Micromix user guide

Contents

• Micromix
• Installing and running
  • Micromix
  • Plugins
• Using Micromix
  • Selecting organism
  • Selecting datasets
  • Uploading datasets
  • Combining datasets
  • Filtering data
  • Visualising data
• Modifying Micromix
  • Preparing a new bacteria
  • How to add a new organism
  • How to add new expression data
  • Modifying or adding gene or pathway annotations
  • Adding new visualisation plugins
  • Database maintenance

Micromix

Background

Micromix is designed as a visualization platform to easily view next-generation sequencing data, such as RNA-seq counts. It primarily focuses on prokaryotic data, such as bacteria, which comes pre-bundled, which comes pre-bundled with Salmonella and Bacteroides. Users can include different bacteria, where associated data can be filtered and/or transformed, then visualized through plugins like heatmaps to examine biological patterns.

Infrastructure

The site comprises a backend (Flask) and a frontend (Vue.js) that communicate with each other, saving data from each session using MongoDB. Plugins within the site are typically set up on separate servers, displaying a visualisation within the site.

Each user session is stored with a unique ID, allowing session information to be re-loaded by passing the unique ID into the URL. For example: https://micromix.helmholtz-hiri.de/bacteroides/?config=667e67422e5a30d66f793d96. These links can be shared with collaborators to examine specific data patterns from data within the site, or unique user data they have manually uploaded.