gcmstools

Getting started

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Getting started

gcmstools is a Python package that reads some GCMS file formats and does simple fitting and calibration. The source code for this project can be found on GitHub. If you are reading this in PDF format, there is online documentation as well.

This user guide is broken into a few sections.

  1. Installation: Information about getting a Python installation up and running and installing gcmstools.
  2. Basic Setup: Go here first to learn about the basic setup and to get some sample data. This is necessary to follow this documentation.
  3. File Types: This covers the supported file types, their properties, and some simple plotting.
  4. Referenceing and Fitting: Incorporate reference data into your GCMS dataset and use this to fit the data.
  5. Data Storage: Create a storage container for your processed GCMS datasets. These containers are necessary for the next step in the process.
  6. Calibration: Generate calibration curves and use this information to extract concentration information from you sample datasets.
  7. Isotopic Analysis: Calculate the isotopic distribution of a sample using a series of reference mass spectra.
  8. Batch Processing: A simple function for automating this entire process is presented. You can skip to this section if all you want to do is automate some data extractions. It is not necessary to understand the basics of data manipulation, calibration, etc.
  9. Appendix A: Command line basics. The examples presented in this document require a basic working knowledge of using a command-line terminal interface and of running Python commands from an IPython interpreter. This section covers some of the basics.
  10. Appendix B: Examples. Basic data extraction and plotting examples are presented. Check out this section if you want some ideas about processing, plotting, or extracting data.

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