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http://www.immunexpresso.org

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   

•   Source: SciCrunch Registry

https://dice-database.org

Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis.

Proper citation: Database of Immune Cell Epigenomes (RRID:SCR_018259) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/timezone1/

Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes.

Proper citation: TimeZone (RRID:SCR_018564) Copy   

•   Source: SciCrunch Registry

https://www.epimodel.org/

Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics.

Proper citation: EpiModel (RRID:SCR_018539) Copy   

•   Source: SciCrunch Registry

http://tools.dice-database.org/GOnet/)

Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.

Proper citation: GOnet (RRID:SCR_018977) Copy   

•   Source: SciCrunch Registry

http://pathema.jcvi.org/Pathema/index.html

Pathema is one of the eight Bioinformatics Resource Centers designed to serve as a core resource for the bio-defense and infectious disease research community. Pathema strives to support basic research and accelerate scientific progress for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens: Category A priority pathogens; Bacillus anthracis and Clostridium botulinum, and Category B priority pathogens; Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens and Entamoeba histolytica. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying databases developed to target the specific data and analysis needs of each scientific community. All publicly available complete genome projects of phylogenetically related organisms are also represented, providing a comprehensive collection of organisms for comparative analyses. Pathema facilitates the scientific exploration of genomic and related data through its integration with web-based analysis tools, customized to obtain, display, and compute results relevant to ongoing pathogen research. Pathema serves the bio-defense and infectious disease research community by disseminating data resulting from pathogen genome sequencing projects and providing access to the results of inter-genomic comparisons for these organisms. The Pathema BRC contract ends in December 2009. At that time JCVI will cease maintenance of the Pathema web resource and data. The PATRIC team, located at the Virginia Bioinformatics Institute, created and maintains a consolidated BRC for all of the NIAID category A-C priority pathogenic bacteria. The EuPathDB team at the University of Pennsylvania will support all eukaryotic pathogens. Pathema transferred all data and software to PATRIC and EuPathDB for incorporation into their new Web-based bioinformatics resource.

Proper citation: Pathema (RRID:SCR_010585) Copy   

•   Source: SciCrunch Registry

https://www.niaid.nih.gov/diseases-conditions/coronaviruses

Information about coronaviruses, including COVID-19. NIAID provides research funding and resources for scientific community to facilitate development of vaccines, therapeutics, and diagnostics for infectious diseases, including those caused by coronaviruses.

Proper citation: NIAID Overview of Coronaviruses (RRID:SCR_018290) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/gernerlab/cytomap/-/wikis/home

Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information.

Proper citation: CytoMAP (RRID:SCR_021227) Copy   

•   Source: SciCrunch Registry

https://github.com/zdk123/SpiecEasi

Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse.

Proper citation: SpiecEasi (RRID:SCR_022712) 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://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   

•   Source: SciCrunch Registry

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   

•   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://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   

•   Source: SciCrunch Registry

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   

•   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

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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.genome.wisc.edu/

The E. coli Genome Project has the goal of completely sequencing the E. coli and human genomes. They began isolation of an overlapping lambda clonebank of E. coli K-12 strain MG1655. Those clones served as the starting material in our initial efforts to sequence the whole genome. Improvements in sequencing technology have since reached the point where whole-genome sequencing of microbial genomes is routine, and the human genome has in fact been completed. They initiated additional sequencing efforts, concentrating on pathogenic members of the family Enterobacteriaceae -- to which E. coli belongs. They also began a systematic functional characterization of E. coli K-12 genes and their regulation, using the whole genome sequence to address how the over 4000 genes of this organism act together to enable its survival in a wide range of environments.

Proper citation: E. coli Genome project (RRID:SCR_008139) Copy   

•   Source: SciCrunch Registry