Science Score: 57.0%
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✓CITATION.cff file
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✓codemeta.json file
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Found 3 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (13.6%) to scientific vocabulary
Repository
Retention Order Support Vector Machine (ROSVM)
Basic Info
Statistics
- Stars: 2
- Watchers: 0
- Forks: 1
- Open Issues: 4
- Releases: 1
Metadata Files
README.md
Retention Order Support Vector Machine (ROSVM)
ROSVM is a Ranking Support Vector Machine (RankSVM) implementation for retention order prediction of liquid chromatography (LC) retention times (RT). It was initally proposed by Bach et al. (2018).
This library aims to be a more self-contained implementation, allowing the user to easily train models and make predictions.
Install
Using conda in a new environment
1) Create a new conda environment using:
bash
conda env create --file conda/environment.yml
2) Active the environment:
bash
conda activate rosvm
3) Install the package into the environment:
bash
pip install .
4) (optional) Use the environment in Jupyter notebooks to run the examples: 1) Install the IPython kernel:
```bash
conda install ipykernel
```
2) Make the environment available as notebook kernel:
```bash
python -m ipykernel install --user --name=rosvm
```
Using pip
You can install the package directly using:
bash
pip install .
However, the installation of rdkit can be a bit tricky. You can find installation instructions for various operating systems here.
Citation
If you are using the library please cite:
- For the general approach of retention order prediction
bibtex
@article{Bach2018,
author = {Bach, Eric and Szedmak, Sandor and Brouard, Céline and Böcker, Sebastian and Rousu, Juho},
title = "{Liquid-chromatography retention order prediction for metabolite identification}",
journal = {Bioinformatics},
volume = {34},
number = {17},
pages = {i875-i883},
year = {2018},
month = {09},
issn = {1367-4803},
doi = {10.1093/bioinformatics/bty590},
url = {https://doi.org/10.1093/bioinformatics/bty590},
eprint = {https://academic.oup.com/bioinformatics/article-pdf/34/17/i875/25702364/bty590.pdf},
}
- For the actual ROSVM implementation:
bibtex
@software{Bach_Retention_Order_Support_2020,
author = {Bach, Eric},
month = {5},
title = {{Retention Order Support Vector Machine (ROSVM)}},
url = {https://github.com/bachi55/rosvm},
version = {0.5.0},
year = {2020}
}
Owner
- Name: Eric Bach
- Login: bachi55
- Kind: user
- Location: Espoo, Finnland
- Company: Aalto University
- Website: https://www.linkedin.com/in/eric-bach-ml/
- Repositories: 10
- Profile: https://github.com/bachi55
Doctoral student in the field of Machine Learning, Bioinformatics and Computational Metabolomics.
Citation (CITATION.cff)
cff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: - family-names: "Bach" given-names: "Eric" email: eric.bach@aalto.fi affiliation: Aalto University, Espoo, Finland title: "Retention Order Support Vector Machine (ROSVM)" version: 0.4.0 date-released: 2021-11-10 url: "https://github.com/bachi55/rosvm"
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Dependencies
- cvxpy
- joblib
- numpy
- pandas
- pip
- rdkit
- scikit-learn
- scipy
- cvxpy *
- joblib *
- numpy *
- pandas *
- scikit-learn *
- scipy *