microGalaxy

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microgalaxy@lists.galaxyproject.org

March 2024

2 participants
2 discussions

microGalaxy paper writing - Who is interested in contributing actively?
by Bérénice Batut 16 Sep '24

16 Sep '24

Hi all, In the paper WG meeting yesterday, we discussed about the 2 papers we would like to write in the next months You can find below a quick description about the aims and timelines for both and more details in the paper WG notes <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…>. If you are interested in contributing actively in any or both papers, let us know either by answering this email or adding your name in the paper WG notes <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…> on page 2 and 3 We will after that organise separate meetings for each paper. Best, Bérénice User-oriented paper What? (Opinion) paper showing that Galaxy is used for microbial data analysis and how with overview of publications using Galaxy, result of survey, use cases Where? Open-access user oriented journal (e.g. BMC Microbiology) When? November - December 2023 Process the survey and use cases Clarify the paper outline Beginning of 2024: write the manuscript Technical paper What? A technical paper presenting resources/infrastructure (tools, workflows, training, etc) available for microbial data analysis in Galaxy Where? NAR webserver <https://academic.oup.com/nar/pages/submission_webserver> When? Deadlines for NAR webserver Submission of one-page summary by December, 20th Submission of full manuscript 3 weeks after the date of the approval email or 31 January Timeline November - December: Collect tools, workflows, database and training available in Galaxy Write a 1st draft of the paper Write the summary Make a nice looking subdomain microgalaxy.usegalaxy.eu with links to workflows and training and selection of tools January Finalize the draft Submit the manuscript

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Online Hackathon - March 11-15, 2024 - Improving the annotation of Galaxy resources for microbial data analysis and beyond
by Bérénice Batut 11 Mar '24

11 Mar '24

Hi all, We organize an Online Hackathon in March to improve the annotation of Galaxy resources for microbial data analysis and beyond: https://galaxyproject.org/events/2024-03-11-hackathon-galaxy-resources-anno… Objectives The objective of this hackathon is to improve the annotation of the Galaxy resources (tools, training, workflows) for microbial data analysis by: • Linking microbial Galaxy tools <https://galaxyproject.github.io/galaxy_tool_metadata_extractor/microgalaxy/> to bio.tools <http://bio.tools/> to obtain EDAM ontology annotation <https://edamontology.org/page> • Improving bio.tools annotations • Annotating existing microbial-related tutorials <https://training.galaxyproject.org/training-material/search2?query=microgal…> with EDAM terms • Reflecting on the addition of EDAM terms to workflows • Reflecting on missing terms in the EDAM ontology for microbial data analyses • Brainstorming about a way to connect tool annotations to improve training and workflow annotations All this work will be beneficial to structure the tools, workflows, and training we have to display them on the microGalaxy landing page <https://microgalaxy.usegalaxy.eu/>, structure the Galaxy tool panel, and create figures and tables for the technical paper <https://docs.google.com/document/d/1uVQ8E_8HpIuHDYHwR82jU8pCvj0tnebFKyS0juA…> we are working on. General information • Date: March 11th - 15th 2024 (full week) • Location: Online with a • a Zoom room, open the whole week • 2 daily stand-ups to accommodate different time zones • Several brainstorming meetings • microGalaxy Matrix chat <https://matrix.to/#/%23galaxyproject_microGalaxy:gitter.im> for communication • Time: full day, 9/10am CET to open end • Cost: Free Preliminary Schedule The schedule is quite flexible. There is no requirement to join the whole week. See the event page for more details about the planned schedule (stand-ups, brainstorming meetings): https://galaxyproject.org/events/2024-03-11-hackathon-galaxy-resources-anno…. Participation To participate, add your name, your affiliation, your availability during the week, and your email in the "Participation" section of the organizational GDoc so we can include you in further communication: https://docs.google.com/document/d/1B125dSKhB6AevnyShSi_zXIXUQd49tvNYfWHuyq… We hope to see a lot of you even if it is just to say hi :) Best, Paul and Bérénice

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