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 L_o 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 L_o 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

   plane.
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 (L_o and L_d) 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 L_o and L_d 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.