Science Score: 33.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: nature.com -
✓Committers with academic emails
17 of 25 committers (68.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.7%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: rxncon
- License: lgpl-3.0
- Language: Python
- Default Branch: master
- Size: 5.15 MB
Statistics
- Stars: 10
- Watchers: 1
- Forks: 2
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
rxncon
The purpose of rxncon is to provide a framework to collect, visualise and model experimental data on cellular networks. In the rxncon framework, cellular signal transduction networks are described at the same granularity as empirical data. The key feature is strict separation of elemental reactions from contingencies, which define contextual constrains on these reactions, and this separation minimises the combinatorial complexity. The user defines the network as one reaction list and one contingency list. From these data mathematical and graphical representation can be generated. The network can be easily modified and extended, and both visualization and mathematical models can be generated automatically at any time.
For more details we refer to the following publications:
Tiger, C.-F., Krause, F., Cedersund, G., Palmér, R., Klipp. E., Hohmann, S., Kitano, H. & Krantz, M. (2012) A framework for mapping, visualisation and automatic model creation of signal transduction networks. Molecular Systems Biology 8, 578.
Romers, J.C. & Krantz, M. (2017) rxncon 2.0: a language for executable molecular systems biology. bioRxiv:107136
Installation
This software requires Python 3.5 or higher. Installation is straightforward
through the Python Package Index.
If the pip command is linked to your Python 3 installation, run pip install rxncon,
otherwise run pip3 install rxncon.
This should install all libraries and the command-line tools to interface with them on your machine.
Usage
Please clone our models repository to find an example model describing the insulin pathway, as well as an example Excel sheet that you can use to create your own models.
In what follows we assume the Excel file containing your network description
is called model.xls
Compiling to a boolean network
To compile the rxncon system to a boolean network, run the command
rxncon2boolnet.py model.xls
This will generate three files model.boolnet, model_symbols.csv and model_initial_vals.csv
Compiling to a rule-based model
Generating graphs
For devs
We accept pull requests. Some things to keep in mind:
Please write tests for your code. The directory structure in
rxncon/test/mirrors the structure in therxncon/directory, and we try to cover each module. Feel free to look around. The testing framework we use is pytestPlease provide some documentation for each module, class, method and function. Don't overdo it either: one-liner functions don't require 5 lines of documentation.
Please use Python 3.5's type annotations in your code. The shell script
typecheck.shruns the mypy type checker with the strictest options. This should give no errors.
Owner
- Login: rxncon
- Kind: user
- Repositories: 2
- Profile: https://github.com/rxncon
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jesper Romers | j****s@g****m | 334 |
| thieme | s****e@h****e | 226 |
| Jesper Romers | j****s@h****e | 157 |
| Sebastian | s****e@b****e | 114 |
| jesperromers | j****s@j****l | 114 |
| Basti | d****l@l****t | 72 |
| Jesper Romers | j****r@j****l | 16 |
| Mathias Wajnberg | m****g@f****e | 12 |
| Mathias Wajnberg | m****g@h****e | 7 |
| jesperromers | j****s@c****e | 7 |
| Marcus | m****5@g****m | 6 |
| jesperromers | j****s@c****e | 6 |
| Mathias Wajnberg | M****g@h****e | 5 |
| jesperromers | j****s@c****e | 4 |
| jesperromers | j****s@c****e | 4 |
| jesperromers | j****s@c****e | 3 |
| jesperromers | j****s@c****e | 3 |
| jesperromers | j****s@j****n | 3 |
| jesperromers | j****s@c****e | 2 |
| jesperromers | j****s@c****e | 2 |
| jesperromers | j****s@j****3 | 2 |
| palmerito0 | s****s@g****m | 2 |
| jesperromers | j****s@c****e | 1 |
| jesperromers | j****s@c****e | 1 |
| jesperromers | j****s@c****e | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 1
- Total pull requests: 3
- Average time to close issues: almost 2 years
- Average time to close pull requests: 12 months
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.67
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- palmerito0 (1)
Pull Request Authors
- palmerito0 (2)
- lenarother (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 51 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 17
- Total maintainers: 2
pypi.org: rxncon
The reaction-contingency framework for cellular signalling processes.
- Homepage: https://github.com/rxncon/rxncon
- Documentation: https://rxncon.readthedocs.io/
- License: LGPL
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Latest release: 2.0b19
published over 4 years ago
Rankings
Maintainers (2)
Dependencies
- click *
- click_log ==0.1.8
- colorama *
- networkx *
- numpy *
- pyeda *
- pytest *
- scipy *
- xlrd *