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mtdynamics

Simulation of microtubule growth dynamics in th presence and absence of physical obstacles

https://github.com/florian-huber/mtdynamics

Science Score: 57.0%

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 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.7%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Simulation of microtubule growth dynamics in th presence and absence of physical obstacles

Basic Info
  • Host: GitHub
  • Owner: florian-huber
  • License: apache-2.0
  • Language: Jupyter Notebook
  • Default Branch: master
  • Size: 1000 KB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 1
  • Open Issues: 3
  • Releases: 2
Created over 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License Citation

README.md

Microtubule dynamics simulation

Simulation of microtubule growth dynamics in the presence and absence of physical obstacles.

Work done by: - Simulation code: Florian Huber and Maurits Kok - Experiments run by: Maurits Kok and Svenja-Marei Kalisch - Marileen Dogterom

Reference / citation

You can read more about this simulation in:
Kok, Huber, Kalisch, Dogterom, 2021, bioRxiv, DOI: 10.1101/2021.12.07.471417

Please also cite this article if use the present code or results. Thanks!

Simulation code

GitHub Workflow Status Liscence PyPI fair-software.eu

The full simulation code used to produce the results as published in [coming soon] is provided.\ in this repository.
The code consits of the main simulation code (simulation_main.py and simulation_functions.py). Simulation parameters are specified in simulation_parameters.py. Functions for plotting the results are provided in plotting_functions.py.

Requirements

Python version 3.6 or higher.

Installation

If you work with Anaconda you can create an own environment for mtdynamics by running the following commands:

```

install mtdynamics in a new virtual environment to avoid dependency clashes

conda create --name mtdynamics python=3.7 conda activate mtdynamics pip install mtdynamics pip install jupyter # Optional, if you want to run jupyter notebooks from this environment conda install -c anaconda pywin32 # Optional, if you run into win32api error (e.g. when using Python 3.8) ```

Or simply install mtdynamics in your already existing environment: pip install mtdynamics

Runing the simulation

Jupyter notebook(s) are provided to illustrate how to run the simlation. They can be found in the folder \notebooks.

Making a new release

To create release you need write permission on the repository.

  1. Check author list in citation.cff file.
  2. Update version in setup.py and CHANGELOG.md.
  3. Update the CHANGELOG.md to include changes made.
  4. Goto GitHub release page
  5. Press draft a new release button
  6. Fill version, title and description field
  7. Press the Publish Release button

A GitHub action will run which will publish the new version to pypi.

Owner

  • Name: Florian Huber
  • Login: florian-huber
  • Kind: user
  • Location: Düsseldorf, Germany
  • Company: HSD, Düsseldorf, Germany

Citation (CITATION.cff) 

# YAML 1.2
---
abstract: "Simulation of microtubule growth dynamics in the presence and absence of physical obstacles."
authors:
  -
    affiliation: "Netherlands eScience Center"
    family-names: Huber
    given-names: Florian
    orcid: "https://orcid.org/0000-0002-3535-9406"
  -
    affiliation: "TU Delft"
    family-names: Kok
    given-names: Maurits
    orcid: "https://orcid.org/0000-0002-0564-2614"
  -
    affiliation: "TU Delft, Department of Bionanoscience"
    family-names: Dogterom
    given-names: Marileen
    orcid: "https://orcid.org/0000-0002-8803-5261"


cff-version: "1.1.0"
keywords:
  - python
  - "microtubule dynamics"
  - "simulation"
  - "microtubule catastrophes"
license: "Apache-2.0"
repository-code: "https://github.com/florian-huber/mtdynamics"
title: mtdynamics
...

GitHub Events

Total
Last Year

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 80
  • Total Committers: 2
  • Avg Commits per committer: 40.0
  • Development Distribution Score (DDS): 0.012
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
florian-huber 3****r 79
Maurits Kok m****k@g****m 1

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 6
  • Total pull requests: 4
  • Average time to close issues: 7 days
  • Average time to close pull requests: 2 days
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.67
  • Average comments per pull request: 0.5
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • florian-huber (6)
Pull Request Authors
  • florian-huber (4)
  • mwakok (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

setup.py pypi
  • matplotlib *
  • numpy *
  • pandas *
  • parameters *
  • scipy *
.github/workflows/CI_publish.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
  • pypa/gh-action-pypi-publish master composite
.github/workflows/CI_push.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite