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examplenotebooks

Notebooks demonstrating how to do simple tasks related to free energy calculations.

https://github.com/openfreeenergy/examplenotebooks

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Notebooks demonstrating how to do simple tasks related to free energy calculations.

Basic Info
  • Host: GitHub
  • Owner: OpenFreeEnergy
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 34.3 MB
Statistics
  • Stars: 48
  • Watchers: 2
  • Forks: 8
  • Open Issues: 43
  • Releases: 0
Created over 4 years ago · Last pushed 10 months ago
Metadata Files
Readme License Citation

README.md

Logo full_tests pre-commit.ci status Open In Colab

OpenFE Notebooks

Collection of notebooks for the Open FreeEnergy project. These can be ran in the browser via the Binder links.

| Binder link | Description | | --- | --- | | Open In Colab | Start here. This notebook demonstrates how a free energy calculation can be defined, executed and analyzed using the openfe package. |

Running these notebooks locally

To run these notebooks locally you will need to install the openfe package, this is best done using the instuctions here

Then you can download a copy of the notebooks:

  • wget -O OpenFEExampleNotebooks.tar.gz https://github.com/OpenFreeEnergy/ExampleNotebooks/tarball/main
  • or (depending on your platform)
  • curl -L -k -o OpenFEEXampleNotebooks.tar.gz https://github.com/OpenFreeEnergy/ExampleNotebooks/tarball/main

Unpack, then navigate to the downloaded notebooks:

  • tar -xz OpenFEExampleNotebooks.tar.gz
  • cd OpenFreeEnergy-ExampleNotebooks-b79be48

Then launch the notebook application as:

  • jupyter notebook

This should present a choice of notebooks to follow.

Owner

  • Name: Open Free Energy
  • Login: OpenFreeEnergy
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Gowers"
  given-names: "Richard J."
  orcid: "https://orcid.org/0000-0002-3241-1846"
- family-names: "Alibay"
  given-names: "Irfan"
  orcid: "https://orcid.org/0000-0001-5787-9130"
- family-names: "Swenson"
  given-names: "David W.H."
- family-names: "Henry"
  given-names: "Michael M."
  orcid: "https://orcid.org/0000-0002-3870-9993"
title: "The Open Free Energy Example Notebooks"
version: 0.1
date-released: 2022-03-28
url: "https://openfree.energy/"
license: MIT License
repository-code: "https://github.com/OpenFreeEnergy/ExampleNotebooks"

GitHub Events

Total
  • Create event: 24
  • Release event: 1
  • Issues event: 40
  • Watch event: 14
  • Delete event: 20
  • Issue comment event: 109
  • Push event: 76
  • Pull request review comment event: 70
  • Pull request event: 42
  • Pull request review event: 71
  • Fork event: 2
Last Year
  • Create event: 24
  • Release event: 1
  • Issues event: 40
  • Watch event: 14
  • Delete event: 20
  • Issue comment event: 109
  • Push event: 76
  • Pull request review comment event: 70
  • Pull request event: 42
  • Pull request review event: 71
  • Fork event: 2

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 95
  • Total pull requests: 130
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 17
  • Total pull request authors: 12
  • Average comments per issue: 0.44
  • Average comments per pull request: 2.89
  • Merged pull requests: 107
  • Bot issues: 0
  • Bot pull requests: 9
Past Year
  • Issues: 26
  • Pull requests: 26
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 3 days
  • Issue authors: 11
  • Pull request authors: 5
  • Average comments per issue: 0.73
  • Average comments per pull request: 2.85
  • Merged pull requests: 20
  • Bot issues: 0
  • Bot pull requests: 2
View more stats
Top Authors
Issue Authors
  • IAlibay (26)
  • richardjgowers (20)
  • hannahbaumann (13)
  • mikemhenry (11)
  • atravitz (8)
  • RiesBen (6)
  • jameseastwood (3)
  • jthorton (3)
  • dwhswenson (2)
  • xyzmjf (2)
  • ichxw (2)
  • wenchangzhou-qtx (2)
  • mathilfiker (1)
  • thomas-coudrat (1)
  • satoshikanaoka (1)
Pull Request Authors
  • hannahbaumann (25)
  • IAlibay (23)
  • mikemhenry (20)
  • atravitz (19)
  • dwhswenson (17)
  • richardjgowers (12)
  • pre-commit-ci[bot] (11)
  • RiesBen (7)
  • jthorton (5)
  • Yoshanuikabundi (2)
  • jameseastwood (2)
  • dotsdl (1)
Top Labels
Issue Labels
1.0docdrive (7) bug (3) enhancement (2) documentation (1) high-priority (1)
Pull Request Labels
documentation (4) 1.0docdrive (2) enhancement (2)

Dependencies

.github/workflows/CI.yml actions
  • actions/checkout v2.4.0 composite
  • conda-incubator/setup-miniconda v2.1.1 composite
.github/workflows/binder-badge.yaml actions
  • actions/github-script v3 composite
.github/workflows/build-image.yml actions
  • actions/checkout main composite
  • jupyterhub/repo2docker-action master composite
.binder/environment.yml conda
  • click
  • coverage
  • gufe 0.5.*
  • ipywidgets 7.*
  • lomap2
  • lxml
  • mdanalysis
  • mdtraj
  • nbval
  • networkx
  • nglview
  • notebook
  • numpy
  • openfe 0.5.*
  • openff-forcefields
  • openmm
  • openmmforcefields 0.11.2
  • openmmtools
  • pip
  • plugcli
  • pydantic
  • pymbar
  • pytest
  • pytest-cov
  • pytest-xdist
  • python 3.9.*
  • rdkit
  • typing_extensions