pyhdx

Derive ΔG for single residues from HDX-MS data

https://github.com/jhsmit/pyhdx

Science Score: 77.0%

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
Found 5 DOI reference(s) in README
✓
Academic publication links
Links to: biorxiv.org, zenodo.org
✓
Committers with academic emails
1 of 6 committers (16.7%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (12.3%) to scientific vocabulary

Keywords

hdx-ms protein-dynamics protein-structure

Keywords from Contributors

interactive mesh interpretability profiles sequences generic projection standardization optim embedded

Last synced: 6 months ago · JSON representation ·

Repository

Derive ΔG for single residues from HDX-MS data

Basic Info

Host: GitHub
Owner: Jhsmit
License: mit
Language: Jupyter Notebook
Default Branch: master
Homepage: http://pyhdx.readthedocs.io
Size: 47.4 MB

Statistics

Stars: 28
Watchers: 3
Forks: 14
Open Issues: 63
Releases: 22

Topics

hdx-ms protein-dynamics protein-structure

Created over 6 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog Contributing License Citation

README.md

PyHDX

PyHDX is python project which can be used to derive Gibbs free energy from HDX-MS data.

PyHDX web

PyHDX latest documentation

PyHDX on YouTube

Installation

Installation of the latest stable beta with pip:

bash $ pip install pyhdx

Installation with web interface extra:

bash $ pip install pyhdx[web]

Conda install (includes web interface extra):

bash $ conda install pyhdx

Run PyHDX

Most up-to-date code examples are in the directory pyhdx/templates

To run the web server:

bash $ pyhdx serve

Please refer to the docs for more details on how to run PyHDX.

Web Application

The PyHDX web application is currently hosted at: http://pyhdx.jhsmit.org

A test file can be downloaded from here and here (right click, save as).

A beta version might be available at: http://pyhdx-beta.jhsmit.org

Publication

Our Analytical Chemistry Publication describing PyHDX can be found here

The latest version (v2) of our biorxiv paper: https://doi.org/10.1101/2020.09.30.320887

Python code for analysis and generation the figures in the paper are here: https://github.com/Jhsmit/PyHDX-paper

Other

HDX MS datasets repository and format: https://github.com/Jhsmit/HDX-MS-datasets

HDXMS datasets python bindings: https://github.com/Jhsmit/hdxms-datasets

Owner

Name: Jochem Smit
Login: Jhsmit
Kind: user

Twitter: Jhsmit_
Repositories: 8
Profile: https://github.com/Jhsmit

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: "Smit"
    given-names: "Jochem H."
    orcid: "https://orcid.org/0000-0002-3597-9429"
title: "PyHDX"
version: 0.4.0b5
doi: 10.5281/zenodo.4062031
date-released: 2021-12-01
url: "https://github.com/Jhsmit/PyHDX"
preferred-citation:
  type: article
  authors:
    - family-names: "Smit"
      given-names: "Jochem H."
      orcid: "https://orcid.org/0000-0002-3597-9429"
    - family-names: "Krishnamurthy"
      given-names: "Srinath"
      orcid: "https://orcid.org/0000-0001-5492-4450"
    - family-names: "Srinivasu"
      given-names: "Bindu Y."
      orcid: "https://orcid.org/0000-0003-0875-2680"
    - family-names: "Parakra"
      given-names: "Rinky"
      orcid: "https://orcid.org/0000-0001-8690-7073"
    - family-names: "Karamanou"
      given-names: "Spyridoula"
      orcid: "https://orcid.org/0000-0002-8803-1404"
    - family-names: "Economou"
      given-names: "Anastassios"
      orcid: "https://orcid.org/0000-0002-1770-507X"
  doi: "10.1021/acs.analchem.1c02155"
  journal: "Analytical Chemistry"
  month: 9
  start: 12840 # First page number
  end: 12847 # Last page number
  title: "Probing Universal Protein Dynamics Using Hydrogen–Deuterium Exchange Mass Spectrometry-Derived Residue-Level Gibbs Free Energy"
  number: 38
  volume: 93
  year: 2021
  url: "https://doi.org/10.1021/acs.analchem.1c02155"

GitHub Events

Total

Delete event: 5
Issue comment event: 10
Push event: 29
Pull request event: 19
Fork event: 2
Create event: 12

Last Year

Delete event: 5
Issue comment event: 10
Push event: 29
Pull request event: 19
Fork event: 2
Create event: 12

Committers

Last synced: 9 months ago

All Time

Total Commits: 2,149
Total Committers: 6
Avg Commits per committer: 358.167
Development Distribution Score (DDS): 0.024

Past Year

Commits: 26
Committers: 2
Avg Commits per committer: 13.0
Development Distribution Score (DDS): 0.231

Top Committers

Name	Email	Commits
Jochem Smit	j**t@g**m	2,097
dependabot[bot]	4****]	22
Jochem Smit	j**t@r**l	13
sajetan	s**n@g**m	12
sebaztiano	s**0@h**m	3
Philipp Rudiger	p**r@a**m	2

Committer Domains (Top 20 + Academic)

anaconda.com: 1 rug.nl: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 87
Total pull requests: 97
Average time to close issues: 10 months
Average time to close pull requests: about 1 month
Total issue authors: 7
Total pull request authors: 5
Average comments per issue: 0.93
Average comments per pull request: 0.33
Merged pull requests: 65
Bot issues: 0
Bot pull requests: 43

Past Year

Issues: 3
Pull requests: 22
Average time to close issues: 3 days
Average time to close pull requests: 18 days
Issue authors: 2
Pull request authors: 2
Average comments per issue: 1.67
Average comments per pull request: 0.23
Merged pull requests: 4
Bot issues: 0
Bot pull requests: 19

View more stats

Top Authors

Issue Authors

Jhsmit (77)
ococrook (3)
Neel6164 (2)
JZbacklife1 (2)
Arthanis58 (1)
tuttlelm (1)
Shakrim (1)

Pull Request Authors

Jhsmit (54)
dependabot[bot] (50)
tuttlelm (2)
CFisicaro (1)
philippjfr (1)

Top Labels

Issue Labels

enhancement (37) GUI (31) bug (17) Fitting (4) documentation (3) good first issue (2) investigate (2) discussion (2) invalid (1)

Pull Request Labels

dependencies (50) python (50)

Packages

Total packages: 2
Total downloads:
- pypi 93 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 24
Total maintainers: 1

pypi.org: pyhdx

Derive ΔG for single residues from HDX-MS data

Documentation: https://pyhdx.readthedocs.io/en/stable/
License: mit
Latest release: 0.4.3
published about 2 years ago

Versions: 17
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 93 Last month

Rankings

Dependent packages count: 10.1%

Forks count: 11.4%

Stargazers count: 12.3%

Average: 16.1%

Dependent repos count: 21.6%

Downloads: 25.0%

Maintainers (1)

Jhsmit

Last synced: 7 months ago

conda-forge.org: pyhdx

Homepage: https://github.com/Jhsmit/PyHDX
License: MIT
Latest release: 0.4.1
published almost 4 years ago

Versions: 7
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent repos count: 34.0%

Average: 44.4%

Forks count: 46.0%

Stargazers count: 46.3%

Dependent packages count: 51.2%

Last synced: 7 months ago

Dependencies

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pyproject.toml pypi

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dask >=2022.12.1
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requirements/requirements-macOS-latest-3.9.txt pypi

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bleach ==6.0.0 test
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certifi ==2023.7.22 test
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requirements/requirements-windows-latest-3.9.txt pypi

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