Interactive tutorials

To help you get the most out of lipyphilic, we have created a set of interactive tutorials in the form of Jupyter Notebooks. There is no need to download or install anything, simply click the link below:

We currently have tutorials on the following topics:

  1. Basic usage: Illustrates basic usage of lipyphilic, including how to store results for later usage.
    Also shows how to assign lipids to leaflets, which is required for many other analyses.
  2. Flip-flop rate: Shows how to use lipyphilic to calculate the rate of cholesterol flip-flop, as well as
    identify the frames at which each flip-flop event begins and ends.
  3. Local lipid environments: Illustrates how to determine the local lipid environment of each lipid
    over time, as well as the enrichment/depletion index.
  4. Lipid domains: Shows how to calculate the largest cluster of specific lipids over time. Examples
    include finding the largest ganglioside cluster in a neuronal plasma membrane and identifying
    the largest domain of Lo lipids in a phase separated membrane.
  5. Interleaflet registration: This notebook shows how to calculate the interleaflet registration over
    time. The example shows how to calculate the registration of Lo lipids across leaflets.
  6. Lateral diffusion: Illustrates how to perform “nojump” trajectory unwrapping with LiPyphilic,
    then use the unwrapped coordinates to calculate the mean-squared displacement and lateral
    diffusion coefficient of lipids in a membrane.
  7. Coarse-grained lipid order parameter: Shows how to calculate the coarse-grained order
    parameter, and how to create a two-dimensional projection of these values onto the membrane
  8. Projection plots: Shows how to create two-dimensional projections of arbitrary lipid properties
    onto the membrane plane. Examples include projecting local membrane thicknesses calculated
    using FATSLiM onto the membrane plane, and projecting the ordered state (Lo and Ld) of lipids
    onto the membrane plane.
  9. Potential of mean force (PMF): This notebook illustrates how to use lipyphilic to calculate the
    height and orientation of sterols in a membrane, and subsequently plot the two-dimensional
    PMF of sterol height and orientation.
  10. Hidden Markov Models (HMM): Learn how to use the output of lipyphilic to construct HMMs
    with HMMLearn. We will create a HMM based on lipid thicknesses to detect Lo and Ld lipids in a
    phase separated membrane. The output from this is can be used as input to other
    analyses in lipyphilic, such as calculating interleaflet registration or local lipid environments.