fairmd-lipids 1.3.3a0

FAIRMD Lipids project (formerly NMRlipids) contains the core functionality for managing and accessing the Database.

FAIRMD Lipids

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.

Installation

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-lipids

Install fairmd-lipids package from repo:

pip install git+https://github.com/NMRLipids/FAIRMD_lipids.git

or from pypi:

pip install fairmd-lipids

Note 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.rc

Then you can work with the standalone scripts as well as use fairmd-lipids package in your python code.

Documentation

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.

How to use

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.

Web UI

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.

Upload Portal

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.

Contribution

The project is open for contributions!

Please consult CONTRIBUTION.md and Data Contribution for further information.

Do not hesitate contacting us via [e-mail] if you have any questions or inquiries!