diff --git a/mdakits/domhmm/metadata.yaml b/mdakits/domhmm/metadata.yaml new file mode 100644 index 00000000..9d461168 --- /dev/null +++ b/mdakits/domhmm/metadata.yaml @@ -0,0 +1,98 @@ +# DomHMM - Detect, Analyze, Understand +# -------------------- +# TL;DR: DomHMM provides an automated workflow to identify liquid-ordered (Lo) domains from Molecular Dynamics simulations of bio-membranes. :-) +# +# Nano- and microdomains in lipid membranes are of great interest for understanding biological processes such as small molecule binding and signal transduction. +# Molecular Dynamics (MD) present a powerful tool for studying membranes with various lipid compositions at different levels of resolution. +# However, detecting these domains can be challenging, as most workflows are described in papers without available or maintained implementations. +# The MDAKit "DomHMM" faciliates the analysis of domains in your simulation trajectories by providing an automated workflow for the detection of lateral heterogeneities (i.e., liquid-ordered domains). +# It is a versatile tool to handle different use case scenarios, such as simulations of asymmetric membranes or membranes including small proteins. It utilizes therefore unsupervised machine learning algorithms, +# including Gaussian Mixture Models and Gaussian-based Hidden Markov Models, to detect ordered lipids based on their structural properties. Identified lipids are then clustered into domains using spatial autocorrelation analysis. +# More details about the method can be found here: https://doi.org/10.1016/bs.mie.2024.03.006. +# +#------------------------------------------------------------ +# Required entries +#------------------------------------------------------------ +## Name of the repository +project_name: domhmm + +## List of DomHMM's authors +authors: + - https://github.com/BioMemPhys-FAU/domhmm/blob/main/AUTHORS.md + +## List of DomHMM's maintainers +maintainers: + - m-a-r-i-u-s + - yusuferentunc + - biomemphys + +## What is DomHMM +description: > + TL;DR: DomHMM provides an automated workflow to identify liquid-ordered (Lo) domains from Molecular Dynamics simulations of bio-membranes. :-) + Nano- and microdomains in lipid membranes are of great interest for understanding biological processes such as small molecule binding and signal transduction. + Molecular Dynamics (MD) present a powerful tool for studying membranes with various lipid compositions at different levels of resolution. + However, detecting these domains can be challenging, as most workflows are described in papers without available or maintained implementations. + The MDAKit DomHMM faciliates the analysis of domains in your simulation trajectories by providing an automated workflow for the detection of lateral heterogeneities (i.e., liquid-ordered domains). + It is a versatile tool to handle different use case scenarios, such as simulations of asymmetric membranes or membranes including small proteins. It utilizes therefore unsupervised machine learning algorithms, + including Gaussian Mixture Models and Gaussian-based Hidden Markov Models, to detect ordered lipids based on their structural properties. Identified lipids are then clustered into domains using spatial autocorrelation analysis. + +## Keywords that relate to DomHMM +keywords: + - membranes + - molecular dynamics + - nanodomains + - microdomains + - machine learning + +license: GPL-2.0-or-later + +## You can find DomHMM on our GitHub repository: +project_home: https://github.com/BioMemPhys-FAU/domhmm + +## You can find the documentation of DomHMM here: +documentation_home: https://domhmm.readthedocs.io + +documentation_type: UserGuide + API + +src_install: + - pip install git+https://github.com/BioMemPhys-FAU/domhmm@main + +import_name: domhmm + +python_requires: ">=3.9" + +mdanalysis_requires: ">=2.0.0" + +## The repositiory of DomHMM includes some unit tests to ensure that the package runs as intended. Please note that we are using pytest to run the tests. +run_tests: + - pytest --pyargs domhmm + +test_dependencies: + - mamba install pytest + +## Computational Biology - Department Biologie - Friedrich-Alexander-Universität Erlangen-Nürnberg +project_org: BioMemPhys-FAU + +#------------------------------------------------------------ +# Optional entries +#------------------------------------------------------------ +## List(str): a list of commands to use when installing the latest +## release of the code. Note: only one installation method can currently +## be defined. We suggest using mamba where possible (e.g. +## mamba -c conda-forge install MYPROJECT +## for a conda package installation). +## Here we use a simple PyPi installation: +# More to come! +# install: +# - git clone latest +# - pip install . + +development_status: Production/Stable + +publications: + - https://doi.org/10.1016/bs.mie.2024.03.006 + +# We welcome your feedback on the code or any other aspects of the project. :-) +community_home: https://github.com/BioMemPhys-FAU/domhmm/discussions/ + +changelog: https://github.com/BioMemPhys-FAU/domhmm/blob/main/CHANGELOG.md