New seminar series / graduate course

Over the last year we had the opportunity to participate in 4 doctoral school classes and it appears that some features of that can be used to solve research projects are not well known. For this reason we will organize some short (max 30 min) seminars by Zoom ( on regular base. They will take place Monday at 5PM (Swiss time) by Zoom.


If you want to obtain credits for the course we ask you to make significant improvements to the documentation (i.e., to go beyond fixing a few typos). Please register in the poll and let us know in case you have issues with updating/writing documentation. See the blog post about documentation for more details.

See the recording for the Q&A session.


18.1.2021: General introduction to


The first seminar will focus on the “big picture”

  • Philosophy
  • Store / retrieve original data
  • Extract knowledge
  • Publish information to Zenodo

1.2.2021: Add a new sample


  • Biological sample, material sample.
  • Chemical structure, stereochemistry, mixture of isomers.
  • Natural or modified peptidic and nucleic sequences.
  • Keywords and meta information.

15.2.2021: Managing chemical libraries of synthesized products


  • Find synthesized chemicals from former colleagues.
  • How to create labels for new products (with chemical structure)?
  • Define a location and status.
  • Update the stock.


1.3.2021: Monoisotopic mass


  • Determine possible molecular formula from monoisotopic mass
  • Problem of ionization.
  • Difference of mass and corresponding molecular formula.
  • Pubchem lookup.

15.3.2021: Mass spectrometry of polymers


  • Polymer, copolymer, ⍺ and ⍵ end groups.
  • Kendrick chart.
  • Advanced reporting.

29.3.2021: Electronic laboratory notebook


  • Calculation of quantities.
  • Definition of shortcuts.

12.4.2021: Mass spectrometry of natural or non-natural peptides


  • How to enter a sequence?
  • Fragmentation and internal fragmentation.
  • Create a report for publication.

26.4.2021: Image analysis

  • Bit depth, mask, ROI, resolution
  • Hull, MBR, Ferret min, Ferret max, Compactness

10.5.2021: XRD and PXRD (Kevin Jablonka)

  • Find topology of a periodic net
  • Predict PXRD patterns / change cell parameters
  • Match to pattern in database using Deep Learning
  • Look up PXRD patterns form database

25.5.2021: Multiple spectra analysis

  • Superimpose hundreds of spectra in one click
  • Integration, relative spectra
  • Export data for kinetic analysis

14.6.2021: Machine learning on spectra and data exportation

  • Preprocessing and normalization of spectra
  • Principal component Analysis (PCA)
  • Uniform Manifold Approximation and Projection (UMAP)
  • Create reports
  • Export to Zenodo
  • Download files as a ZIP