2014
This notebook uses a subset of the available processing features in NMRLab (+Metabolab) to process 1D NMR spectra. The output is saved as a CSV file that can be imported into pandas, PLS_Toolbox or any other package for subsequent analysis.
To use this workbook you will need an installation of …
This notebook contains snippets of code that are useful when working with MATLAB in IPython Notebooks.
Displaying images from MATLAB
Passing variables into cells using the %%matlab magic requires h5py which is tricky to install. If you only need to pass in simple variables (strings) you can instead pass it …
This short demo shows analysis of a publically available GEO dataset using Pathomx, with a workflow build using the new visual editor (available in the next release).
You can download the example dataset from here.
Pathomx is an open-source workflow-based scientific analysis application. Source code is available here with packaged …
2013
Short demo of an experimental analysis of metabolomic (NMR) data using Pathomx. Metabolomic test dataset produced from THP-1 cells grown under normal and hypoxic conditions. Spectra (2D 1H JRES) have been pre-processed and quantified using the BML-NMR service.
The video shows an example analysis from processed data through to metabolic …
A Python implementation of the Icoshift algorithm, a versatile tool for the rapid alignment of 1D NMR spectra
Icoshift is a Matlab-based algorithm for the alignment of NMR spectra developed by Francesco Savorani and Giorgio Tomasi. It performs correlation shifting of spectral intervals using an FFT engine that aligns …
On MacOS X 10.5 there is considerable slow-down in the MATLAB editor and other GUI elements. The issue is related to a change in the default Mac Java 2D rendering engine from Quartz2D (10.4) and Sun2D (10.5). This newer rendering engine improves performance for figure drawing, but …
Established 1980