v1.1.7

This update adds an ability to view past searches and predictions, plus other improvements.

• Viewing past searches and predictions
  • Searches and predictions are now saved as computation jobs, which are viewable in History tab
  • Computation jobs are saved up to 30 days
• Other improvements
  • Navigation
    • Pages can now be accessed directly via static URLs
  • User interface
    • An animated loading screen is now shown when loading content
  • Error fixes
    • Random forest model for gram stain has been replaced with the correct model

v1.1.6

This update features better compatibility with other apps for microbial analysis. Other improvements have been made to the database, predictive tools, and plots.

• Compatibility with other apps
  • Output from other apps can be inputted for analysis
  • Four apps supported in total
    • IMG/M (newly supported)
    • KEGG Automatic Annotation Server (KAAS) (better supported via error fixes)
    • QIIME2 (previously supported)
    • DADA2 (previously supported)
• Database
  • Added information on fermentation for n = 1,343 organisms
    • Data are from BacDive
• Features for predictive tools
  • Predict traits from taxonomy
    • Now capable of predicting probability of a trait (not just presence/absence)
  • Predict traits using machine learning
    • Now comes with 21 pre-trained models for predicting traits
• Plots
  • Plots now expand to fit window
• Other improvements
  • Improved file structure
    • R scripts now in hierarchical folders
  • Error fixes
    • Fixed errors in selecting organisms and unbalanced intermediates in Predict traits from networks

v1.1.5

This update features an expanded database and more features for predictive tools.

• Database
  • Number of organisms increased from n = 8,350 to 20,806
  • Number of genome sequences increased from n = 4,354 to 13,967
  • Names and strain information now comes from the List of Prokaryotic names with Standing in Nomenclature (LPSN)
  • Phenotypic information comes from an additional source
    • Anaerobe Laboratory Manual
  • Taxonomy now comes from 4 sources in total
    • LPSN
    • NCBI
    • GTDB
    • Bergey's Manual
  • Code for database construction is now included with app
• Features for predictive tools
  • Predict traits from taxonomy
    • Query taxa can now be selected from the database
    • Taxonomy from 4 aforementioned sources now supported
  • Predict traits with machine learning
    • Gene functions can now be selected from the database
• Other improvements
  • Faster start up time
    • Slowly-loading content (module UI and data) is now loaded on demand rather than at app start up
  • More intuitive user interface
    • Better layout of navigation tabs within predictive tools
    • Better use of dropdown elements for user input

v1.1.1

v1.1.1

v1.1.0

v1.1.0

This is the first major update since the original release. This update features more data, more ways to visualize results, and more predictive tools.

• Data
  • Traits (substrates and end products) have been added for 141 species of methanogens
• Plots
  • Plots now fully interactive
    • Built using Plotly
  • New types of plots
    • 3D network plot
    • Heatmap
• Predictive tools
  • New tool
    • Predict traits with machine learning
      • Built using randomForest package of R
  • Expanded tools
    • Predict traits from taxonomy
      • Range of traits has been extended
  • Predict traits with metabolic networks
    - Range of metabolism types has been extended
• Other improvements
  • User interface now built on bslib package of R
  • Search database tool uses an improved query builder from jqbr package of R
  • Predict traits from taxonomy tool has been refactored and processes queries faster
  • All functions are documented with roxygen comments

v1.0.3

v1.0.3

v1.0.2

v1.0.2

v1.0.1

v1.0.1

v1.0.0

v1.0.0