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http://sites.huji.ac.il/malaria/

Data set of metabolic pathways for the malaria parasite based on the present knowledge of parasite biochemistry and on pathways known to occur in other unicellular eukaryotes. This site extracted the pertinent information from the universal sites and presented them in an educative and informative format. The site also includes, cell-cell interactions (cytoadherence and rosetting), invasion of the erythrocyte by the parasite and transport functions. It also contains an artistic impression of the ultrastructural morphology of the interaerythrocytic cycle stages and some details about the morphology of mitochondria and the apicoplast. Most pathways are relevant to the erythrocytic phase of the parasite cycle. All maps were checked for the presence of enzyme-coding genes as they are officially annotated in the Plasmodium genome (http://plasmodb.org/). The site is constructed in a hierarchical pattern that permits logical deepening: * Grouped pathways of major chemical components or biological process ** Specific pathways or specific process *** Chemical structures of substrates and products or process **** Names of enzymes and their genes or components of process Each map is linked to other maps thus enabling to verify the origin of a substrate or the fate of a product. Clicking on the EC number that appears next to each enzyme, connects the site to BRENDA, SWISSPROT ExPASy ENZYME, PlasmoDB and to IUBMB reaction scheme. Clicking of the name of a metabolite, connects the site to KEGG thus providing its chemical structure and formula. Next to each enzyme there is a pie that depicts the stage-dependent transcription of the enzyme''s coding gene. The pie is constructed as a clock of the 48 hours of the parasite cycle, where red signifies over-transcription and green, under-transcription. Clicking on the pie links to the DeRisi/UCSF transcriptome database.

Proper citation: Malaria Parasite Metabolic Pathways (RRID:SCR_007072) Copy   

•   Source: SciCrunch Registry

http://www.datamonkey.org/

Web-based suite of phylogenetic analysis tools for use in evolutionary biology. Web application for comparative analysis of sequence alignments using statistical models. Used for analyzing evolutionary signatures in sequence data. Datamonkey 2.0 provides curated collection of methods for interrogating coding-sequence alignments for imprints of natural selection, packaged as a responsive (i.e. can be viewed on tablet and mobile devices), fully interactive, and API-enabled web application.

Proper citation: Datamonkey (RRID:SCR_010278) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/IMMDIS

Ontology generated as part of the Bioinformatics Integration Support Contract (BISC) that is based on the National Library of Medicine (NLM) Medical Subject Headings; National Cancer Institute Thesaurus; International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM); ICD-10; and other open source public databases. Specific information may be available about a class, including Preferred_Name, DEFINITION, Synonym, etc.

Proper citation: Immune Disorder Ontology (RRID:SCR_010344) Copy   

•   Source: SciCrunch Registry

http://www.immuneprofiling.org/

Consortium established to capitalize on recent advances in immune profiling methods in order to create a novel public resource that characterizes diverse states of the human immune system following infection; prior to and following vaccination against an infectious disease; or prior to and following treatment with an immune adjuvant that targets a known innate immune receptor(s). Through this program, well-characterized human cohorts are studied using a variety of modern analytic tools, including multiplex transcriptional, cytokine, and proteomic assays; multiparameter phenotyping of leukocyte subsets; assessment of leukocyte functional status; and multiple computational methods. Centralized research resources and a comprehensive, centralized database will be constructed for use by the greater scientific community. The information gained from the program will provide a comprehensive understanding of the human immune system and its regulation, and will reveal novel associations between components of the immune system and other biological systems, identify novel immune mediators and pathways, establish predictors of vaccine safety in different populations, and enable the rapid evaluation of different vaccine formulations and administration regimens in human populations.

Proper citation: Human Immunology Project Consortium (RRID:SCR_001491) Copy   

•   Source: SciCrunch Registry

https://david.ncifcrf.gov/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis.

Proper citation: DAVID (RRID:SCR_001881) Copy   

•   Source: SciCrunch Registry

http://mummer.sourceforge.net/

Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.

Proper citation: MUMmer (RRID:SCR_018171) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/NetMHCpan/

Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs).

Proper citation: NetMHCpan Server (RRID:SCR_018182) Copy   

•   Source: SciCrunch Registry

https://www.immport.org/home

Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology.

Proper citation: The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) Copy   

•   Source: SciCrunch Registry

https://bioweb.pasteur.fr/packages/pack@Tracer@v1.6

Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more.

Proper citation: Tracer (RRID:SCR_019121) Copy   

•   Source: SciCrunch Registry

https://github.com/datatagsuite

Software suite to enable discoverability of datasets. Enables submission of metadata on datasets to DataMed. Has core set of elements, which are generic and applicable to any type of dataset, and extended set that can accommodate more specialized data types. Platform independent model developed by NIH BD2K bioCADDIE project for DataMed Data Discovery Index prototype being developed. Also available as annotated serialization in schema.org, which in turn is widely used by major search engines like Google, Microsoft, Yahoo and Yandex.

Proper citation: DatA Tag Suite (RRID:SCR_019236) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/ap_seg_2013_nih/

A MATLAB GUI for segmenting and quantifying PET images with multi-focal and diffuse uptakes. It imports a PET image and allows the user to draw region of interests (ROIs) in 2D or 3D to roughly separate the object of interest from the background. The areas are then segmented using a PET image segmentation method based on Affinity Propagation clustering to cluster the image intensities into meaningful groups. For quantification, the Standardized Uptake Value measurements of the binary or the user defined ROI are SUVmax, SUVmean, and Volume (mm^3) and can be exported into an excel sheet.

Proper citation: NIH-CIDI Segmentation of PET Images based on Affinity Propagation Clustering (RRID:SCR_014151) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://cedar.metadatacenter.org/

Web application for creating, collecting, testing, and sharing metadata. It provides templates for metadata models or structures, and is capable of testing those models quickly using real data.

Proper citation: CEDAR Workbench (RRID:SCR_016270) Copy   

•   Source: SciCrunch Registry

http://web.cbio.uct.ac.za/~darren/rdp.html

Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes.

Proper citation: Recombination Detection Program (RRID:SCR_018537) Copy   

•   Source: SciCrunch Registry

https://software.broadinstitute.org/software/discovar/blog/

Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes.

Proper citation: Discovar assembler (RRID:SCR_016755) Copy   

•   Source: SciCrunch Registry

http://research.mssm.edu/integrative-network-biology/Software.html

Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles.

Proper citation: proMODMatcher (RRID:SCR_017219) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://niaid.github.io/spice/

Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically.

Proper citation: SPICE (RRID:SCR_016603) Copy   

•   Source: SciCrunch Registry

http://www.usidnet.org/

Research consortium to advance scientific research in the primary immune deficiency diseases (PIDD) and: * Assemble and maintain a registry of patients with primary immunodeficiency diseases to provide a minimum estimate of the prevalence of each disorder in the United States. Provide a comprehensive clinical picture of each disorder and act as a resource for clinical and laboratory research. * Establish a multifaceted mentoring program to introduce new investigators into the field and stimulate interest and research in primary immune deficiency diseases. * Establish an advisory/review committee to maintain a cell/DNA Repository of biologic material from well-characterized PIDD patients for the advancement of scientific research USIDNET operates a large database of patient information for your use. The purpose and scope of this project is to assemble and maintain a registry of residents with primary immunodeficiency diseases. The project was started with the Registry of U.S. Residents with Chronic Granulomatous Disease. Since then, the registry has been expanded and now collects data on all primary immunodeficiency disorders. The following are just a few of the diseases housed in the registry: Chronic Granulomatous Disease, Common Variable Immunodeficiency Disease, DiGeorge Anomaly, Hyper IgM Syndrome, Leukocyte Adhesion Defect, Severe Combined Immunodeficiency Disease, Wiskott-Aldrich Syndrome, X-Linked Agammaglobulinemia Physicians who would like to register their patients or access the registry are encouraged to contact Onika Davis or Lamar Hamilton, USIDNET team, at odavis (at) primaryimmune.org, or lhamilton (at) primaryimmune.org

Proper citation: USIDNET: US Immunodeficiency Network (RRID:SCR_004672) Copy   

•   Source: SciCrunch Registry

http://hiv-web.lanl.gov/

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.

Proper citation: HIV Sequence Database (RRID:SCR_002906) Copy   

•   Source: SciCrunch Registry