+
+
+
+
+
Legacy
+
+ Archived Apps
+
+
+ These projects are kept for reference. They still work, but are no longer updated or supported by the community.
+
+
+
+
+
+ {{< webapps-archived-catalog >}}
+
+
Detailed view
-### Code of Conduct (Detailed View)
+ Part 1 — Introduction
-#### Part 1 - Introduction
+ OpenMS is a community-led project. We value the involvement of everyone in the community. We are committed to creating a friendly and respectful place for learning, teaching and contributing. All participants in our events and communications are expected to show respect and courtesy to others.
-OpenMS is a community-led project. We value the involvement of everyone in the community. We are committed to creating a friendly and respectful place for learning, teaching and contributing. All participants in our events and communications are expected to show respect and courtesy to others.
+ To make clear what is expected, everyone participating in OpenMS activities is required to conform to the Code of Conduct. This Code of Conduct applies to all spaces managed by OpenMS including, but not limited to, workshops, email lists, and online forums such as GitHub, Discord and LinkedIn. Workshop hosts are expected to assist with the enforcement of the Code of Conduct.
-To make clear what is expected, everyone participating in OpenMS activities is required to conform to the Code of Conduct. This Code of Conduct applies to all spaces managed by OpenMS including, but not limited to, workshops, email lists, and online forums such as GitHub, Slack and Twitter. Workshop hosts are expected to assist with the enforcement of the Code of Conduct.
+ The OpenMS Code of Conduct Committee is responsible for enforcing the Code of Conduct. It can be contacted by emailing open-ms-c_o_c@lists.sourceforge.net. All reports will be reviewed by the Code of Conduct Committee and will be kept confidential. See the report handling manual for how reports are followed up.
-The OpenMS Code of Conduct Committee is responsible for enforcing the Code of Conduct. It can be contacted by emailing open-ms-c_o_c@lists.sourceforge.net. All reports will be reviewed by the Code of Conduct Committee and will be kept confidential.
+ Part 2 — OpenMS Code of Conduct
-#### Part 2 - OpenMS Code of Conduct
+ OpenMS is dedicated to providing a welcoming and supportive environment for all people, regardless of background or identity. As such, we do not tolerate behaviour that is disrespectful to our teachers or learners or that excludes, intimidates, or causes discomfort to others. We do not tolerate discrimination or harassment based on characteristics that include, but are not limited to, gender identity and expression, sexual orientation, disability, physical appearance, body size, citizenship, nationality, ethnic or social origin, pregnancy, familial status, veteran status, genetic information, religion or belief (or lack thereof), membership of a national minority, property, age, education, socio-economic status, technical choices, and experience level.
-OpenMS is dedicated to providing a welcoming and supportive environment for all people, regardless of background or identity. As such, we do not tolerate behaviour that is disrespectful to our teachers or learners or that excludes, intimidates, or causes discomfort to others. We do not tolerate discrimination or harassment based on characteristics that include, but are not limited to, gender identity and expression, sexual orientation, disability, physical appearance, body size, citizenship, nationality, ethnic or social origin, pregnancy, familial status, veteran status, genetic information, religion or belief (or lack thereof), membership of a national minority, property, age, education, socio-economic status, technical choices, and experience level.
+ Everyone who participates in OpenMS activities is required to conform to this Code of Conduct. It applies to all spaces managed by OpenMS including, but not limited to, workshops, email lists, and online forums such as GitHub, Discord and LinkedIn. Workshop hosts are expected to assist with the enforcement of the Code of Conduct. By participating, participants indicate their acceptance of the procedures by which OpenMS resolves any Code of Conduct incidents, which may include storage and processing of their personal information.
-Everyone who participates in OpenMS activities is required to conform to this Code of Conduct. It applies to all spaces managed by OpenMS including, but not limited to, workshops, email lists, and online forums such as GitHub, Gitter and Twitter. Workshop hosts are expected to assist with the enforcement of the Code of Conduct. By participating, participants indicate their acceptance of the procedures by which OpenMS resolves any Code of Conduct incidents, which may include storage and processing of their personal information.
+ Part 2.1 — Expected behaviour
-#### Part 2.1 - Expected behaviour
+ All participants in our events and communications are expected to show respect and courtesy to others. All interactions should be professional regardless of platform: either online or in-person. In order to foster a positive and professional learning environment we encourage the following kinds of behaviours in all OpenMS events and platforms:
-All participants in our events and communications are expected to show respect and courtesy to others. All interactions should be professional regardless of platform: either online or in-person. In order to foster a positive and professional learning environment we encourage the following kinds of behaviours in all OpenMS events and platforms:
+
+ - Use welcoming and inclusive language
+ - Be respectful of different viewpoints and experiences
+ - Gracefully accept constructive criticism
+ - Focus on what is best for the community
+ - Show courtesy and respect towards other community members
+
-- Use welcoming and inclusive language
-- Be respectful of different viewpoints and experiences
-- Gracefully accept constructive criticism
-- Focus on what is best for the community
-- Show courtesy and respect towards other community members
+ Note: See the four social rules for further recommendations.
-Note: See the four [social rules](https://www.recurse.com/manual#sub-sec-social-rules) for further recommendations.
+ Part 2.2 — Unacceptable behaviour
-#### Part 2.2 - Unacceptable behaviour
+ Examples of unacceptable behaviour by participants at any OpenMS event/platform include:
-Examples of unacceptable behaviour by participants at any OpenMS event/platform include:
+
+ - written or verbal comments which have the effect of excluding people on the basis of membership of any specific group
+ - causing someone to fear for their safety, such as through stalking, following, or intimidation
+ - violent threats or language directed against another person
+ - the display of sexual or violent images
+ - unwelcome sexual attention
+ - nonconsensual or unwelcome physical contact
+ - sustained disruption of talks, events or communications
+ - insults or put downs
+ - sexist, racist, homophobic, transphobic, ableist, or exclusionary jokes
+ - excessive swearing
+ - incitement to violence, suicide, or self-harm
+ - continuing to initiate interaction (including photography or recording) with someone after being asked to stop
+ - publication of private communication without consent
+
-- written or verbal comments which have the effect of excluding people on the basis of membership of any specific group
-- causing someone to fear for their safety, such as through stalking, following, or intimidation
-- violent threats or language directed against another person
-- the display of sexual or violent images
-- unwelcome sexual attention
-- nonconsensual or unwelcome physical contact
-- sustained disruption of talks, events or communications
-- insults or put downs
-- sexist, racist, homophobic, transphobic, ableist, or exclusionary jokes
-- excessive swearing
-- incitement to violence, suicide, or self-harm
-- continuing to initiate interaction (including photography or recording) with someone after being asked to stop
-- publication of private communication without consent
+ Part 2.3 — Consequences of unacceptable behaviour
-#### Part 2.3 Consequences of Unacceptable behaviour
+ Participants who are asked to stop any inappropriate behaviour are expected to comply immediately. This applies to any OpenMS events and platforms, either online or in-person. If a participant engages in behaviour that violates this code of conduct, the organisers may warn the offender, ask them to leave the event or platform (without refund), or engage OpenMS Code of Conduct Committee to investigate the Code of Conduct violation and impose appropriate sanctions.
+
-Participants who are asked to stop any inappropriate behaviour are expected to comply immediately. This applies to any OpenMS events and platforms, either online or in-person. If a participant engages in behaviour that violates this code of conduct, the organisers may warn the offender, ask them to leave the event or platform (without refund), or engage OpenMS Code of Conduct Committee to investigate the Code of Conduct violation and impose appropriate sanctions.
+
+ Incident reporting, resolution & enforcement
-### Incident reporting resolution & Code of Conduct enforcement
+ This section summarizes the most important points; more details are in the OpenMS Code of Conduct — How to follow up on a report.
-_This section summarizes the most important points, more details can be found in_ [OpenMS Code of Conduct - How to follow up on a report](/report-handling-manual).
+ We will investigate and respond to all complaints. The OpenMS Code of Conduct Committee and the OpenMS Executive Committee (if involved) will protect the identity of the reporter, and treat the content of complaints as confidential (unless the reporter agrees otherwise).
-We will investigate and respond to all complaints. The OpenMS Code of Conduct Committee and the OpenMS Executive Committee (if involved) will protect the identity of the reporter, and treat the content of complaints as confidential (unless the reporter agrees otherwise).
+ In case of severe and obvious breaches, e.g. personal threat or violent, sexist or racist language, we will immediately disconnect the originator from OpenMS communication channels; please see the manual for details.
-In case of severe and obvious breaches, e.g. personal threat or violent, sexist or racist language, we will immediately disconnect the originator from OpenMS communication channels; please see the manual for details.
+ In cases not involving clear severe and obvious breaches of this Code of Conduct the process for acting on any received Code of Conduct violation report will be:
-In cases not involving clear severe and obvious breaches of this Code of Conduct the process for acting on any received Code of Conduct violation report will be:
+
+ - Acknowledge report is received,
+ - Reasonable discussion/feedback,
+ - Mediation (if feedback didn't help, and only if both reporter and reportee agree to this),
+ - Enforcement via transparent decision (see Resolutions) by the Code of Conduct Committee.
+
-1. Acknowledge report is received,
-2. Reasonable discussion/feedback,
-3. Mediation (if feedback didn’t help, and only if both reporter and reportee agree to this),
-4. Enforcement via transparent decision (see [Resolutions](/report-handling-manual/#resolutions)) by the Code of Conduct Committee.
+ The Committee will respond to any report as soon as possible, and at most within 72 hours.
+
-The Committee will respond to any report as soon as possible, and at most within 72 hours.
-
-### About this Document
+## About this Document
This document is adapted from guidelines written by the [The Carpentries Project](https://github.com/carpentries/handbook/blob/master/topic_folders/policies/code-of-conduct.md), which was itself based on the [Django Project](https://www.djangoproject.com/conduct/enforcement-manual/) and [Ada Initiative](http://geekfeminism.wikia.com/wiki/Conference_anti-harassment/Responding_to_reports) template and the [PyCon 2013 Procedure for Handling Harassment Incidents](https://us.pycon.org/2013/about/code-of-conduct/harassment-incidents/).
-[licensed CC BY 3.0](http://creativecommons.org/licenses/by/3.0/)
\ No newline at end of file
+[licensed CC BY 3.0](http://creativecommons.org/licenses/by/3.0/)
diff --git a/content/en/communication.md b/content/en/communication.md
deleted file mode 100644
index deb590c7..00000000
--- a/content/en/communication.md
+++ /dev/null
@@ -1,74 +0,0 @@
----
-title: Community
-sidebar: false
----
-
-## Welcome to OpenMS!
-
-@OpenMS is an open-source C++ software library for LC-MS data management and analysis with python wrappers, a large modular toolset and workflows for e.g., Galaxy, KNIME and nextflow.
-
-OpenMS is a community-driven open source project developed by a diverse group of [contributors](/contributors). The OpenMS leadership has made a strong commitment to creating an open, inclusive, and positive community. Please read the [OpenMS Code of Conduct](/code-of-conduct) for guidance on how to interact with others in a way that makes the community thrive.
-
-Here's how to get started:
-
-- 📚 Browse through the main library code under [OpenMS/OpenMS](https://github.com/openms/openms/issues)
-- 👩💻 Check out the [documentation](https://openms.readthedocs.io/en/latest/index.html).
-- 🙋♀️ Come and say hi on our [](https://discord.gg/v9tv5BxPch) channel.
-- 🍿 Tune in for news about developer/user meetings and events, [get involved]({{< ref "news.md" >}})!
-- 🌈 Please abide by our [community code of conduct](https://github.com/OpenMS/OpenMS/blob/develop/CODE_OF_CONDUCT.md)
-
-We offer several communication channels to learn, share your knowledge and connect with others within the OpenMS community.
-
-***
-
-###
+
+
+
+
+
Community tools
+
+ Featured Apps
+
+
+ GUI or Command Line Apps actively maintained by the OpenMS core development team.
+
+
+
+
+
+ {{< webapps-featured-catalog >}}
+
+
Discussion
+ OpenMS mailing list
+
+ The main forum for longer-form discussions — new features, roadmap changes,
+ and project-wide decisions. Announcements about releases, developer meetings,
+ sprints, and conference talks are also made here.
+
+
+ Join the mailing list
+ ·
+ Search the archive
+
+
+ Please use bottom posting, reply to the list (rather than to another sender),
+ and do not reply to digests.
+
+
+
+ Development
+ GitHub issue tracker
+
+ Use the tracker for bug reports, documentation issues (e.g. unclear sections),
+ and feature requests (e.g. new interpolation methods).
+
+
+ Open issues on GitHub
+
+
+
+ C++ / OpenMS
+ OpenMS documentation
+
+ Documentation for the newest release — all classes, functions, and build
+ instructions for several operating systems. Includes an introduction to core
+ data structures and algorithms for new developers.
+
+
+ Browse the docs
+ ·
+ Developer tutorial
+
+
+
+ Python
+ pyOpenMS documentation
+
+ Documentation on how to use OpenMS in Python.
+
+
+ Read pyOpenMS docs
+
+
+
diff --git a/content/en/news/_index.md b/content/en/news/_index.md
new file mode 100644
index 00000000..1ea2f362
--- /dev/null
+++ b/content/en/news/_index.md
@@ -0,0 +1,6 @@
+---
+title: News
+subtitle: Announcements, releases, workshops, and community updates from OpenMS.
+hidePageTitle: true
+hideShortcuts: true
+---
diff --git a/content/en/news/gsoc2025.md b/content/en/news/gsoc2025.md
index c545adb1..4cef78a8 100644
--- a/content/en/news/gsoc2025.md
+++ b/content/en/news/gsoc2025.md
@@ -3,6 +3,7 @@ title: GSoC 2025 – Two Projects Accepted!
authors: ["Matteo Pilz, Timo Sachsenberg"]
date: 2025-05-20
summary: We're thrilled to announce that two OpenMS projects have been accepted for Google Summer of Code 2025! 🚀
+type: news
---
🎉 OpenMS is part of GSoC 2025 – Two Projects Accepted!
diff --git a/content/en/openms-lib.md b/content/en/openms-lib.md
new file mode 100644
index 00000000..eda22faa
--- /dev/null
+++ b/content/en/openms-lib.md
@@ -0,0 +1,69 @@
+---
+title: OpenMS-lib
+hidePageTitle: true
+hideShortcuts: true
+sidebar: false
+---
+
+
+
+
+
+
+
OpenMS-lib
+
+ The open source toolkit for mass spectrometry.
+
+
+ OpenMS-lib is a mature and reliable C++ framework for omics-based mass spectrometry data analysis.
+
+
+
+
+
+
+ {{< openms-lib-highlights >}}
+
+
+ {{< openms-lib-topp >}}
+
+
+ {{< openms-lib-getting-started >}}
+
+
+ {{< openms-lib-developers >}}
+
+
diff --git a/content/en/our-sponsors.md b/content/en/our-sponsors.md
new file mode 100644
index 00000000..6515d2fa
--- /dev/null
+++ b/content/en/our-sponsors.md
@@ -0,0 +1,6 @@
+---
+title: Our Sponsors
+sidebar: false
+hideShortcuts: true
+hidePageTitle: true
+---
diff --git a/content/en/privacy.md b/content/en/privacy.md
index 4a30d7dc..2df6eb22 100644
--- a/content/en/privacy.md
+++ b/content/en/privacy.md
@@ -1,6 +1,8 @@
---
title: Privacy Policy
sidebar: false
+hidePageTitle: true
+hideShortcuts: true
---
### WHO WE ARE
diff --git a/content/en/publications.md b/content/en/publications.md
index 40ae701e..dca1dcba 100644
--- a/content/en/publications.md
+++ b/content/en/publications.md
@@ -1,237 +1,227 @@
-# List of OpenMS Publications
-
-## 2025
-
-
-- Müller, Tom David; Siraj, Arslan; Walter, Axel; Kim, Jihyung; Wein, Samuel; von Kleist, Johannes; Feroz, Ayesha; Pilz, Matteo; Jeong, Kyowon; Sing, Justin Cyril; *OpenMS WebApps: Building User-Friendly Solutions for MS Analysis*. Journal of Proteome Research. 2025. [Link](https://www.ncbi.nlm.nih.gov/pubmed/39881492)
-
-- Sing, Justin Cyril; Charkow, Joshua; Walter, Axel; Gao, Mingxuan; Muller, Tom David; Bittremieux, Wout; Sachsenberg, Timo; Röst, Hannes Luc; *pyOpenMS-viz: Streamlining Mass Spectrometry Data Visualization with pandas*. Journal of Proteome Research. 2025. [Link](https://www.ncbi.nlm.nih.gov/pubmed/40019346)
-***
-## 2024
-
-
-- Kim, Jihyung; Jeong, Kyowon; Kaulich, Philipp T; Winkels, Konrad; Tholey, Andreas; Kohlbacher, Oliver; *FLASHQuant: a fast algorithm for proteoform quantification in top-down proteomics*. Analytical Chemistry. 2024. [Link](https://www.ncbi.nlm.nih.gov/pubmed/39424290)
-
-- Siraj, Arslan; Bouwmeester, Robbin; Declercq, Arthur; Welp, Luisa; Chernev, Aleksandar; Wulf, Alexander; Urlaub, Henning; Martens, Lennart; Degroeve, Sven; Kohlbacher, Oliver; *Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links*. Proteomics. 2024. [Link](https://www.ncbi.nlm.nih.gov/pubmed/38629965)
-
-- Pfeuffer, Julianus; Bielow, Chris; Wein, Samuel; Jeong, Kyowon; Netz, Eugen; Walter, Axel; Alka, Oliver; Nilse, Lars; Colaianni, Pasquale Domenico; McCloskey, Douglas; *OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data*. Nature methods. 2024. [Link](https://www.ncbi.nlm.nih.gov/pubmed/38366242)
-
-- Dai, Chengxin; Pfeuffer, Julianus; Wang, Hong; Zheng, Ping; Käll, Lukas; Sachsenberg, Timo; Demichev, Vadim; Bai, Mingze; Kohlbacher, Oliver; Perez-Riverol, Yasset; *quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data*. Nature Methods. 2024. [Link](https://www.ncbi.nlm.nih.gov/pubmed/38965444)
-***
-## 2023
-
-
-- Kontou, Eftychia E; Walter, Axel; Alka, Oliver; Pfeuffer, Julianus; Sachsenberg, Timo; Mohite, Omkar S; Nuhamunada, Matin; Kohlbacher, Oliver; Weber, Tilmann; *UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis*. Journal of Cheminformatics. 2023. [Link](https://www.ncbi.nlm.nih.gov/pubmed/37173725)
-
-- Bittremieux, Wout; Levitsky, Lev; Pilz, Matteo; Sachsenberg, Timo; Huber, Florian; Wang, Mingxun; Dorrestein, Pieter C; *Unified and standardized mass spectrometry data processing in Python using spectrum_utils*. Journal of proteome research. 2023. [Link](https://www.ncbi.nlm.nih.gov/pubmed/36688502)
-***
-## 2022
-
-
-- Luo, Xiyang; Bittremieux, Wout; Griss, Johannes; Deutsch, Eric W; Sachsenberg, Timo; Levitsky, Lev I; Ivanov, Mark V; Bubis, Julia A; Gabriels, Ralf; Webel, Henry; *A comprehensive evaluation of consensus spectrum generation methods in proteomics*. Journal of proteome research. 2022. [Link](https://www.ncbi.nlm.nih.gov/pubmed/35549218)
-
-- Jeong, Kyowon; Babović, Maša; Gorshkov, Vladimir; Kim, Jihyung; Jensen, Ole N; Kohlbacher, Oliver; *FLASHIda enables intelligent data acquisition for top–down proteomics to boost proteoform identification counts*. Nature communications. 2022. [Link](https://www.ncbi.nlm.nih.gov/pubmed/35906205)
-
-- Umer, Husen M; Audain, Enrique; Zhu, Yafeng; Pfeuffer, Julianus; Sachsenberg, Timo; Lehtiö, Janne; Branca, Rui M; Perez-Riverol, Yasset; *Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides*. Bioinformatics. 2022. [Link](https://www.ncbi.nlm.nih.gov/pubmed/34904638)
-
-- Jeong, Kyowon; Kim, Jihyung; Kohlbacher, Oliver; *Mass Deconvolution of Top-Down Mass Spectrometry Datasets by FLASHDeconv*. Proteoform Identification: Methods and Protocols. 2022. [Link](https://www.ncbi.nlm.nih.gov/pubmed/35657592)
-***
-## 2021
-
-
-- Dai, Chengxin; Füllgrabe, Anja; Pfeuffer, Julianus; Solovyeva, Elizaveta M; Deng, Jingwen; Moreno, Pablo; Kamatchinathan, Selvakumar; Kundu, Deepti Jaiswal; George, Nancy; Fexova, Silvie; *A proteomics sample metadata representation for multiomics integration and big data analysis*. Nature Communications. 2021. [Link](https://www.ncbi.nlm.nih.gov/pubmed/34615866)
-
-- Bichmann, Leon; Gupta, Shubham; Rosenberger, George; Kuchenbecker, Leon; Sachsenberg, Timo; Ewels, Phil; Alka, Oliver; Pfeuffer, Julianus; Kohlbacher, Oliver; Rost, Hannes; *DIAproteomics: A multifunctional data analysis pipeline for data-independent acquisition proteomics and peptidomics*. Journal of proteome research. 2021
-
-- Marcu, Ana; Bichmann, Leon; Kuchenbecker, Leon; Kowalewski, Daniel Johannes; Freudenmann, Lena Katharina; Backert, Linus; Mühlenbruch, Lena; Szolek, András; Lübke, Maren; Wagner, Philipp; *HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy*. Journal for immunotherapy of cancer. 2021
-***
-## 2020
-
-
-- Wein, Samuel; Andrews, Byron; Sachsenberg, Timo; Santos-Rosa, Helena; Kohlbacher, Oliver; Kouzarides, Tony; Garcia, Benjamin A; Weisser, Hendrik; *A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry*. Nature communications. 2020. [Link](https://www.ncbi.nlm.nih.gov/pubmed/32066737)
-
-- Stützer, Alexandra; Welp, Luisa M; Raabe, Monika; Sachsenberg, Timo; Kappert, Christin; Wulf, Alexander; Lau, Andy M; David, Stefan-Sebastian; Chernev, Aleksandar; Kramer, Katharina; *Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry*. Nature communications. 2020. [Link](https://www.ncbi.nlm.nih.gov/pubmed/33067435)
-
-- Jeong, Kyowon; Kim, Jihyung; Gaikwad, Manasi; Hidayah, Siti Nurul; Heikaus, Laura; Schlüter, Hartmut; Kohlbacher, Oliver; *FLASHDeconv: ultrafast, high-quality feature deconvolution for top-down proteomics*. Cell Systems. 2020
-
-- Nothias, Louis-Félix; Petras, Daniel; Schmid, Robin; Dührkop, Kai; Rainer, Johannes; Sarvepalli, Abinesh; Protsyuk, Ivan; Ernst, Madeleine; Tsugawa, Hiroshi; Fleischauer, Markus; *Feature-based molecular networking in the GNPS analysis environment*. Nature methods. 2020
-
-- Rurik, Marc; Alka, Oliver; Aicheler, Fabian; Kohlbacher, Oliver; *Metabolomics data processing using OpenMS*. Computational Methods and Data Analysis for Metabolomics. 2020
-
-- Netz, Eugen; Dijkstra, Tjeerd MH; Sachsenberg, Timo; Zimmermann, Lukas; Walzer, Mathias; Monecke, Thomas; Ficner, Ralf; Dybkov, Olexandr; Urlaub, Henning; Kohlbacher, Oliver; *OpenPepXL: an open-source tool for sensitive identification of cross-linked peptides in XL-MS*. Molecular & Cellular Proteomics. 2020. [Link](https://www.ncbi.nlm.nih.gov/pubmed/33067342)
-
-- Scheidt, Tamara; Alka, Oliver; Gonczarowska-Jorge, Humberto; Gruber, Wolfgang; Rathje, Florian; Dell’Aica, Margherita; Rurik, Marc; Kohlbacher, Oliver; Zahedi, René P; Aberger, Fritz; *Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells*. Cell Communication and Signaling. 2020
-
-- Kutuzova, Svetlana; Colaianni, Pasquale; Rost, Hannes; Sachsenberg, Timo; Alka, Oliver; Kohlbacher, Oliver; Burla, Bo; Torta, Federico; Schrubbers, Lars; Kristensen, Mette; *SmartPeak automates targeted and quantitative metabolomics data processing*. Analytical Chemistry. 2020. [Link](https://www.ncbi.nlm.nih.gov/pubmed/33269929)
-
-- Starke, Robert; Oliphant, Kaitlyn; Jehmlich, Nico; Schäpe, Stephanie Serena; Sachsenberg, Timo; Kohlbacher, Oliver; Allen-Vercoe, Emma; von Bergen, Martin; *Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities*. Journal of Proteomics. 2020
-***
-## 2019
-
-
-- Pfeuffer, Julianus; Sachsenberg, Timo; Dijkstra, Tjeerd MH; Serang, Oliver; Reinert, Knut; Kohlbacher, Oliver; *EPIFANY-A method for efficient high-confidence protein inference*. Journal of proteome research. 2019
-
-- Cain, Nicolas; Alka, Oliver; Segelke, Torben; von Wuthenau, Kristian; Kohlbacher, Oliver; Fischer, Markus; *Food fingerprinting: Mass spectrometric determination of the cocoa shell content (Theobroma cacao L.) in cocoa products by HPLC-QTOF-MS*. Food chemistry. 2019. [Link](https://www.ncbi.nlm.nih.gov/pubmed/31260999)
-
-- Bichmann, Leon; Nelde, Annika; Ghosh, Michael; Heumos, Lukas; Mohr, Christopher; Peltzer, Alexander; Kuchenbecker, Leon; Sachsenberg, Timo; Walz, Juliane S; Stevanovic, Stefan; *MHCquant: automated and reproducible data analysis for immunopeptidomics*. Journal of proteome research. 2019. [Link](https://www.ncbi.nlm.nih.gov/pubmed/31589052)
-
-- Löffler, Markus W; Mohr, Christopher; Bichmann, Leon; Freudenmann, Lena Katharina; Walzer, Mathias; Schroeder, Christopher M; Trautwein, Nico; Hilke, Franz J; Zinser, Raphael S; Mühlenbruch, Lena; *Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma*. Genome medicine. 2019. [Link](https://www.ncbi.nlm.nih.gov/pubmed/31039795)
-
-- Gruening, Bjorn; Sallou, Olivier; Moreno, Pablo; da Veiga Leprevost, Felipe; Ménager, Hervé; Søndergaard, Dan; Röst, Hannes; Sachsenberg, Timo; O'connor, Brian; Madeira, Fábio; *Recommendations for the packaging and containerizing of bioinformatics software*. F1000Research. 2019. [Link](https://www.ncbi.nlm.nih.gov/pubmed/31543945)
-
-- Hulstaert, Niels; Shofstahl, Jim; Sachsenberg, Timo; Walzer, Mathias; Barsnes, Harald; Martens, Lennart; Perez-Riverol, Yasset; *ThermoRawFileParser: modular, scalable, and cross-platform RAW file conversion*. Journal of proteome research. 2019. [Link](https://www.ncbi.nlm.nih.gov/pubmed/31755270)
-
-- Licha, David; Vidali, Silvia; Aminzadeh-Gohari, Sepideh; Alka, Oliver; Breitkreuz, Leander; Kohlbacher, Oliver; Reischl, Roland J; Feichtinger, René G; Kofler, Barbara; Huber, Christian G; *Untargeted metabolomics reveals molecular effects of ketogenic diet on healthy and tumor xenograft mouse models*. International journal of molecular sciences. 2019. [Link](https://www.ncbi.nlm.nih.gov/pubmed/31398922)
-***
-## 2018
-
-
-- Kahles, André; Lehmann, Kjong-Van; Toussaint, Nora C; Hüser, Matthias; Stark, Stefan G; Sachsenberg, Timo; Stegle, Oliver; Kohlbacher, Oliver; Sander, Chris; Caesar-Johnson, Samantha J; *Comprehensive analysis of alternative splicing across tumors from 8,705 patients*. Cancer cell. 2018. [Link](https://www.ncbi.nlm.nih.gov/pubmed/30078747)
-***
-## 2017
-
-
-- Röst, Hannes L; Aebersold, Ruedi; Schubert, Olga T; *Automated SWATH data analysis using targeted extraction of ion chromatograms*. Proteomics: Methods and Protocols. 2017. [Link](https://www.ncbi.nlm.nih.gov/pubmed/28188537)
-
-- da Veiga Leprevost, Felipe; Grüning, Björn A; Alves Aflitos, Saulo; Röst, Hannes L; Uszkoreit, Julian; Barsnes, Harald; Vaudel, Marc; Moreno, Pablo; Gatto, Laurent; Weber, Jonas; *BioContainers: an open-source and community-driven framework for software standardization*. Bioinformatics. 2017. [Link](https://www.ncbi.nlm.nih.gov/pubmed/28379341)
-
-- Audain, Enrique; Uszkoreit, Julian; Sachsenberg, Timo; Pfeuffer, Julianus; Liang, Xiao; Hermjakob, Henning; Sanchez, Aniel; Eisenacher, Martin; Reinert, Knut; Tabb, David L; *In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics*. Journal of proteomics. 2017. [Link](https://www.ncbi.nlm.nih.gov/pubmed/27498275)
-
-- Pfeuffer, Julianus; Sachsenberg, Timo; Alka, Oliver; Walzer, Mathias; Fillbrunn, Alexander; Nilse, Lars; Schilling, Oliver; Reinert, Knut; Kohlbacher, Oliver; *OpenMS–a platform for reproducible analysis of mass spectrometry data*. Journal of biotechnology. 2017
-
-- Weisser, Hendrik; Choudhary, Jyoti S; *Targeted feature detection for data-dependent shotgun proteomics*. Journal of proteome research. 2017
-
-- Vizcaíno, Juan Antonio; Mayer, Gerhard; Perkins, Simon R; Barsnes, Harald; Vaudel, Marc; Perez-Riverol, Yasset; Ternent, Tobias; Uszkoreit, Julian; Eisenacher, Martin; Fischer, Lutz; *The mzIdentML data standard version 1.2, supporting advances in proteome informatics*. Molecular & Cellular Proteomics. 2017
-***
-## 2016
-
-
-- Navarro, Pedro; Kuharev, Jörg; Gillet, Ludovic C; Bernhardt, Oliver M; MacLean, Brendan; Röst, Hannes L; Tate, Stephen A; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; *A multicenter study benchmarks software tools for label-free proteome quantification*. Nature biotechnology. 2016. [Link](https://www.ncbi.nlm.nih.gov/pubmed/27701404)
-
-- Weisser, Hendrik; Wright, James C; Mudge, Jonathan M; Gutenbrunner, Petra; Choudhary, Jyoti S; *Flexible data analysis pipeline for high-confidence proteogenomics*. Journal of Proteome Research. 2016. [Link](https://www.ncbi.nlm.nih.gov/pubmed/27786492)
-
-- Veit, Johannes; Sachsenberg, Timo; Chernev, Aleksandar; Aicheler, Fabian; Urlaub, Henning; Kohlbacher, Oliver; *LFQProfiler and RNPxl: open-source tools for label-free quantification and protein–RNA cross-linking integrated into proteome discoverer*. Journal of proteome research. 2016. [Link](https://www.ncbi.nlm.nih.gov/pubmed/27476824)
-
-- Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; *OpenMS: a flexible open-source software platform for mass spectrometry data analysis*. Nature methods. 2016
-
-- Perez-Riverol, Yasset; Gatto, Laurent; Wang, Rui; Sachsenberg, Timo; Uszkoreit, Julian; da Veiga Leprevost, Felipe; Fufezan, Christian; Ternent, Tobias; Eglen, Stephen J; Katz, Daniel S; *Ten simple rules for taking advantage of Git and GitHub*. PLoS computational biology. 2016
-***
-## 2015
-
-
-- Röst, Hannes L; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars; *Efficient visualization of high-throughput targeted proteomics experiments: TAPIR*. Bioinformatics. 2015. [Link](https://www.ncbi.nlm.nih.gov/pubmed/25788625)
-
-- Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars; *Fast and efficient XML data access for next-generation mass spectrometry*. PloS one. 2015. [Link](https://www.ncbi.nlm.nih.gov/pubmed/25927999)
-
-- Sachsenberg, Timo; Herbst, Florian-Alexander; Taubert, Martin; Kermer, Rene; Jehmlich, Nico; Von Bergen, Martin; Seifert, Jana; Kohlbacher, Oliver; *MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics*. Journal of proteome research. 2015. [Link](https://www.ncbi.nlm.nih.gov/pubmed/25412983)
-
-- Ranninger, Christina; Rurik, Marc; Limonciel, Alice; Ruzek, Silke; Reischl, Roland; Wilmes, Anja; Jennings, Paul; Hewitt, Philip; Dekant, Wolfgang; Kohlbacher, Oliver; *Nephron toxicity profiling via untargeted metabolome analysis employing a high performance liquid chromatography-mass spectrometry-based experimental and computational pipeline*. Journal of Biological Chemistry. 2015. [Link](https://www.ncbi.nlm.nih.gov/pubmed/26055719)
-
-- Aicheler, Fabian; Li, Jia; Hoene, Miriam; Lehmann, Rainer; Xu, Guowang; Kohlbacher, Oliver; *Retention time prediction improves identification in nontargeted lipidomics approaches*. Analytical chemistry. 2015. [Link](https://www.ncbi.nlm.nih.gov/pubmed/26145158)
-
-- Nilse, Lars; Sigloch, Florian Christoph; Biniossek, Martin L; Schilling, Oliver; *Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling*. PROTEOMICS–Clinical Applications. 2015. [Link](https://www.ncbi.nlm.nih.gov/pubmed/25931027)
-
-- Aiche, Stephan; Sachsenberg, Timo; Kenar, Erhan; Walzer, Mathias; Wiswedel, Bernd; Kristl, Theresa; Boyles, Matthew; Duschl, Albert; Huber, Christian G; Berthold, Michael R; *Workflows for automated downstream data analysis and visualization in large‐scale computational mass spectrometry*. Proteomics. 2015
-***
-## 2014
-
-
-- Kenar, Erhan; Franken, Holger; Forcisi, Sara; Wörmann, Kilian; Häring, Hans-Ulrich; Lehmann, Rainer; Schmitt-Kopplin, Philippe; Zell, Andreas; Kohlbacher, Oliver; *Automated label-free quantification of metabolites from liquid chromatography–mass spectrometry data*. Molecular & Cellular Proteomics. 2014. [Link](https://www.ncbi.nlm.nih.gov/pubmed/24176773)
-
-- Röst, Hannes L; Rosenberger, George; Navarro, Pedro; Gillet, Ludovic; Miladinović, Saša M; Schubert, Olga T; Wolski, Witold; Collins, Ben C; Malmström, Johan; Malmström, Lars; *OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data*. Nature biotechnology. 2014
-
-- Kramer, Katharina; Sachsenberg, Timo; Beckmann, Benedikt M; Qamar, Saadia; Boon, Kum-Loong; Hentze, Matthias W; Kohlbacher, Oliver; Urlaub, Henning; *Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins*. Nature methods. 2014. [Link](https://www.ncbi.nlm.nih.gov/pubmed/25173706)
-
-- Griss, Johannes; Jones, Andrew R; Sachsenberg, Timo; Walzer, Mathias; Gatto, Laurent; Hartler, Jürgen; Thallinger, Gerhard G; Salek, Reza M; Steinbeck, Christoph; Neuhauser, Nadin; *The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience*. Molecular & Cellular Proteomics. 2014. [Link](https://www.ncbi.nlm.nih.gov/pubmed/24980485)
-
-- Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars; *pyOpenMS: a Python‐based interface to the OpenMS mass‐spectrometry algorithm library*. Proteomics. 2014
-
-- Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk WP; Staes, An; Vandenbussche, Jonathan; *qcML: an exchange format for quality control metrics from mass spectrometry experiments*. Molecular & Cellular Proteomics. 2014. [Link](https://www.ncbi.nlm.nih.gov/pubmed/24760958)
-***
-## 2013
-
-
-- Weisser, Hendrik; Nahnsen, Sven; Grossmann, Jonas; Nilse, Lars; Quandt, Andreas; Brauer, Hendrik; Sturm, Marc; Kenar, Erhan; Kohlbacher, Oliver; Aebersold, Ruedi; *An automated pipeline for high-throughput label-free quantitative proteomics*. Journal of proteome research. 2013
-
-- Walzer, Mathias; Qi, Da; Mayer, Gerhard; Uszkoreit, Julian; Eisenacher, Martin; Sachsenberg, Timo; Gonzalez-Galarza, Faviel F; Fan, Jun; Bessant, Conrad; Deutsch, Eric W; *The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics*. Molecular & Cellular Proteomics. 2013
-
-- Nahnsen, Sven; Bielow, Chris; Reinert, Knut; Kohlbacher, Oliver; *Tools for label-free peptide quantification*. Molecular & Cellular Proteomics. 2013
-***
-## 2012
-
-
-- Nahnsen, Sven; Kohlbacher, Oliver; *In silico design of targeted SRM-based experiments*. BMC bioinformatics. 2012. [Link](https://www.ncbi.nlm.nih.gov/pubmed/23176520)
-
-- Junker, Johannes; Bielow, Chris; Bertsch, Andreas; Sturm, Marc; Reinert, Knut; Kohlbacher, Oliver; *TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data*. Journal of proteome research. 2012. [Link](https://www.ncbi.nlm.nih.gov/pubmed/22583024)
-
-- Jones, Andrew R; Eisenacher, Martin; Mayer, Gerhard; Kohlbacher, Oliver; Siepen, Jennifer; Hubbard, Simon J; Selley, Julian N; Searle, Brian C; Shofstahl, James; Seymour, Sean L; *The mzIdentML data standard for mass spectrometry-based proteomics results*. Molecular & cellular proteomics. 2012
-***
-## 2011
-
-
-- Bielow, Chris; Aiche, Stephan; Andreotti, Sandro; Reinert, Knut; *MSSimulator: Simulation of mass spectrometry data*. Journal of proteome research. 2011. [Link](https://www.ncbi.nlm.nih.gov/pubmed/21526843)
-
-- Bertsch, Andreas; Gröpl, Clemens; Reinert, Knut; Kohlbacher, Oliver; *OpenMS and TOPP: open source software for LC-MS data analysis*. Data Mining in Proteomics: From Standards to Applications. 2011
-
-- Nahnsen, Sven; Bertsch, Andreas; Rahnenführer, Jörg; Nordheim, Alfred; Kohlbacher, Oliver; *Probabilistic consensus scoring improves tandem mass spectrometry peptide identification*. Journal of proteome research. 2011. [Link](https://www.ncbi.nlm.nih.gov/pubmed/21644507)
-***
-## 2010
-
-
-- Bertsch, Andreas; Jung, Stephan; Zerck, Alexandra; Pfeifer, Nico; Nahnsen, Sven; Henneges, Carsten; Nordheim, Alfred; Kohlbacher, Oliver; *Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics*. Journal of proteome research. 2010. [Link](https://www.ncbi.nlm.nih.gov/pubmed/20201589)
-
-- Gesing, Sandra; van Hemert, Jano; Koetsier, Jos; Bertsch, Andreas; Kohlbacher, Oliver; *TOPP goes Rapid The OpenMS Proteomics Pipeline in a Grid-Enabled Web Portal*. Proceedings of the 2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing. 2010
-***
-## 2009
-
-
-- Bertsch, Andreas; Leinenbach, Andreas; Pervukhin, Anton; Lubeck, Markus; Hartmer, Ralf; Baessmann, Carsten; Elnakady, Yasser Abbas; Müller, Rolf; Böcker, Sebastian; Huber, Christian G; *De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation*. Electrophoresis. 2009
-
-- Pfeifer, Nico; Leinenbach, Andreas; Huber, Christian G; Kohlbacher, Oliver; *Improving peptide identification in proteome analysis by a two-dimensional retention time filtering approach*. Journal of proteome research. 2009. [Link](https://www.ncbi.nlm.nih.gov/pubmed/19492844)
-
-- Reinert, Knut; Kohlbacher, Oliver; *OpenMS and TOPP: open source software for LC-MS data analysis*. Proteome Bioinformatics. 2009
-
-- Nilse, Lars; Sturm, Marc; Trudgian, David; Salek, Mogjiborahman; Sims, Paul FG; Carroll, Kathleen M; Hubbard, Simon J; *SILACAnalyzer-a tool for differential quantitation of stable isotope derived data*. International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics. 2009
-
-- Sturm, Marc; Kohlbacher, Oliver; *TOPPView: an open-source viewer for mass spectrometry data*. Journal of proteome research. 2009. [Link](https://www.ncbi.nlm.nih.gov/pubmed/19425593)
-***
-## 2008
-
-
-- Lange, Eva; *Analysis of mass spectrometric data: peak picking and map alignment*. Freie Universtaet Berlin. 2008
-
-- Schulz-Trieglaff, Ole; Hussong, Rene; Gröpl, Clemens; Leinenbach, Andreas; Hildebrandt, Andreas; Huber, Christian; Reinert, Knut; *Computational quantification of peptides from LC-MS data*. Journal of Computational Biology. 2008
-
-- Lange, Eva; Tautenhahn, Ralf; Neumann, Steffen; Gröpl, Clemens; *Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements*. BMC bioinformatics. 2008. [Link](https://www.ncbi.nlm.nih.gov/pubmed/18793413)
-
-- Schulz-Trieglaff, Ole; Pfeifer, Nico; Gröpl, Clemens; Kohlbacher, Oliver; Reinert, Knut; *LC-MSsim–a simulation software for liquid chromatography mass spectrometry data*. BMC bioinformatics. 2008. [Link](https://www.ncbi.nlm.nih.gov/pubmed/18842122)
-
-- Sturm, Marc; Bertsch, Andreas; Gröpl, Clemens; Hildebrandt, Andreas; Hussong, Rene; Lange, Eva; Pfeifer, Nico; Schulz-Trieglaff, Ole; Zerck, Alexandra; Reinert, Knut; *OpenMS–an open-source software framework for mass spectrometry*. BMC bioinformatics. 2008
-***
-## 2007
-
-
-- Schulz-Trieglaff, Ole; Hussong, Rene; Gröpl, Clemens; Hildebrandt, Andreas; Reinert, Knut; *A fast and accurate algorithm for the quantification of peptides from mass spectrometry data*. Research in Computational Molecular Biology: 11th Annual International Conference, RECOMB 2007, Oakland, CA, USA, April 21-25, 2007. Proceedings 11. 2007
-
-- Lange, Eva; Gröpl, Clemens; Schulz-Trieglaff, Ole; Leinenbach, Andreas; Huber, Christian; Reinert, Knut; *A geometric approach for the alignment of liquid chromatography—mass spectrometry data*. Bioinformatics. 2007
-
-- Sturm, Marc; *TOPP The OpenMS Proteomics Pipeline*. Proceedings of the 5th European. 2007
-
-- Kohlbacher, Oliver; Reinert, Knut; Gröpl, Clemens; Lange, Eva; Pfeifer, Nico; Schulz-Trieglaff, Ole; Sturm, Marc; *TOPP—the OpenMS proteomics pipeline*. Bioinformatics. 2007. [Link](https://www.ncbi.nlm.nih.gov/pubmed/17237091)
-***
-## 2006
-
-
-- Lange, Eva; Gröpl, Clemens; Reinert, Knut; Kohlbacher, Oliver; Hildebrandt, Andreas; *High-accuracy peak picking of proteomics data using wavelet techniques*. Biocomputing 2006. 2006. [Link](https://www.ncbi.nlm.nih.gov/pubmed/17094243)
-***
-## 2005
-
-
-- Groepl, Clemens; Lange, Eva; Reinert, Knut; Kohlbacher, Oliver; Sturm, Marc; Huber, Christian G; Mayr, Bettina M; Klein, Christoph L; *Absolute quantification of myoglobin content in blood serum using HPLC/MS through automatic bioinformatics analysis*. MOLECULAR & CELLULAR PROTEOMICS. 2005
-
-- Gröpl, Clemens; Lange, Eva; Reinert, Knut; Kohlbacher, Oliver; Sturm, Marc; Huber, Christian G; Mayr, Bettina M; Klein, Christoph L; *Algorithms for the automated absolute quantification of diagnostic markers in complex proteomics samples*. Computational Life Sciences: First International Symposium, CompLife 2005, Konstanz, Germany, September 25-27, 2005. Proceedings 1. 2005
-
-- Lange, E; Reinert, K; Groepl, C; Kohlbacher, O; Sturm, M; Hildebrandt, A; *OPENMS; a generic open source framework for chromatography/MS-based proteomics*. Molecular & Cellular Proteomics. 2005
-
-- Gröpl, C; Hildebrandt, A; Kohlbacher, O; Lange, E; Lövenich, S; Sturm, M; *OpenMS-Software for Mass Spectrometry*. Poster presented at the MBI Workshop on Computational Proteomics and Mass Spectrometry. 2005
-***
+---
+title: Publications
+sidebar: false
+hideShortcuts: true
+hidePageTitle: true
+---
+
+
+
+
+
+
+
pyopenms_viz
+
+ Seamless plotting directly from pandas dataframes.
+
+
+ Create spectra, chromatograms, and more from just a single line of code.
+
+ df.plot()
+
+
+
+
+
+
+ {{< pyopenms-viz-developers >}}
+
+
diff --git a/content/en/pyopenms.md b/content/en/pyopenms.md
new file mode 100644
index 00000000..931bbaf5
--- /dev/null
+++ b/content/en/pyopenms.md
@@ -0,0 +1,49 @@
+---
+title: pyOpenMS
+hidePageTitle: true
+hideShortcuts: true
+sidebar: false
+---
+
+
+
+
+
+
+
pyOpenMS
+
+ Python bindings for mass spectrometry.
+
+
+ Python bindings to OpenMS-lib. Write custom analysis scripts and integrate OpenMS into Python workflows.
+
+
+
+
+
+
+ {{< pyopenms-highlights >}}
+
+
+ {{< pyopenms-getting-started >}}
+
+
+ {{< pyopenms-developers >}}
+
+
diff --git a/content/en/research-partnerships.md b/content/en/research-partnerships.md
new file mode 100644
index 00000000..7671d057
--- /dev/null
+++ b/content/en/research-partnerships.md
@@ -0,0 +1,82 @@
+---
+title: Research Partnerships
+hidePageTitle: true
+hideShortcuts: true
+sidebar: false
+---
+
+
+
+
+
+
+
OpenMS WebApps
+
+ Build a WebApp to showcase your pipeline.
+
+
+
+
+
+
+ {{< webapps-highlights >}}
+
+
+ {{< webapps-using-template >}}
+
+
+ {{< webapps-developers >}}
+
+
diff --git a/data/community_events.yaml b/data/community_events.yaml
new file mode 100644
index 00000000..de4ab2fb
--- /dev/null
+++ b/data/community_events.yaml
@@ -0,0 +1,69 @@
+# Community calendar — edit this file to add or update events (see docs/common-tasks/update-community-calendar.md)
+events:
+ - title: OpenMS Developer Meeting 2026
+ start: 2026-03-23
+ end: 2026-03-27
+ location: Piotrowice Nyskie Palace, Otmuchów, Poland
+ category: developer-meeting
+ summary: Annual developer meeting with talks, tutorials, and code sprints.
+ url: https://docs.google.com/forms/d/1tyg3uMQoidQ45C7lUqic9GF-AqDCs5cBdIyOzfrl_uA/edit
+ news_url: /news/devmeeting2026/
+
+ - title: OpenMS/CIBI workshops — South Africa
+ start: 2026-02-09
+ end: 2026-02-20
+ location: South Africa
+ category: workshop
+ summary: Four two-day workshops on metabolomics and proteomics for plant biotechnology.
+ news_url: /news/south_africa_roadshow_2026/
+
+ - title: Workshop at University of Helsinki
+ start: 2026-04-30
+ location: University of Helsinki, Finland
+ category: workshop
+ summary: One-day workshop on MS analysis with OpenMS and OpenDIAKiosk.
+ news_url: /news/helsinki_workshop_2026/
+
+ - title: Google Summer of Code 2026
+ start: 2026-06-01
+ end: 2026-08-31
+ location: Remote
+ category: outreach
+ summary: Students collaborate with mentors on OpenMS features, documentation, and tool integrations.
+ news_url: /news/GSoC2026/
+
+ - title: OpenMS Community Code Clinic
+ start: 2026-07-15
+ location: Online
+ category: outreach
+ summary: Drop-in session for workflow questions, troubleshooting, and getting started as a contributor.
+ news_url: /news/cibi_codeclinic/
+
+ - title: OpenMS Autumn Workshop
+ start: 2026-10-14
+ end: 2026-10-16
+ location: Tübingen, Germany
+ category: workshop
+ summary: Hands-on training on proteomics and metabolomics workflows with OpenMS and TOPP tools.
+
+ - title: OpenMS Developer Meeting 2027
+ start: 2027-03-15
+ end: 2027-03-19
+ location: To be announced
+ category: developer-meeting
+ summary: Annual developer meeting with tutorials, talks, and code sprints.
+
+ - title: OpenMS Open House 2025
+ start: 2025-11-09
+ location: University of Toronto, Canada
+ category: outreach
+ summary: Drop-in session on computational mass spectrometry and open-source development.
+ news_url: /news/openhouse2025/
+
+ - title: OpenMS Developer Meeting 2025
+ start: 2025-03-17
+ end: 2025-03-21
+ location: Xewkija, Gozo, Malta
+ category: developer-meeting
+ summary: Developer meeting with tutorials and code sprints.
+ news_url: /news/devmeeting2025/
diff --git a/docs/README.md b/docs/README.md
new file mode 100644
index 00000000..6916f266
--- /dev/null
+++ b/docs/README.md
@@ -0,0 +1,86 @@
+# OpenMS website — maintainer documentation
+
+This guide is for **non–front-end contributors** who update [openms.de](https://openms.de) content: news, text pages, homepage copy, and configuration. You do not need to know React, Vue, or JavaScript for most tasks.
+
+## How the site works (30 seconds)
+
+- The site is built with **[Hugo](https://gohugo.io/)** — a static site generator.
+- **Pages** live as Markdown files under `content/en/`.
+- **Homepage sections** (hero, banner, webapps list, footer links, etc.) live mainly in **`config.yaml`** under `params`.
+- **Layout and styling** live in `layouts/` and `assets/css/` — only change these if you are doing design or structure work (ask the web team first).
+- Changes are merged on GitHub; **Netlify** builds and deploys the live site.
+
+## I want to…
+
+| Task | Guide |
+|------|--------|
+| Add or edit a news article | [Add a news post](common-tasks/add-news-post.md) |
+| Add or update community calendar events | [Update the community calendar](common-tasks/update-community-calendar.md) |
+| Change the yellow announcement bar on the homepage | [Update the news banner](common-tasks/update-news-banner.md) |
+| Change homepage headline, stats, or “What is OpenMS?” | [Edit the homepage hero & key features](common-tasks/edit-homepage-hero.md) |
+| Add or reorder a project on the homepage carousel | [Add a webapp to the homepage](common-tasks/add-webapp-to-homepage.md) |
+| Change footer links, navbar, or social links | [Edit footer or navbar](common-tasks/edit-footer-or-navbar.md) |
+| Add or remove a sponsor logo | [Update sponsors](common-tasks/update-sponsors.md) |
+| Set up Zeffy on the donate page | [Configure the donate page (Zeffy)](common-tasks/configure-donate-zeffy.md) |
+| Edit About, Contribute, Governance, etc. | [Edit a page](common-tasks/edit-a-page.md) |
+| Add or replace an image | [Add images](common-tasks/add-images.md) |
+| Preview the site on my computer | [Preview locally](getting-started/preview-locally.md) |
+| Edit without installing anything | [Edit via GitHub](getting-started/edit-via-github.md) |
+| Open a pull request | [Pull requests](workflow/pull-requests.md) |
+| Understand what happens when we merge | [Deployment](workflow/deployment.md) |
+| Find who can approve or help | [Who to ask](workflow/who-to-ask.md) |
+
+## What you can change safely
+
+| Level | Folders / files | Typical edits |
+|-------|-----------------|---------------|
+| **Safe** | `content/en/**/*.md` | News, about text, application guides |
+| **Config** | `config.yaml` (`languages.en.params`) | Hero, banner, webapps, footer, trusted-by list |
+| **Ask first** | `layouts/`, `assets/css/`, `static/js/` | Layout, colors, partner marquee HTML |
+| **Do not edit** | `themes/scientific-python-hugo-theme/` | Upstream theme (use overrides in `layouts/` instead) |
+
+## Documentation map
+
+```
+docs/
+├── README.md ← you are here
+├── getting-started/
+│ ├── preview-locally.md
+│ └── edit-via-github.md
+├── common-tasks/
+│ ├── add-news-post.md
+│ ├── update-news-banner.md
+│ ├── edit-homepage-hero.md
+│ ├── add-webapp-to-homepage.md
+│ ├── edit-footer-or-navbar.md
+│ ├── update-sponsors.md
+│ ├── edit-a-page.md
+│ └── add-images.md
+├── reference/
+│ ├── content-front-matter.md
+│ ├── config-yaml-guide.md
+│ ├── shortcodes.md
+│ └── file-locations.md
+├── workflow/
+│ ├── pull-requests.md
+│ ├── deployment.md
+│ └── who-to-ask.md
+└── troubleshooting/
+ └── common-errors.md
+```
+
+## Quick start (no local install)
+
+1. Open the file you need on GitHub (e.g. `content/en/news/my-post.md` or `config.yaml`).
+2. Click **Edit** (pencil) or create a new file on a branch.
+3. Save and open a **pull request**.
+4. Wait for the **Netlify deploy preview** on the PR (see [Pull requests](workflow/pull-requests.md)).
+5. Ask a web-team reviewer to merge.
+
+For local preview, see [Preview locally](getting-started/preview-locally.md).
+
+## Related links
+
+- Developer setup (short): [README.md](../README.md) in the repo root
+- OpenMS software docs: [openms.readthedocs.io](https://openms.readthedocs.io/)
+- Hugo docs (advanced): [gohugo.io/documentation](https://gohugo.io/documentation/)
diff --git a/docs/common-tasks/add-images.md b/docs/common-tasks/add-images.md
new file mode 100644
index 00000000..e8b10e59
--- /dev/null
+++ b/docs/common-tasks/add-images.md
@@ -0,0 +1,59 @@
+# Add images
+
+Static files are served from the **`static/`** folder. A file at `static/images/foo.png` is available on the site as **`/images/foo.png`**.
+
+## Where to put images
+
+| Use case | Suggested path |
+|----------|----------------|
+| Logos, general | `static/images/logos/` |
+| Webapp / project logos | `static/images/webapp/logo/` |
+| Application guide screenshots | `static/images/content_images/applications/` |
+| Homepage / hero (referenced by filename in config) | Often `static/images/` or theme assets — match existing entries in `config.yaml` |
+| Favicon | `static/images/favicon.png` |
+
+## Reference in Markdown (content pages)
+
+Use the theme **figure** shortcode:
+
+```markdown
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