Notebooks

Spike Notebook documents

The files contained in this directory are intended to provide a simple access to the basic features of SPIKE.

They provide a simple User Interface, in the popular Jupyter Notebook format. Each Notebook provides a single set of functions, for instance

1D NMR

• Proc1DNMR.ipynb: The basic NoteBook to process your 1D NMR files, (Bruker only so far)
  • with interactive phasing, baseline correction, peak-picking, Integration
  • Composite display with spectral superimposition, zoom and extracts
  • advanced bucketing capabilities
• Proc1DNMR_2Dseries.ipynb: to be used for a set of 1D stored as a pseudo 2D
  For instance
  • a kinetics experiments
  • $T_1$ or $T_2$ relaxation experiments
  • block acquisition for large NS
  • can be used to pre-process a DOSY experiment, or to isolate heavy components of a DOSY

2D NMR

• Proc2DNMR.ipynb: to process 2D experiments and display
  • modulus and phased 2D
  • extract rows and columns
• ProcDOSY.ipynb: to process and display DOSY experiment using the PALMA algorithm

FTICR-MS

Processing and display of a 1D FTICR-MS dataset

• ProcessFTICR-MS.ipynb: to process FTICR-MS experiment
  • choose the apodisation, the zerofiling level
  • correct the baseline
  • peak-pick and do centroid -
  • superimpose theoretical spectrum
• ProcessFTICR-MS-PH.ipynb: same as above but for absorption processing
  • interactive phasing for optimal peak shapes

2D FTICR-MS

Processing and Display of a 2D FT-ICR-MS experiments

• Processing.py a non interactive program to realise the 2D processing of the dataset
  • able to process up to 500GB-1TB files
  • fully parallel - desktop (multiprocessing) and HPC (MPI)
  • tested up to 256 processors (MPI)
  • efficient denoising
  • processing of narrowband / NUS / 2XR acquition

You can display and explore the 2DFTICR map:

• zoom in and out,
• change the level of contour
• extract fragment and precursor spectra

There are two tools to display and explore the 2D experiment. they present the same tools, organized differently.

• EasyDisplayFTICR2D.ipynb: a graphic interface, hiding the python details.
• DisplayFTICR2D.ipynb: the same tools have their python interface presented

utilities

• ReadSMX.ipynb Allow to read 1D and 2D processed NMR datasets from Bruker/Topspin
• Logo.ipynb the code which generates the Spike logo

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This is still an early effort, and the number of recipes should grow rapidly - SPIKE Users are welcome to provide their own !

The Notebooks can be migrated anywhere, as long as spike is installed and available. A typical usage is to copy a version close the data to be analysed, and to keep it there, as a lab-book, holding the analysis, and eventually your comments on the data.

Remarks

1/ Note that the notebooks are kept both as *.ipynb (as reference) and as *.py (to follow the difference between commits.) Both version are identical, if they unfortunately do not correspond, the *.py should be considered as reference.

2/ to use this program, you should have installed the following packages:

• a complete scientific python environment ( tested with python 3.9 / anaconda with no support for python 2.7 )
• spike ( version 0.99.32 minimum )
• ipywidgets ( tested with version 7.6 )
• ipympl ( adds interactivity in the notebook )