Merge pull request #131 from t0mdavid-m/update_citations

Update citations

Author: jcharkow

README.md

@@ -18,6 +18,11 @@ This repository contains a template app for OpenMS workflows in a web applicatio
 
 Documentation for **users** and **developers** is included as pages in [this template app](https://abi-services.cs.uni-tuebingen.de/streamlit-template/), indicated by the 📖 icon.
 
+## Citation
+
+Please cite:
+Müller, T. D., Siraj, A., et al. OpenMS WebApps: Building User-Friendly Solutions for MS Analysis. Journal of Proteome Research (2025). [https://doi.org/10.1021/acs.jproteome.4c00872](https://doi.org/10.1021/acs.jproteome.4c00872)
+
 ## References
 
 - Pfeuffer, J., Bielow, C., Wein, S. et al. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods 21, 365–367 (2024). [https://doi.org/10.1038/s41592-024-02197-7](https://doi.org/10.1038/s41592-024-02197-7)

src/workflow/StreamlitUI.py

@@ -1114,11 +1114,13 @@ def export_parameters_markdown(self):
             version = result.stderr.split("Version: ")[1].split("-")[0]
 
         markdown.append(
-            f"""Data was processed using **{st.session_state.settings['app-name']}** ([{url}]({url})), a web application based on the OpenMS WebApps framework.
-OpenMS ([https://www.openms.de](https://www.openms.de)) is a free and open-source software for LC-MS data analysis [1].
+            f"""Data was processed using **{st.session_state.settings['app-name']}** ([{url}]({url})), a web application based on the OpenMS WebApps framework [1].
+OpenMS ([https://www.openms.de](https://www.openms.de)) is a free and open-source software for LC-MS data analysis [2].
 The workflow includes the **OpenMS {version}** TOPP tools {tools} as well as Python scripts. Non-default parameters are listed in the supplementary section below.
 
-[1] Sachsenberg, Timo, et al. "OpenMS 3 expands the frontiers of open-source computational mass spectrometry." (2023).
+[1] Müller, Tom David, et al. "OpenMS WebApps: Building User-Friendly Solutions for MS Analysis." (2025) [https://doi.org/10.1021/acs.jproteome.4c00872](https://doi.org/10.1021/acs.jproteome.4c00872).
+\\
+[2] Pfeuffer, Julianus, et al. "OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data." (2024) [https://doi.org/10.1038/s41592-024-02197-7](https://doi.org/10.1038/s41592-024-02197-7).
 """
         )
         markdown.append(self.non_default_params_summary())