Galaxy Mass Spectrometry Community - SIG Page first version

content/community/sig/mass-spectrometry/index.md

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+---
+description: "Users, developers, and trainers providing feedback and energy to improve and expand the Galaxy mass spectrometry capabilities."
+autotoc: true
+title: "Galaxy Mass Spectrometry Community (GMSC)"
+---
+
+<slot name="/community/sig/common_linkbox" />
+
+<!-- <img class="img-fluid float-right" src="/community/sig/mass-spectrometry/GalaxyP_logo.png" style="width:200px;" alt="Logo for Galaxy mass spectrometry community."/> -->
+
+## Welcome to the Galaxy Mass Spectrometry Community!
+
+**An Open and Collaborative Community**
+
+We are a vibrant and inclusive network of researchers, developers, and trainers dedicated to advancing the fields of proteomics, metabolomics, exposomics and everything mass spec! Our community is committed to fostering open, reproducible, and accessible research through the use of Galaxy.
+
+**Our Mission**
+
+We believe in the power of collaboration and the importance of sharing knowledge. 
+
+Our mission is to:
+
+- develop a set of well-documented and tested tools for the analysis of mass spectrometry data (both LC-MS/MS and GC-MS/MS),
+- support researchers in their quest to understand complex biological systems using the MS. We provide workflows for various -omics to analyze complex MS data,
+- provide comprehensive training materials describing such tools and workflows,
+- facilitate a collaboration across pipelines and tools,
+- conduct a research in an open and reproducible manner.
+
+**How do we function?**
+
+**Meetings** We meet every 2-3 months. There are two meetings in one day, one for the EU and one for AU time zone - you can choose the one that suits you more or join both! 
+
+<!-- **Emails** We send out emails to the mailing list after each meeting, at the mid-way point between meetings, and the day before meetings as a reminder. -->
+
+**Notes** We keep rolling notes on a googledoc and monitor our work in a github project.
+
+**Chat Forum** We have a chat forum on [Matrix](https://matrix.to/#/#galaxyproject_mass-spectrometry:matrix.org), where you can discuss news and ideas or ask for a help. 
+
+
+
+<!-- <iframe src="https://calendar.google.com/calendar/embed?height=600&wkst=1&bgcolor=%239E69AF&ctz=Europe%2FBerlin&title=Galaxy%20Single%20Cell%20Community%20of%20Practice&showNav=1&showPrint=0&showTabs=1&showCalendars=0&mode=AGENDA&src=Z2FsYXh5LnNjLmNvcEBnbWFpbC5jb20&color=%23039BE5" style="border:solid 1px #777" width="800" height="300" frameborder="0" scrolling="no"></iframe> -->
+
+
+**Join Us!**
+
+We invite you to become a part of our community! Whether you are a seasoned researcher or just starting, there are numerous opportunities to connect, learn, and contribute. Everybody with an interest in mass spectrometry is welcome!
+
+Follow us on [Twitter](https://x.com/usegalaxyp)
+
+## I would like to... 
+
+## ... analyze my MS data!
+
+You can start with the [introduction to proteomics](https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/introduction/slides.html#1) or [introduction to metabolomics](https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/introduction/slides.html#1). Then follow with other tutorials: analysis of [proteomic](https://training.galaxyproject.org/training-material/topics/proteomics/) or [metabolomic](https://training.galaxyproject.org/training-material/topics/metabolomics/) data in Galaxy.
+
+Also, the GalaxyP team provides slides to [conference talks](https://galaxyp.org/conference-presentations/#presentations) or materials from [workshops](https://galaxyp.org/workshops/).
+
+## ... learn more about Galaxy!
+
+If you are completely new to Galaxy, these two tutorials are great point to start!
+
+- [Introduction to Galaxy Analyses](https://training.galaxyproject.org/training-material/topics/introduction/)
+- [Using Galaxy and Managing your Data](https://training.galaxyproject.org/training-material/topics/galaxy-interface/)
+
+## ... develop new tools!
+
+We keep all the source code on Github:
+
+- General [Galaxy repository](https://github.com/galaxyproject).
+- Github repository for [proteomics tools](https://github.com/galaxyproteomics)
+- Github repository for metabolomics tools from [workflow4metabolomics](https://github.com/workflow4metabolomics/tools-metabolomics)
+- GitHub repository for functional exposomics at [RECETOX](https://github.com/RECETOX/galaxytools).
+
+To start with the new tools development, check out the [development training materials](https://training.galaxyproject.org/training-material/topics/dev/) 
+
+## ... contribute to trainings!
+
+If you would like to create new training materials or hold a training at your institute - we obviously have a [training](https://training.galaxyproject.org/training-material/topics/contributing/) for that!
+
+## ... participate in events!
+
+Events related to MS data processing will be published here.
+
+## Important links
+
+ - <i class="fa fa-book" aria-hidden="true"></i>&nbsp; &nbsp;[Proteomics training material](https://training.galaxyproject.org/training-material/topics/proteomics/)
+ - <i class="fa fa-book" aria-hidden="true"></i>&nbsp; &nbsp;[Metabolomics training material](https://training.galaxyproject.org/training-material/topics/metabolomics/)
+ - <i class="fa fa-tv" aria-hidden="true"></i>&nbsp;&nbsp; [Proteomics Galaxy instance](https://proteomics.usegalaxy.eu/)
+ - <i class="fa fa-question-circle-o" aria-hidden="true"></i>&nbsp; &nbsp;[Metabolomics help forum](https://help.galaxyproject.org/tag/metabolomics)
+ - <i class="fa fa-comments-o" aria-hidden="true"></i>&nbsp; &nbsp;[Mass spectrometry user community chat room](https://matrix.to/#/#galaxyproject_mass-spectrometry:matrix.org)
+ <!-- - <i class="fa fa-calendar" aria-hidden="true"></i>&nbsp;&nbsp; [Google Calendar](https://calendar.google.com/calendar/embed?src=galaxy.sc.cop%40gmail.com&ctz=Europe%2FLondon) <-- Subscribe! -->
+ - <i class="fa fa-list-alt" aria-hidden="true"></i>&nbsp;&nbsp; [Meeting Notes doc](https://docs.google.com/document/d/1EvGFC39qT8tp-TbLqlXGZehgPm0VXZEYnlac13gBXO0/edit) <--- There's a section here called 'New here?' that gives tips on how to start contributing as well!
+
+## Recent publications
+
+- Hecht, H., Rojas, W. Y., Ahmad, Z., Křenek, A., Klánová, J., & Price, E. J. (2024). Quantum Chemistry-Based Prediction of Electron Ionization Mass Spectra for Environmental Chemicals. Analytical Chemistry, 96(33), 13652–13662. [link](https://doi.org/10.1021/acs.analchem.4c02589)
+- Galvis, J., Guyon, J., Dartigues, B., Hecht, H., Grüning, B., Specque, F., Soueidan, H., Karkar, S., Daubon, T., & Nikolski, M. (2024). DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data. Bioinformatics, 40(5). [link](https://doi.org/10.1093/bioinformatics/btae282)
+- Metaproteomics for Coinfections in the Upper Respiratory Tract: The Case of COVID-19. Bihani S et al. (2024) doi: 10.1007/978-1-0716-3910-8_15. [link](https://pubmed.ncbi.nlm.nih.gov/38941023/)
+- An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease. Kruk et al. (2024) doi: 10.1128/msystems.00929-23. [link](https://pubmed.ncbi.nlm.nih.gov/38934598/)
+- A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease. Do et al. (2024) doi: 10.1128/msphere.00793-23. [link](https://pubmed.ncbi.nlm.nih.gov/38780289/)
+- The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update. Galaxy Community (2024). doi: 10.1093/nar/gkae410. [link](https://pubmed.ncbi.nlm.nih.gov/38769056/)
+- The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020) Jagtap et al. (2023) doi: 10.7171/3fc1f5fe.a058bad4. [link](https://pubmed.ncbi.nlm.nih.gov/37969874/)
+- A Galaxy of informatics resources for MS-based proteomics. Mehta et al. (2023). doi: 10.1080/14789450.2023.2265062. [link](https://pubmed.ncbi.nlm.nih.gov/37787106/)
+- Create, run, share, publish, and reference your LC–MS, FIA–MS, GC–MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics. Guitton et al. (2017) doi: 10.1016/j.biocel.2017.07.002. [link](https://www.sciencedirect.com/science/article/pii/S1357272517301577?via%3Dihub)
+
+## Key words
+
+Mass Spectrometry
+Proteomics
+Metabolomics
+Data-dependent acquisition
+Data-independent acquisition
+Metaproteomics
+Proteogenomics
+Exposomics
+ELIXIR
+EIRENE

content/projects/mass-spectrometry/index.md

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+---
+description: "Users, developers, and trainers providing feedback and energy to improve and expand the <>."
+autotoc: true
+title: "Galaxy Mass Spectrometry Community of Practice"
+---
+
+We are a mix of users, developers, and trainers providing feedback and energy to improve and expand the processing of mass spectrometry data with Galaxy. Do you use Galaxy in your research? Do you have feedback for us? Want to be a tester of new resources? Want to impact the future of computational mass spectrometry in Galaxy? Are you a developer looking for a place to play? Are you developing Galaxy materials and want to stay aware of what others are doing in this field?
+
+**Welcome to the Galaxy Mass Spectrometry Community of Practice!**
+
+## I'm just trying to learn to analyse my data, how did I get here?
+Hello user! You'll be interested in the following resources:
+
+ - [Learning pathway for getting to grips with Galaxy and <>]()
+ - [Proteomics training material](https://training.galaxyproject.org/training-material/topics/proteomics)
+ - [Metabolomics training material](https://training.galaxyproject.org/training-material/topics/metabolomics)
+ - Galaxy instance: [<> instance]()
+ - [Matrix channel for asking for help](https://matrix.to/#/#galaxyproject_mass-spectrometry:matrix.org)
+
+Saying that, we'd absolutely love to have users feedback on their experiences to help us improve. You'd be very welcome to join the Community of Practice to help improve the processing of mass spectrometry data in Galaxy!
+
+# What are the goals of the Mass Spectrometry community of practice?
+
+🎯Goals
+- Prevent work duplication
+- Collaborate across pipeline, ensuring users feedback to developers
+- Identify community needs
+- Tool & tutorial development
+- Testing
+- Build & support user community
+- <Modify/adapt the above>
+
+# Who are we looking for?
+
+Anyone with energy! We love hearing from users, developers, trainers, and everyone in between who is using or developing Galaxy for mass spectrometry analysis.
+
+# How do we function?
+
+<Change/adapt/edit this section>
+
+We meet every <3 weeks (alternating USA and AU time zones) for 1 hour>.
+
+Our meeting agenda is:
+ - Random intro chatter & introductions
+ - Updates from Trello site (what people are working on / asking for help)
+    - 🐛Help/bugs
+    - Status reports & new stuff that’s happening
+ - Other cool stuff (example: Smorgasbord)
+ - Ongoing actions to send out
+
+We send out emails to the mailing list after each meeting, at the mid-way point between meetings, and the day before meetings as a reminder.
+
+We keep rolling notes on a googledoc and monitor our work on Trello.
+
+When people ask for help or are working across institutes, we set up chat sub-channels to bring them together.
+
+We have a chat forum to discuss news and ideas, and are represented in the Galaxy Community Reps chat group.
+
+# How can you join & other important links
+
+Start by joining our [💬Matrix channel](https://matrix.to/#/#galaxyproject_mass-spectrometry:matrix.org) and introduce yourself! (Or you can just lurk there for a bit!)
+
+ - 📪[Mailing list]()
+ - ✅[Trello site]()
+ - 🗓️[SC-CoP Google Calendar]() <-- Subscribe!
+ - 📝[Meeting Notes doc](https://docs.google.com/document/d/1EvGFC39qT8tp-TbLqlXGZehgPm0VXZEYnlac13gBXO0/edit#heading=h.vxfnvlhpiq7n) <--- There's a section here called 'New here?' that gives tips on how to start contributing as well!
+ - 🧑🏽‍🏫[User Matrix Channel](https://matrix.to/#/#galaxyproject_mass-spectrometry:matrix.org)
+
+ # How is Galaxy used for Mass Spectrometry based Omics?
+
+ ## Projects / Showcases
+
+ Below is a list of projects involving members of this community:
+
+ | Project | Description | Techniques | Sequencing | Analyses | People involved | Funding | Status |
+ |---------|-------------|------------|------------|----------|-----------------|---------|--------|
+ | [IRIDA](https://irida.ca/) | The Integrated Rapid Infectious Disease Analysis | | | | Aaron Petkau
+ Foodborne pathogen detection | | Metagenomics | Long reads | | Bérénice Batut, Engy Nasr | EOSC-Life for 2022 | Ongoing
+
+ ## Partners
+
+ | Partners | Description | People involved |
+ |----------|-------------|-----------------|
+ | [Seq4AMR](https://www.jpiamr.eu/projects/seq4amr/) | [JPIAMR]() Network for Integrating Microbial Sequencing and Platforms for Antimicrobial Resistance | Saskia Hilteman
+ | [ELIXIR Emerging Microbiome Community](https://elixir-europe.org/communities/marine-metagenomics) | | Bérénice Batut
+ | µbioinfo Slack | |
+
+ <img class="img-fluid float-right" src="/projects/microbial/microgalaxy-logo.png" style="width:200px;" alt="Logo for microgalaxy"/>
+
+## Key words