2023-02-07

This is Maëlle's DBGI daily open-notebook.

Today is 2023.02.07

meeting with pma

Start of Master thesis!

See open-notebook.pmallard.2023.02.07.md

Regulations: Must do a formal written thesis (~30-40 pages) and an oral presentation

TODO

• Read articles/look examples from open-notebook.pmallard.2023.02.07.md

  • https://microbeatlas.org/
  • https://www.nature.com/articles/s41592-021-01339-5
  • https://pubmed.ncbi.nlm.nih.gov/34662515/
  • https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-00445-4
  • https://pubs.acs.org/doi/full/10.1021/acs.jnatprod.8b00767
  • https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giac124/6980761

• Familiarize with tools

  • datawarrior
  • tmap
  • molplotly
  • vega grammar

CODE

NOTES

tmap

python

Visualization => Python package Faerun for large scale data sets - Faster than matplotlib/pyplot - interactive plots

molplotly

python

allows 2D images of molecules to be shown in plotly figures when hovering over the data points

vega

visualizations are described in JSON, and generate interactive views using either HTML5 Canvas or SVG

Lots of possible plots => geographic maps, tree diagrams & network diagrams might be interesting

datawarrior

Important features:

• Plots interacting with each other
• 'contains' ...
• Search by structure
• Check for similarity

Features needed for the vizualisation project

• Plots interacting with each other (datawarrior)
• 'contains' ... (datawarrior)
• Search by structure (datawarrior)
• Check for similarity (datawarrior)
• phylogeny by MASST (https://masst.gnps2.org/microbemasst/) (NP classifier)

TODO NEXT

• prepare presentation for DBGI meeting
• Search for best way to create dashboard
  • Java
  • Python
  • HTML
• Read articles/look examples from open-notebook.pmallard.2023.02.07.md
  • https://microbeatlas.org/
  • https://www.nature.com/articles/s41592-021-01339-5
  • https://pubmed.ncbi.nlm.nih.gov/34662515/
  • https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-00445-4
  • https://pubs.acs.org/doi/full/10.1021/acs.jnatprod.8b00767
  • https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giac124/6980761