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http://rast.nmpdr.org

A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes.

Proper citation: RAST Server (RRID:SCR_014606) Copy   

•   Source: SciCrunch Registry

http://www.ctotstudies.org

Project portal for a cooperative research program to improve short and long-term graft and patient survival. CTOT is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for transplant recipients.

Proper citation: Clinical Trials in Organ Transplantation (CTOT) (RRID:SCR_015859) Copy   

•   Source: SciCrunch Registry

http://www.ctotc.org

Project portal for a cooperative research program sponsored by the National Institute of Allergy and Infectious Diseases (NIAID). CTOT-C is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for pediatric heart, lung, or kidney transplant recipients.

Proper citation: Clinical Trials in Organ Transplantation in Children (CTOT-C) (RRID:SCR_015860) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://bloodexposome.org

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   

•   Source: SciCrunch Registry

http://10kimmunomes.org

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   

•   Source: SciCrunch Registry

https://vdjbase.org/

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   

•   Source: SciCrunch Registry

http://www.uniprot.org/

Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.

Proper citation: UniProt (RRID:SCR_002380) Copy   

•   Source: SciCrunch Registry

http://compbio.uthsc.edu/miRSNP/

Database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational repression or mRNA destabilization. SNPs and INDELs in miRNAs and their target sites may affect miRNA-mRNA interaction, and hence affect miRNA-mediated gene repression. The PolymiRTS database was created by scanning 3'UTRs of mRNAs in human and mouse for SNPs and INDELs in miRNA target sites. Then, the potential downstream effects of these polymorphisms on gene expression and higher-order phenotypes are identified. Specifically, genes containing PolymiRTSs, cis-acting expression QTLs, and physiological QTLs in mouse and the results of genome-wide association studies (GWAS) of human traits and diseases are linked in the database. The PolymiRTS database also includes polymorphisms in target sites that have been supported by a variety of experimental methods and polymorphisms in miRNA seed regions.

Proper citation: PolymiRTS (RRID:SCR_003389) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.urmc.rochester.edu/microbiology-immunology/xenopus-laevis.aspx

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.

Proper citation: Xenopus laevis Research Resource for Immunobiology (XLRR) (RRID:SCR_014354) Copy   

•   Source: SciCrunch Registry

https://github.com/EpistasisLab/ReBATE

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 .

Proper citation: ReBATE (RRID:SCR_017139) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Maaslin2.html

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.

Proper citation: MaAsLin2 (RRID:SCR_023241) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://bnaber.org

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   

•   Source: SciCrunch Registry

http://www.violinet.org

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

Proper citation: VIOLIN: Vaccine Investigation and Online Information Network (RRID:SCR_012749) Copy   

•   Source: SciCrunch Registry

http://toxodb.org/toxo/

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

Proper citation: ApiDB ToxoDB (RRID:SCR_013453) Copy   

•   Source: SciCrunch Registry

http://msub.csbio.unc.edu/

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.

Proper citation: Mouse Phylogeny Viewer (RRID:SCR_014071) Copy   

•   Source: SciCrunch Registry

http://www.patricbrc.org/portal/portal/patric/Home

A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available.

Proper citation: Pathosystems Resource Integration Center (RRID:SCR_004154) Copy   

•   Source: SciCrunch Registry