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http://www.jcvi.org/charprotdb/index.cgi/home

The Characterized Protein Database, CharProtDB, is designed and being developed as a resource of expertly curated, experimentally characterized proteins described in published literature. For each protein record in CharProtDB, storage of several data types is supported. It includes functional annotation (several instances of protein names and gene symbols) taxonomic classification, literature links, specific Gene Ontology (GO) terms and GO evidence codes, EC (Enzyme Commisssion) and TC (Transport Classification) numbers and protein sequence. Additionally, each protein record is associated with cross links to all public accessions in major protein databases as ��synonymous accessions��. Each of the above data types can be linked to as many literature references as possible. Every CharProtDB entry requires minimum data types to be furnished. They are protein name, GO terms and supporting reference(s) associated to GO evidence codes. Annotating using the GO system is of importance for several reasons; the GO system captures defined concepts (the GO terms) with unique ids, which can be attached to specific genes and the three controlled vocabularies of the GO allow for the capture of much more annotation information than is traditionally captured in protein common names, including, for example, not just the function of the protein, but its location as well. GO evidence codes implemented in CharProtDB directly correlate with the GO consortium definitions of experimental codes. CharProtDB tools link characterization data from multiple input streams through synonymous accessions or direct sequence identity. CharProtDB can represent multiple characterizations of the same protein, with proper attribution and links to database sources. Users can use a variety of search terms including protein name, gene symbol, EC number, organism name, accessions or any text to search the database. Following the search, a display page lists all the proteins that match the search term. Click on the protein name to view more detailed annotated information for each protein. Additionally, each protein record can be annotated.

Proper citation: CharProtDB: Characterized Protein Database (RRID:SCR_005872) Copy   

•   Source: SciCrunch Registry

http://cryptodb.org/cryptodb/

An integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining. Organisms included in CryptoDB are Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and environmental isolate sequences from numerous species. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-funded Bioinformatics Resource Center. Tools include: * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Cryptosporidium Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * CryptoCyc: Explore Automatically Defined Metabolic Pathways * Searches via Web Services: Web service access to our data

Proper citation: ApiDB CryptoDB (RRID:SCR_013455) Copy   

•   Source: SciCrunch Registry

http://immport.org/immport-open/public/reference/cytokineRegistry

A registry of cytokines, chemokines, and receptors generated for the purpose of collecting, integrating, and mapping between entity names and synonyms from several resources. These resources include MeSH, the Protein Ontology, EntrezGene, HGNC, MGI, UniProt and others.

Proper citation: Cytokine Registry (RRID:SCR_014368) Copy   

•   Source: SciCrunch Registry

http://imed.med.ucm.es/epimhc/

Database of naturally processed MHC-restricted peptide ligands and epitopes for customized computational vaccinology.

Proper citation: EPIMHC (RRID:SCR_016279) Copy   

•   Source: SciCrunch Registry

https://dbaasp.org

Collection of manually curated data regarding structure and antimicrobial activity of natural and synthetic peptides. Provides the information and analytical resources to develop antimicrobial compounds with the high therapeutic index.

Proper citation: Database of Antimicrobial Activity and Structure of Peptides (RRID:SCR_016600) Copy   

•   Source: SciCrunch Registry

https://www.immgen.org/

Project combines immunology and computational biology laboratories in effort to establish complete road map of gene-expression and regulatory networks in all immune cells. Project will generate, with rigorously standardized conditions, complete compendium of genome-wide data sets showing expression of protein-coding genes for all defined cell populations of mouse immune system.

Proper citation: ImmGen (RRID:SCR_021792) Copy   

•   Source: SciCrunch Registry

http://www.niaid.nih.gov/about/organization/dait/pages/csgadp.aspx

Collaborative network of investigators with a focus on prevention of autoimmune disease, defined as halting the development of autoimmune disease prior to clinical onset by means other than global immunosuppression, and an emphasis on Type 1 diabetes. Its mission is to engage in scientific discovery that significantly advances knowledge for the prevention and regulation of autoimmune disease. The specific goals enunciated in pursuit of this mission are: * To create improved models of disease pathogenesis and therapy to better understand immune mechanisms that will provide opportunities for prevention strategies * To use these models as validation platforms with which to test new tools applicable to human studies * To encourage core expertise and collaborative projects designed for rapid translation from animal to human studies, emphasizing the development of surrogate markers for disease progression and/or regulation which can be utilized in the context of clinical trials

Proper citation: Cooperative Study Group for Autoimmune Disease Prevention (RRID:SCR_006803) Copy   

•   Source: SciCrunch Registry

http://www.cbil.upenn.edu/apidots/

Note: ApiDots is currently unavailable. For data on apicomplexan EST assemblies, please see EuPathDB ApiDots is a database integrating mRNA/EST sequences from numerous Apicomplexan parasites. ESTs and mRNAs were clustered and further assembled to generate consensus sequences. These consensus sequences were then subjected to database searches against protein sequences and protein domain sequences. The underlying relational structure of this database allows researchers to analyze these data and pose biologically interesting questions.

Proper citation: ApiDots (RRID:SCR_001778) Copy   

•   Source: SciCrunch Registry

http://www.hiv.lanl.gov/content/immunology/index

An annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites, plus related tools and information. The goal of this database is to provide a comprehensive listing of defined HIV epitopes. These data are also printed in the HIV Molecular Immunology compendium, which is updated yearly and provided free of charge to scientific researchers, both by online download and as a printed copy. The data included in this database are extracted from the HIV immunology literature. HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three sections, CTL (CD8+), T helper (CD4+), and antibody. Within these sections, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein sub-section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each section. The annotation includes information such as cross-reactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, tables and maps of all defined linear epitopes relative to the HXB2 reference proteins are provided. Alignments of CTL, helper T-cell, and antibody epitopes are available through the search interfaces. Only responses to HIV-1 and HIV-2 are included in the database.

Proper citation: HIV Molecular Immunology Database (RRID:SCR_002893) Copy   

•   Source: SciCrunch Registry

http://www.hiv.lanl.gov/content/vaccine/home.html

An overview of HIV and SIV vaccine trials and their outcomes. It was developed as a tool for compilation, search and comparison of published studies on SIV, HIV and SHIV vaccine trials in nonhuman primates. We used a set of criteria to scan Pubmed for relevant studies to enter into the database. In selecting studies for entry, priority was given to recently published studies in journals generally regarded as the primary source of information pertaining to HIV and SIV vaccine research in nonhuman primates. In most cases, we give priority to challenge studies, where the animals received a live virus to measure the "efficacy" of the immunogen(s) inoculated during the course of the investigation. 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 *Publication of the data and analyses on this site and in a yearly printed publication, the HIV sequence Compendium, which is available free of charge

Proper citation: Nonhuman Primate HIV/SIV Vaccine Trials Database (RRID:SCR_002274) 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

https://www.archrproject.com/

Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing.

Proper citation: ArchR (RRID:SCR_020982) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/salsa

Software tool for scaffold long read assemblies with Hi-C data.

Proper citation: SALSA (RRID:SCR_022013) Copy   

•   Source: SciCrunch Registry

https://github.com/JamieHeather/stitchr

Software Python tool for stitching coding T cell receptors nucleotide sequences from V,J,CDR3 information. Produces complete coding sequences representing fully spliced TCR cDNA given minimal V,J,CDR3 information.

Proper citation: Stitchr (RRID:SCR_022139) Copy   

•   Source: SciCrunch Registry

https://github.com/immunogenomics/harmony

Software R package to project cells into shared embedding in which cells group by cell type rather than dataset specific conditions. Harmony simultaneously accounts for multiple experimental and biological factors. Used for integration of single cell data.

Proper citation: Harmony (RRID:SCR_022206) Copy   

•   Source: SciCrunch Registry

https://github.com/wyp1125/MCScanx

Software toolkit for detection and evolutionary analysis of gene synteny and collinearity.

Proper citation: MCScanX (RRID:SCR_022067) Copy   

•   Source: SciCrunch Registry

https://masst.gnps2.org/microbemasst/

Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns.

Proper citation: microbeMASST (RRID:SCR_024713) Copy   

•   Source: SciCrunch Registry

http://www.sb.cs.cmu.edu/drem

The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations

Proper citation: Dynamic Regulatory Events Miner (RRID:SCR_003080) Copy   

•   Source: SciCrunch Registry