Merge pull request #102 from draeger-lab/dev

Adds publication badge, how to cites, some bug fixes and some new features

CITATION.cff

@@ -0,0 +1,39 @@
+cff-version: 1.2.0
+message: "If you use refineGEMs, please cite it as below."
+authors:
+- family-names: "Bäuerle"
+  given-names: "Famke"
+  orcid: "https://orcid.org/0000-0003-1387-0251"
+- family-names: "Döbel"
+  given-names: "Gwendolyn O."
+  orcid: "https://orcid.org/0000-0002-8206-2576"
+title: "refineGEMs"
+version: 1.3.1
+doi: 10.5281/zenodo.8270303 
+date-released: 2023-10-30
+url: "https://github.com/github-linguist/linguist"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Bäuerle"
+    given-names: "Famke"
+    orcid: "https://orcid.org/0000-0003-1387-0251"
+  - family-names: "Döbel"
+    given-names: "Gwendolyn O."
+    orcid: "https://orcid.org/0000-0002-8206-2576"
+  - family-names: "Camus"
+    given-names: "Laura"
+    orcid: "https://orcid.org/0000-0003-1335-8901"
+  - family-names: "Heilbronner"
+    given-names: "Simon"
+    orcid: "https://orcid.org/0000-0002-6774-2311"
+  - family-names: "Dräger"
+    given-names: "Andreas"
+    orcid: "https://orcid.org/0000-0002-1240-5553"
+  doi: "10.3389/fbinf.2023.1214074"
+  journal: "Front. Bioinform."
+  month: 10
+  title: "Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum"
+  issn: 2673-7647
+  volume: 3
+  year: 2023

README.md

@@ -1,51 +1,61 @@
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-![GitHub Pipenv locked dependency version](https://img.shields.io/github/pipenv/locked/dependency-version/draeger-lab/refinegems/refinegems?label=refineGEMs&color=B4A069)
-![GitHub Pipenv locked Python version](https://img.shields.io/github/pipenv/locked/python-version/draeger-lab/refinegems)
+![PyPI - Version](https://img.shields.io/pypi/v/refineGEMs?label=refineGEMs&color=B4A069&style=flat-square)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2Fdraeger-lab%2Frefinegems%2Fmain%2Fpyproject.toml)
 [![Documentation Status](https://readthedocs.org/projects/refinegems/badge/?version=latest)](https://refinegems.readthedocs.io/en/latest/?badge=latest)
 ![GitHub last commit (branch)](https://img.shields.io/github/last-commit/draeger-lab/refinegems/main)
 ![Repo Size](https://img.shields.io/github/repo-size/draeger-lab/refinegems)
 ![PyPI version](https://img.shields.io/pypi/v/refinegems?label=PyPI%20package&color=neongreen)
 ![PyPI - Format](https://img.shields.io/pypi/format/refinegems)
-[![PyPI downloads](https://img.shields.io/pypi/dm/refinegems.svg)](https://pypistats.org/packages/refinegems)
-[![DOI](https://zenodo.org/badge/359867657.svg)](https://zenodo.org/badge/latestdoi/359867657)
+[![PyPI downloads](https://img.shields.io/pypi/dm/refinegems.svg)](https://pypistats.org/packages/refinegems)  
+[![Zenodo DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.8270303-B4A069?style=flat-square&logo=zenodo&logoColor=white)](https://zenodo.org/badge/latestdoi/359867657)  
+[![Frontiers DOI](https://img.shields.io/badge/Frontiers%20DOI-10.3389%2Ffbinf.2023.1214074-B4A069?style=flat-square)](https://www.frontiersin.org/articles/10.3389/fbinf.2023.1214074/full)
 
 <p align="center">
 <img src="https://github.com/draeger-lab/refinegems/raw/main/docs/source/images/refineGEMs_logo.png" height="200"/>
 </p>
 
 # refineGEMs
-`refineGEMs` is a python package inteded to help with the curation of genome-scale metabolic models (GEMS).
+`refineGEMs` is a python package intended to help with the curation of genome-scale metabolic models (GEMS). </br>
+The documentation can be found [here](https://refinegems.readthedocs.io/en/latest/).
 
-## Documentation
-The docs can be found [here](https://refinegems.readthedocs.io/en/latest/).
+## Table of contents
+1. [Overview](#overview)
+2. [Installation](#installation)
+3. [How to cite](#how-to-cite)
+4. [Repositories using refineGEMs](#repositories-using-refinegems)
 
 ## Overview
 
 Currently `refineGEMs` can be used for the investigation of a GEM, it can complete the following tasks:
-- loading GEMS with `cobrapy` and `libSBML`
+
+- loading GEMs with `COBRApy` and `libSBML`
 - report number of metabolites, reactions and genes
 - report orphaned, deadends and disconnected metabolites
 - report mass and charge unbalanced reactions
 - report [Memote](https://memote.readthedocs.io/en/latest/index.html) score
-- compare the genes present in the model to the genes found in the [KEGG](https://www.genome.jp/kegg/kegg1.html) Database (Note: this requires a gff file of your organism and the KEGG identifier of your organism)
-- compare the charges and masses of the metabolites present in the model to the charges and masses denoted in the [ModelSEED](https://modelseed.org/) Database
+- compare the genes present in the model to the genes found in:
+  - the [KEGG](https://www.genome.jp/kegg/kegg1.html) Database (Note: This requires the GFF file and the KEGG identifier of your organism.)
+  - Or the [BioCyc](https://biocyc.org) Database (Note: This requires that a database entry for your organism exists in BioCyc.)
+- compare the charges and masses of the metabolites present in the model to the charges and masses denoted in the [ModelSEED](https://modelseed.org/) Database.
+
+Other applications of `refineGEMs` to curate a given model include: 
 
-Other applications of `refineGEMs` include curation of a given model these include:
-- correction of a model created with [CarveMe](https://github.com/cdanielmachado/carveme) v.1.5.1 (for example moving all relevant information from the notes to the annotation field) this includes automated annotation of NCBI genes to the GeneProtein section of the model
-- addition of [KEGG](https://www.genome.jp/kegg/kegg1.html) Pathways as Groups (using the [libSBML](https://synonym.caltech.edu/software/libsbml/5.18.0/docs/formatted/python-api/classlibsbml_1_1_groups_model_plugin.html) Groups Plugin)
-- SBO-Term annotation based on a script by Elisabeth Fritze
-- annotation of metabolites based using a table created by the user `data/manual_annotations.xlsx`
+- The correction of a model created with [CarveMe](https://github.com/cdanielmachado/carveme) v1.5.1 or v1.5.2 (for example moving all relevant information from the notes to the annotation field or automatically annotating the GeneProduct section of the model with the respective NCBI gene/protein identifiers from the GeneProduct identifiers),
+- The addition of [KEGG](https://www.genome.jp/kegg/kegg1.html) Pathways as Groups (using the [libSBML](https://synonym.caltech.edu/software/libsbml/5.18.0/docs/formatted/python-api/classlibsbml_1_1_groups_model_plugin.html) Groups Plugin),
+- Updating the SBO-Term annotations based on [SBOannotator](https://github.com/draeger-lab/SBOannotator),
+- Updating the annotation of metabolites and extending the model with reactions (for the purpose of filling gaps) based on a table filled by the user `data/manual_annotations.xlsx` (Note: This only works when the structure of the [example Excel file](https://github.com/draeger-lab/refinegems/blob/5eac900d9848b5ae5faf0055db72a986e7ba64e8/data/manual_curation.xlsx) is used.),
+- And extending the model with all information surrounding reactions including the corresponding GeneProducts and metabolites by filling in the table `data/modelName_gapfill_analysis_date_example.xlsx` (Note: This also only works when the structure of the [example Excel file](https://github.com/draeger-lab/refinegems/blob/5eac900d9848b5ae5faf0055db72a986e7ba64e8/data/modelName_gapfill_analysis_date_example.xlsx) is used).
 
 ## Installation
 
 You can install `refineGEMs` via pip:
 
 ```bash
-pip install refinegems
+pip install refineGEMs
 
 ```
 
-or to a local conda environment where `refineGEMs` is distributed via this github repository and all dependencies are denoted in the `setup.py` file:
+or to a local conda environment where `refineGEMs` is distributed via this GitHub repository and all dependencies are denoted in the `setup.py` file:
 
 ```bash
 # clone or pull the latest source code
@@ -62,3 +72,15 @@ which pip
 pip install .
 
 ```
+
+## How to cite
+When using `refineGEMs`, please cite the latest publication:
+
+Famke Bäuerle, Gwendolyn O. Döbel, Laura Camus, Simon Heilbronner, and Andreas Dräger. 
+Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium
+striatum. Front. Bioinform., oct 2023. [doi:10.3389/fbinf.2023.1214074](https://doi.org/10.3389/fbinf.2023.1214074).
+
+## Repositories using refineGEMs
+- [C_striatum_GEMs](https://github.com/draeger-lab/C_striatum_GEMs)
+- draeger-lab/Shaemolyticus - `private`
+- draeger-lab/Ssanguinis - `private`