contingent-evolution-2020
Custom scripts for data analysis and generating figures for "Contingent evolution of alternate metabolic network topologies determines whether crossfeeding evolves" (2020) Jeroen Meijer, Bram van Dijk, Paulien Hogeweg
Science Score: 31.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 6 DOI reference(s) in README -
○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.2%) to scientific vocabulary
Repository
Custom scripts for data analysis and generating figures for "Contingent evolution of alternate metabolic network topologies determines whether crossfeeding evolves" (2020) Jeroen Meijer, Bram van Dijk, Paulien Hogeweg
Basic Info
Statistics
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
contingent-evolution-2020
Scripts for analysis and generating figures supporting:
"Contingent evolution of alternate metabolic network topologies determines whether crossfeeding evolves" (2020) Jeroen Meijer, Bram van Dijk, Paulien Hogeweg. Communications Biology, https://doi.org/10.1038/s42003-020-1107-x
Also includes an archived version of VirtualMicrobes 0.2.5 which was used in this study.
Project organization
``` . ├── .gitignore ├── CITATION.md ├── LICENSE.md ├── README.md ├── requirements.txt ├── data <- All project data, ignored by git │ ├── raw <- The original, immutable data dump. Not included here. │ └── temp <- Intermediate data that has been transformed. ├── figures <- Figures for the paper, generated by src ├── src <- R scripts used for analysis and making figures └── VirtualMicrobes <- VirtualMicrobes 0.2.5 (version used in this study), including config files
```
How to use
- Open a terminal and clone this repository with
git clone https://github.com/meijer-jeroen/contingent-evolution-2020 - Download the raw data from https://doi.org/10.5281/zenodo.3840463
- Extract the data and place it in the folder 'contingent-evolution-2020/data/raw'
- make subdirectories 'contingent-evolution-2020/figures' and 'contingent-evolution-2020/data/temp'
- Use Rstudio to open the contingent-evolution-2020.Rproj file found in main folder, and run individual scripts in the 'src' folder to generate the figures. Some figures might require pre-processing of data with supplied scripts.
VirtualMicrobes
This study includes the VirtualMicrobes Python module v0.2.5. Information about VirtualMicrobes and installation instructions are available at https://bitbucket.org/thocu/virtual-microbes/
Data
Raw data is available at https://doi.org/10.5281/zenodo.3840463
License
This project is licensed under the terms of the MIT License
Citation
Owner
- Name: Jeroen Meijer
- Login: meijer-jeroen
- Kind: user
- Location: Utrecht, the Netherlands
- Company: Utrecht University
- Twitter: jeroen_evo
- Repositories: 1
- Profile: https://github.com/meijer-jeroen
Citation (CITATION.md)
Please cite this project as follows: Jeroen Meijer (2020), contingent-evolution-2020 - version 0.1.0. url: github.com/meijer-jeroen/contingent-evolution-2020