Dear Bérénice et al, Many thanks for all these. I am sorry but I could not join so far the meetings. I went through the draft and did some comments and suggestions. As to the user cases; our collaborators in Tanzania who have sequencers but no servers or programming skills are using the M.tuberculosis variant calling, clustering and phylogenetics Galaxy workflows of Peter, Galo and C.Stritt to analyse sequences obtained from clinical specimens. Would that be interesting? Please let me know in case you think so and we can add a paragraph. We are also working on a new workflow which we would like to put into a ms but that will take some time.
Kind regards Daniela
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Daniela Brites, PhD Tuberculosis Research Unit Swiss Tropical and Public Health Institute Kreuzstrasse 2 4123 Allschwil, Switzerland phone: +41(0) 612848185 email: d.brites@swisstph.ch or d.brites@unibas.ch
-----"Bérénice Batut" berenice.batut@gmail.com wrote: ----- To: microgalaxy@lists.galaxyproject.org From: "Bérénice Batut" berenice.batut@gmail.com Date: 10/10/2024 11:28AM Cc: "Pierre AMATO" pierre.amato@uca.fr, anshu@imtech.res.in, blanked2@ccf.org, evan.bolyen@nau.edu, d.brites@swisstph.ch, galo.goig@swisstph.ch, "Björn Grüning" bjoern.gruening@gmail.com, pjagtap@umn.edu, "Pierre Marin" pierre.marin@uca.fr, smehta@umn.edu, kimberlymetris@gmail.com, asimejamesoba@gmail.com, "Pechlivanis Nikolaos" nikosp41@certh.gr, "Raphaëlle Peguilhan" raphaelle.peguilhan@univ-pau.fr, "Psomopoulos Fotis" fpsom@certh.gr, "Valerie Schiml" valerie.schiml@nmbu.no, anthony.simard@nau.edu, "Nicola Soranzo" nicola.soranzo@earlham.ac.uk, pvanheusden@uwc.ac.za, bmirauta@gmail.com, "Saskia Hiltemann" saskiahiltemann@gmail.com, "Clea SIGURET" clea.siguret@uca.fr Subject: [microGalaxy] microGalaxy technical paper - Updates & Meetings on November, 15th
Hi all,
I hope you are all doing fine! Below is a summary of the key points discussed in our recent meeting: 1. Manuscript for Nature Microbiology: https://docs.google.com/document/d/1jFOzIm8aE0XBM2PTaQqO3JzAsd8WW16qXDPgFzRu... of Scope: The manuscript will be more user-oriented, focusing on the microbiology aspect and be written for Nature Microbiology. Most technical details will be included in the Supplementary materials. Please read, add suggestions and commentsUse Cases: We would like to add published use cases (including preprints) in the manuscript within the tools, workflows, and training Result sections. Any use cases mentioned should be included in the Use Case table (in Supplementary)Overview Figure (Fig 1): Please provide comments and suggestions for changes in the manuscript. You can use Excalidraw or sketch manually to draft your ideas.Supplementary Materials: Comments and suggestions on tables (related platforms, training events) and figures should be added as comments in the manuscript.2. Coordination: Assign yourself to the tasks you wish to work on and tick them off upon completion: https://docs.google.com/document/d/1TCGcooxVo_4FfPUdB7xv5n01UfkIIYz0z8Ydo1Gy... 3. Upcoming Hackathon: A one-day hackathon to add workflows to IWC is scheduled for November. Further details will be shared in a separate invitation email. 4. Lab/Subdomain: Please comment on the provided sketch: Excalidraw Sketch. 5. Timeline:Workflow hackathon in November. Deadline for tasks: end of November (to be confirmed). 6. Next Meeting: The next meeting is scheduled for November 15th with 2 meetings (to accommodate different timezones):
November 15 th at 8am UTC / 5pm AEST / 9am CET (your timezone) - Zoom - NotesNovember 15 th at 3pm UTC / 4pm CET / 10am EDT (your timezone) - Zoom - NotesCalendar with all meetings
Anyone interested in participating in the paper is more than welcome!
I hope to see you around
Best,
Bérénice
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