKIT (RRID:SCR_026411) Copy
https://github.com/ScilifelabDataCentre/node-pathogens-portal
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.
Proper citation: Pathogens Portal Node Toolbox (RRID:SCR_027086) Copy
https://curie.utmb.edu/prosurf.html
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.
Proper citation: InterProSurf (RRID:SCR_027791) Copy
http://www.genome.ou.edu/cneo.html
Cryptococcus neoformans is an encapsulated yeast that infects the human host via the respiratory tract where it usually causes an inapparent infection. In the susceptible host, it may disseminate, typically producing a chronic and life-threatening meningitis. The Cryptococcus neoformans serotypes A and D are responsible for the overwhelming majority of pulmonary infections in AIDS patients. Cryptococcus neoformans strain H99 Latest Data Release - May 19, 2004 To date, we have isolated ca. 3750 cDNA clones from Cryptococcus neoformans strain H99 in collaboration with Drs. Juneann Murphy and Dave Dyer at the University of Oklahoma Health Sciences Center''s Department of Microbiology and Immunology in Oklahoma City and Kent Buchanan at the Tulane University Medical School, New Orleans, LA. The Cryptococcus neoformans strain H99 EST''s have been generated by Doris Kupfer, Heather Bell, Sunkyoung So, Yuong Tang, and Jennifer Lewis at the University of Oklahoma''s Advanced Center for Genome Technology, in the Department of Chemistry and Biochemistry. We now have end sequenced all available templates (ca. 7500 reactions) from both ends of the directionally cloned inserts after excision into pBlueScript SK-. . All of our data is available from our ftp site, and we now have added the ability to perform blast searches on this data. A keyword search of a blastx search of GenBank with this data also is available but we have not yet linked this to a unigene database as the number of EST''s sequenced doesn''t warrent this yet.
Proper citation: Cryptococcus Neoformans cDNA Sequencing (RRID:SCR_008462) Copy
https://omics.pnl.gov/software/ms-gf
Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
Proper citation: MS-GF+ (RRID:SCR_015646) Copy
https://github.com/epistasislab/hibachi
Software tool that creates data sets with particular characteristics. Method and open source software for simulating complex biological and biomedical data to aid in comparing and evaluating machine learning methods.
Proper citation: Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (RRID:SCR_017140) Copy
https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/
Open, global repository as central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). Committed to sharing knowledge related to multiplexed imaging. Antibody validation community knowledgebase.
Proper citation: IBEX Knowledge Base (RRID:SCR_025296) Copy
A consortium of university groups to characterize human immune populations. The Human Immunology Project Consortium (HIPC) program, established in 2010 by the NIAID Division of Allergy, Immunology, and Transplantation, is a major collaborative effort that is generating large amounts of cross-center and cross-assay data including high-dimensional data to characterize the status of the immune system in diverse populations under both normal conditions and in response to stimuli. This large data problem has given birth to ImmuneSpace, a powerful data management and analysis engine where datasets can be easily explored and analyzed using state-of-the-art computational tools.
Proper citation: ImmuneSpace (RRID:SCR_010508) Copy
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