Implementations

ResistoXplorer is developed based on three open source programming languages - Java, R and JavaScript. In particular, the web framework was developed based on the Java Server Faces technology using the PrimeFaces (version: 6.1) and BootsFaces (version: 1.2.0) component library. The interactive networks and other 3D visualization is implemented based on the sigma.js (version: 1.2.0) , CanvasXpress.js (version: 7.8) and D3.js (version: 3.5.17) JavaScript libraries. The backend statistical computation is implemented using the R (version: 3.6.3) scripts, and the packages from the Bioconductor project. Here is the list of R packages that been mainly used for analysis and visualization purposes:

  • reshape (0.8.8), dplyr (0.8.5) & tidyr (1.0.2): for data manipulation and processing;
  • ggplot2 (3.3.0) & gplots (3.0.3): data visualization;
  • igraph (1.2.5): for network creation and layout;
  • pheatmap (1.0.12): for heatmap visualization;
  • viridis (0.5.1) & RColorBrewer (1.1-2): color palettes for generating nice graphics;
  • Cairo (1.5-11):create a new Cairo-based graphics device;
  • RJSONIO (1.3-1.4) & jsonlite (1.6.1): to convert the result data to JSON object for visualization;
  • phyloseq (1.30.0): storing data as S4 class object and general data manipulation;
  • compositions (1.40-4): for log-ratio transformations;
  • vegan (2.5-6): for rarefaction curve, diversity and procrustes analysis;
  • metagenomeSeq (1.28.2),edgeR (3.28.1),DESeq2 (1.26.0) & ALDEx2 (1.18.0): differential abundance testing of metagenomic data;
  • randomForest (4.6-14): for random Forest classification;
  • mixOmics (6.10.8): for vertical data integrative analysis (sPLS & rCCA);
  • made4 (1.64.0): for co-inertia analysis;
  • minerva (1.5.8): for Maximal Information Coeffecient (MIC) correlation analysis;
  • And several other open source R scripts from their respective GitHub repositories.

The R code repository for the ResistoXplorer web server to perform downstream analysis is accessible from: https://github.com/FCPLab007/ResistoXplorerR

ResistoXplorer is hosted on a remote dedicated server running Ubuntu OS 18.04 LTS with 8GB RAM and 4 CPU cores (3.1 GHz each). The application server is Glassfish 5.0. Please note, the client-side data visualization requires a modern browser that supports HTML5 canvas and JavaScript. ResistoXplorer has been tested under Google Chrome (5.0+), Firefox (3.0+), and Internet Explorer (9.0+).

Database statistics

Detailed statistics on data collection and organization of information across databases (present in ARG Table module for functional annotation mapping):

Database Version Date No. of Features Annotation Header No. of functional levels Functional levels Note Link
ResFinder 4.1 2021-01-20 3128 ARG name_Accession 3 Class, Mechanism & Gene - Link
CARD 2.0 (2020) 2019-11-27 2624 ARG accession 3 Mechanism, Family & Gene only ARGs present in “nucleotide fasta protein homolog” model Link
ARDB 1.1 2009-07-03 377 ARG type 2 Class & Mechanism - Link
ARG-ANNOT 4.0 2018-05 2025 ARG name 1 Class - Link
MegaRes (Full) 2.0 2019-10-14 7868 MegaRes ID (Accession) 4 Type, Class, Mechanism & Group drugs, biocide and metal resistance genes Link
MegaRes (Drugs) 2.0 2019-10-14 7126 MegaRes ID (Accession) 3 Class, Mechanism & Group only drugs related resistance genes Link
MegaRes 1.0.1 2016-12-01 3824 MegaRes ID (Accession) 3 Class, Mechanism & Group - Link
AMRFinder 1.0 2019-11-04 4156 ARG name 2 Class & Mechanism - Link
SARG 2.0 2019-12-07 12085 ARG name 2 Type & SubType - Link
DeepARG-DB 1.0 2020-02-07 4511 ARG name 2 Subtypes & Types - Link
ARGminer 1.1.1 2019-04-24 14872 Accession 3 Class, Mechanism & ARG_NAME only contain known ARGs Link
BacMet 2.0 2018-03-11 607 Biocide & Metal resistance gene name 2 Mechanism & Class only experimentally confirmed genes Link
Antimicrobial peptide (AMP) dataset - - 131 AMP gene name 1 Mechanism - Link

Acknowledgements

The work is financed by the INDNOR and INTPART programs funded by The Research Council of Norway, grant numbers 273833 and 274867, and the Olav Thon foundation, and supported by the University of Oslo.

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