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:
- 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.
- Flip-flop rate: Shows how to use lipyphilic to calculate the rate of cholesterol flip-flop, as well asidentify the frames at which each flip-flop event begins and ends.
- Local lipid environments: Illustrates how to determine the local lipid environment of each lipidover time, as well as the enrichment/depletion index.
- Lipid domains: Shows how to calculate the largest cluster of specific lipids over time. Examplesinclude finding the largest ganglioside cluster in a neuronal plasma membrane and identifyingthe largest domain of Lo lipids in a phase separated membrane.
- Interleaflet registration: This notebook shows how to calculate the interleaflet registration overtime. The example shows how to calculate the registration of Lo lipids across leaflets.
- Lateral diffusion: Illustrates how to perform “nojump” trajectory unwrapping with LiPyphilic,then use the unwrapped coordinates to calculate the mean-squared displacement and lateraldiffusion coefficient of lipids in a membrane.
- Coarse-grained lipid order parameter: Shows how to calculate the coarse-grained orderparameter, and how to create a two-dimensional projection of these values onto the membraneplane.
- Projection plots: Shows how to create two-dimensional projections of arbitrary lipid propertiesonto the membrane plane. Examples include projecting local membrane thicknesses calculatedusing FATSLiM onto the membrane plane, and projecting the ordered state (Lo and Ld) of lipidsonto the membrane plane.
- Potential of mean force (PMF): This notebook illustrates how to use lipyphilic to calculate theheight and orientation of sterols in a membrane, and subsequently plot the two-dimensionalPMF of sterol height and orientation.
- Hidden Markov Models (HMM): Learn how to use the output of lipyphilic to construct HMMswith HMMLearn. We will create a HMM based on lipid thicknesses to detect Lo and Ld lipids in aphase separated membrane. The output from this is can be used as input to otheranalyses in lipyphilic, such as calculating interleaflet registration or local lipid environments.