This is the FAIRMD Lipids — an API package for the community-driven catalogue FAIRMD Lipid Databank (formerly NMRlipids Databank) containing atomistic MD simulations of biologically relevant lipid membranes emerging from the NMRlipids Open Collaboration.
The code has been tested in Linux and MacOS environment with python 3.10 or newer. Recent Gromacs version should be available in the system. All dependecies are listed in pyproject.toml.
We recommend installing python libraries into an environment, for example, using conda:
conda create --name fairmd-lipids python==3.10 -c conda-forge
conda activate fairmd-lipidsInstall fairmd-lipids package from repo:
pip install git+https://github.com/NMRLipids/FAIRMD_lipids.gitor from pypi:
pip install fairmd-lipidsNote that the data is stored as a separated repository and should be loaded after
cloning. Default data storage is
BilayerData. You MUST specify
FMDL_DATA_PATH before start working. The easiest way to start is to use
fmdl_initialize_data script provided with the package:
fmdl_initialize_data stable
source databank_env.rcThen you can work with the standalone scripts as well as use fairmd-lipids package in
your python code.
The FAIRMD Lipids project documentation is available in here. More information and example applications are available from the FAIRMD Lipids manuscript.
The fairmd-lipids python module provides programmatic access to all simulation data in
the FAIRMD Lipids. It allows to request data to construct various datasets on the base
of experimental and simulation data from the database that allow one to learn various
models about lipid bilayer properties. It also allows to design and effectively run
automated analysis across all the simulations in the database.
A jupyter template notebook can be used to get started with the analyses utilizing the FAIRMD Lipids.
Connection of Universal molecule and atom naming
conventions
with simulation specific names delivered by mapping files can be used to perform
automatic analyses over large sets of simulations. The results for large analyses can be
stored using the same structure as used for README.yaml files as done, for example,
for water
permeation
and lipid
flip-flop
rates in the repository related to the FAIRMD Lipids
manuscript.
FAIRMD Lipids-webUI provides an easy access to the FAIRMD Lipids content. Simulations can be searched based on their molecular composition, force field, temperature, membrane properties, and quality; the search results are ranked based on the simulation quality as evaluated against experimental data when available. Web-UI provides basic graphical reports for the computed properties as well as graphical comparison between simulation and experimental data.
The Web-UI is being developed in the repository BilayerGUI_laravel.
The FAIRMD Upload-Portal enables researchers to easily contribute new simulation metadata to the BilayerData Repository. Users can upload simulation metadata, which is automatically validated and processed through workflows within the data repository.
The project is open for contributions!
Please consult CONTRIBUTION.md and Data Contribution for further information.
Do not hesitate contacting us via [email protected] if you have any questions or inquiries!