All Applications



The NIH 3D Print Exchange provides models in formats that are readily compatible with 3D printers and offers a set of tools to create and share 3D-printable models related to biomedical science including molecule structures and prosthetics.


Nephele brings together microbiome data and analysis tools and aims to address a major challenge facing researchers today namely, analyzing, transferring, and storing biomedical big data through the use of cloud-based resources.


ChemokineDB is a comprehensive resource of chemokines and receptors with detailed information including taxonomy, nomenclature, structure, physiological function, tissue information, and phenotype, collected from IUPHAR/BPS, UniGene, and UniProt.


The PapillomaVirus Episteme (PaVE) provides curated genomics information and tools to the scientific community. It consists of a database and web applications that support the storage, annotation, analysis, and exchange of information.


The TB Portals contain integrated clinical, imaging, and bacterial genomic information from TB patient cases around the world. They also feature custom-built computational tools to perform meta-domain and domain-specific analyses of this large TB meta dataset.


The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) provides information and analytical resources to researchers to accelerate the development of antimicrobial compounds with a high therapeutic index.


OMics Compendia Commons (OMiCC) is a community-based, biologist-friendly web platform for creating and (meta-) analyzing annotated gene-expression data compendia.


The Simplified Presentation of Incredibly Complex Evaluations (SPICE) program is a data mining application that analyzes large FLOWJO data sets from polychromatic flow cytometry and organizes the normalized data graphically.


CARD is a comprehensive web-application for integrated analysis and interactive visualization of RNA interference (RNAi) screening data.


SPADE is a web tool for applying statistical analysis of gene expression data and visualizing the results.


The Throughput Ranking by Iterative Analysis of Genomic Enrichment (TRIAGE) platform is designed to facilitate prediction, analysis, and hypothesis generation from genome-wide perturbation studies like those designed with RNAi and CRISPR technologies.


MAD BEE is a mAdb microarray data management and analysis system.


Simplified Analysis of Gene Expression (SAGE) is browser-based program for rapidly analyzing and archiving qPCR data. It parses raw, ungrouped data exported from real-time qPCR instruments and analyzes relative gene expression values.


Phasespace Explorer provides a computational framework for understanding behaviors of dynamical models by combining machine learning techniques and massive computational simulation.


PATRIC provides integrated data and analysis tools to support biomedical research on bacterial infectious diseases.


ViPR, the Virus Pathogen Resource, is a publicly available, NIAID-sponsored, one-stop database and analysis resource that supports the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases.


VectorBase is a National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Center (BRC) providing genomic, phenotypic and population-centric data to the scientific community for invertebrate vectors of human pathogens.


The EuPathDB Bioinformatics Resource Center provides a portal for accessing genomic-scale datasets associated with the diverse eukaryotic microbes.


The Influenza Research Database (IRD) is a freely available, NIAID funded resource that supports the research efforts of influenza scientists. IRD provides a diverse set of integrated data sets (both publicly available and computed), and novel bioinformatics tools for analysis and visualization of data sets.


Metascape is comprised of a set of reliable, productive and intuitive tools that help biomedical research community to analysis gene/protein lists and make better data-driven decisions.


This site explores the heterogeniety of human immune cells through figures and a data browser.


JOINSOLVER analyzes human immunoglobulin V(D)J recombination and performs IG nucleotide and amino acid alignment, as well as extensive mutation and CDR3 analysis.


The ImmPort project provides advanced information technology support in the archiving and exchange of scientific data for the diverse community of life science researchers and serves as a long-term, sustainable archive of research and clinical data.


Three statistical tools designed to estimate titer levels from neutralization assays, compute Student’s T-tests from summarized data or compute contingency table analyses for 2 x 2 tables.


Simmune is designed to easily define the interactions between individual molecules in a large network or the behaviors of cells in response to external signals. It consists of three components: Modeler, Cell Designer and Simulator.


The Neutralization Epitope Prediction (NEP) method predicts antibody-specific epitopes at the residue level based on neutralization panels of diverse viral strains (the antigen), incorporating information from an unbound structure.


ABC-BAC is a compilation of classified bacterial ATP-binding cassette (ABC) transporter systems.  The transporter systems identified fulfill the three roles characterized by the nucleotide-binding domain (NBD) , transmembrane domain (TMD), and solute-binding protein (SBP) domains. 


The Networks on Circular Chromosome (NetCirChro) plugin enables users of the network visualization platform Cytoscape to overlay networks onto a circular chromosomal map. Data selection is synchronized between Cytoscape and NetCirChro.


Three-dimensional reconstruction via stereoscopy for the study of mosquito swarms


The Hemagglutinin Structure Prediction (HASP) server allows researchers to visualize their phylogenetic, biochemical, and immunological hemagglutinin data in the three-dimensional context of high quality homology models.


The Desktop cDNA Annotation System (dCAS) allows one to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results.


The N-linked Glycosylation Prediction Server aims to discriminate between glycosylated and non-glycosylated N-X-(T/S) sequons byt incorporating structural information and patterns.


This site contains transcriptomes of vector arthropods and non-vector, medically important arthropods and snakes.

Free Applications



The NIH 3D Print Exchange provides models in formats that are readily compatible with 3D printers and offers a set of tools to create and share 3D-printable models related to biomedical science including molecule structures and prosthetics.


Nephele brings together microbiome data and analysis tools and aims to address a major challenge facing researchers today namely, analyzing, transferring, and storing biomedical big data through the use of cloud-based resources.


ChemokineDB is a comprehensive resource of chemokines and receptors with detailed information including taxonomy, nomenclature, structure, physiological function, tissue information, and phenotype, collected from IUPHAR/BPS, UniGene, and UniProt.


The PapillomaVirus Episteme (PaVE) provides curated genomics information and tools to the scientific community. It consists of a database and web applications that support the storage, annotation, analysis, and exchange of information.


The TB Portals contain integrated clinical, imaging, and bacterial genomic information from TB patient cases around the world. They also feature custom-built computational tools to perform meta-domain and domain-specific analyses of this large TB meta dataset.


The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) provides information and analytical resources to researchers to accelerate the development of antimicrobial compounds with a high therapeutic index.


OMics Compendia Commons (OMiCC) is a community-based, biologist-friendly web platform for creating and (meta-) analyzing annotated gene-expression data compendia.


The Simplified Presentation of Incredibly Complex Evaluations (SPICE) program is a data mining application that analyzes large FLOWJO data sets from polychromatic flow cytometry and organizes the normalized data graphically.


The Throughput Ranking by Iterative Analysis of Genomic Enrichment (TRIAGE) platform is designed to facilitate prediction, analysis, and hypothesis generation from genome-wide perturbation studies like those designed with RNAi and CRISPR technologies.


MAD BEE is a mAdb microarray data management and analysis system.


Simplified Analysis of Gene Expression (SAGE) is browser-based program for rapidly analyzing and archiving qPCR data. It parses raw, ungrouped data exported from real-time qPCR instruments and analyzes relative gene expression values.


Metascape is comprised of a set of reliable, productive and intuitive tools that help biomedical research community to analysis gene/protein lists and make better data-driven decisions.


JOINSOLVER analyzes human immunoglobulin V(D)J recombination and performs IG nucleotide and amino acid alignment, as well as extensive mutation and CDR3 analysis.


The ImmPort project provides advanced information technology support in the archiving and exchange of scientific data for the diverse community of life science researchers and serves as a long-term, sustainable archive of research and clinical data.


Three statistical tools designed to estimate titer levels from neutralization assays, compute Student’s T-tests from summarized data or compute contingency table analyses for 2 x 2 tables.


Simmune is designed to easily define the interactions between individual molecules in a large network or the behaviors of cells in response to external signals. It consists of three components: Modeler, Cell Designer and Simulator.


The Neutralization Epitope Prediction (NEP) method predicts antibody-specific epitopes at the residue level based on neutralization panels of diverse viral strains (the antigen), incorporating information from an unbound structure.


ABC-BAC is a compilation of classified bacterial ATP-binding cassette (ABC) transporter systems.  The transporter systems identified fulfill the three roles characterized by the nucleotide-binding domain (NBD) , transmembrane domain (TMD), and solute-binding protein (SBP) domains. 


The Networks on Circular Chromosome (NetCirChro) plugin enables users of the network visualization platform Cytoscape to overlay networks onto a circular chromosomal map. Data selection is synchronized between Cytoscape and NetCirChro.


The Hemagglutinin Structure Prediction (HASP) server allows researchers to visualize their phylogenetic, biochemical, and immunological hemagglutinin data in the three-dimensional context of high quality homology models.


The Desktop cDNA Annotation System (dCAS) allows one to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results.


The N-linked Glycosylation Prediction Server aims to discriminate between glycosylated and non-glycosylated N-X-(T/S) sequons byt incorporating structural information and patterns.


This site contains transcriptomes of vector arthropods and non-vector, medically important arthropods and snakes.


Biological Imaging



The TB Portals contain integrated clinical, imaging, and bacterial genomic information from TB patient cases around the world. They also feature custom-built computational tools to perform meta-domain and domain-specific analyses of this large TB meta dataset.


Structural Biology



The NIH 3D Print Exchange provides models in formats that are readily compatible with 3D printers and offers a set of tools to create and share 3D-printable models related to biomedical science including molecule structures and prosthetics.


ChemokineDB is a comprehensive resource of chemokines and receptors with detailed information including taxonomy, nomenclature, structure, physiological function, tissue information, and phenotype, collected from IUPHAR/BPS, UniGene, and UniProt.


The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) provides information and analytical resources to researchers to accelerate the development of antimicrobial compounds with a high therapeutic index.


JOINSOLVER analyzes human immunoglobulin V(D)J recombination and performs IG nucleotide and amino acid alignment, as well as extensive mutation and CDR3 analysis.


The Neutralization Epitope Prediction (NEP) method predicts antibody-specific epitopes at the residue level based on neutralization panels of diverse viral strains (the antigen), incorporating information from an unbound structure.


ABC-BAC is a compilation of classified bacterial ATP-binding cassette (ABC) transporter systems.  The transporter systems identified fulfill the three roles characterized by the nucleotide-binding domain (NBD) , transmembrane domain (TMD), and solute-binding protein (SBP) domains. 


The Hemagglutinin Structure Prediction (HASP) server allows researchers to visualize their phylogenetic, biochemical, and immunological hemagglutinin data in the three-dimensional context of high quality homology models.


The N-linked Glycosylation Prediction Server aims to discriminate between glycosylated and non-glycosylated N-X-(T/S) sequons byt incorporating structural information and patterns.


Genomics



Nephele brings together microbiome data and analysis tools and aims to address a major challenge facing researchers today namely, analyzing, transferring, and storing biomedical big data through the use of cloud-based resources.


The PapillomaVirus Episteme (PaVE) provides curated genomics information and tools to the scientific community. It consists of a database and web applications that support the storage, annotation, analysis, and exchange of information.


The TB Portals contain integrated clinical, imaging, and bacterial genomic information from TB patient cases around the world. They also feature custom-built computational tools to perform meta-domain and domain-specific analyses of this large TB meta dataset.


OMics Compendia Commons (OMiCC) is a community-based, biologist-friendly web platform for creating and (meta-) analyzing annotated gene-expression data compendia.


CARD is a comprehensive web-application for integrated analysis and interactive visualization of RNA interference (RNAi) screening data.


SPADE is a web tool for applying statistical analysis of gene expression data and visualizing the results.


The Throughput Ranking by Iterative Analysis of Genomic Enrichment (TRIAGE) platform is designed to facilitate prediction, analysis, and hypothesis generation from genome-wide perturbation studies like those designed with RNAi and CRISPR technologies.


MAD BEE is a mAdb microarray data management and analysis system.


PATRIC provides integrated data and analysis tools to support biomedical research on bacterial infectious diseases.


ViPR, the Virus Pathogen Resource, is a publicly available, NIAID-sponsored, one-stop database and analysis resource that supports the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases.


VectorBase is a National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Center (BRC) providing genomic, phenotypic and population-centric data to the scientific community for invertebrate vectors of human pathogens.


The EuPathDB Bioinformatics Resource Center provides a portal for accessing genomic-scale datasets associated with the diverse eukaryotic microbes.


The Influenza Research Database (IRD) is a freely available, NIAID funded resource that supports the research efforts of influenza scientists. IRD provides a diverse set of integrated data sets (both publicly available and computed), and novel bioinformatics tools for analysis and visualization of data sets.


Metascape is comprised of a set of reliable, productive and intuitive tools that help biomedical research community to analysis gene/protein lists and make better data-driven decisions.


Microbiome



Nephele brings together microbiome data and analysis tools and aims to address a major challenge facing researchers today namely, analyzing, transferring, and storing biomedical big data through the use of cloud-based resources.


Biostatistics



The TB Portals contain integrated clinical, imaging, and bacterial genomic information from TB patient cases around the world. They also feature custom-built computational tools to perform meta-domain and domain-specific analyses of this large TB meta dataset.


The Simplified Presentation of Incredibly Complex Evaluations (SPICE) program is a data mining application that analyzes large FLOWJO data sets from polychromatic flow cytometry and organizes the normalized data graphically.


SPADE is a web tool for applying statistical analysis of gene expression data and visualizing the results.


The Throughput Ranking by Iterative Analysis of Genomic Enrichment (TRIAGE) platform is designed to facilitate prediction, analysis, and hypothesis generation from genome-wide perturbation studies like those designed with RNAi and CRISPR technologies.


Three statistical tools designed to estimate titer levels from neutralization assays, compute Student’s T-tests from summarized data or compute contingency table analyses for 2 x 2 tables.


Simmune is designed to easily define the interactions between individual molecules in a large network or the behaviors of cells in response to external signals. It consists of three components: Modeler, Cell Designer and Simulator.


Flow Cytometry



The Simplified Presentation of Incredibly Complex Evaluations (SPICE) program is a data mining application that analyzes large FLOWJO data sets from polychromatic flow cytometry and organizes the normalized data graphically.


Pathway Analysis



Simmune is designed to easily define the interactions between individual molecules in a large network or the behaviors of cells in response to external signals. It consists of three components: Modeler, Cell Designer and Simulator.


The Networks on Circular Chromosome (NetCirChro) plugin enables users of the network visualization platform Cytoscape to overlay networks onto a circular chromosomal map. Data selection is synchronized between Cytoscape and NetCirChro.


Sequence Analysis



Simplified Analysis of Gene Expression (SAGE) is browser-based program for rapidly analyzing and archiving qPCR data. It parses raw, ungrouped data exported from real-time qPCR instruments and analyzes relative gene expression values.


The Desktop cDNA Annotation System (dCAS) allows one to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results.


Proteomics Analysis



This site explores the heterogeniety of human immune cells through figures and a data browser.