https://github.com/spaam-community/spaam-blog
*Thread Reply:* I would definitely be interested in reading this!
*Thread Reply:* Maybe you could gather all the blog post ideas and put them as issues on the GitHub repository 🙂
*Thread Reply:* Then you can assign people to it etc.
*Thread Reply:* I should've made you and @Shreya admins on it already
*Thread Reply:* Thanks James, will do this when I get a chance, feel like I have hype myself up for github. Maybe we should try and organise a meeting soon Shreya 🙂
*Thread Reply:* Breadth vs depth of coverage (this is just turning into a list of things I google)
*Thread Reply:* you can do it!
*Thread Reply:* @Ele i've made a few issues of my own ideas as to what I meant, I think you can hype yourself up for that for the momemnt
https://github.com/SPAAM-community/spaam-blog/issues
(I'm happy to join the meeting to show you how adding the posts themselves would work :))
*Thread Reply:* Yes, let’s touch base and set up a plan @Ele and it would be awesome if @James Fellows Yates could pop in!
*Thread Reply:* I am out of town this week but back next Monday!
*Thread Reply:* Hope that's ok @Nikolay Oskolkov, don't want to jump ahead of you if you have something ready. I just thought maybe your ideas were more complicated so might take longer
*Thread Reply:* Ha-ha, no problems at all, please go ahead
*Thread Reply:* Maybe you could make a doodle or something?
*Thread Reply:* Would be easier, especially with time zones for @Shreya
*Thread Reply:* Good luck with the review btw!
*Thread Reply:* I’ll make a Doodle! Good luck Ele!
*Thread Reply:* https://www.when2meet.com/?12877619-B8I9g
*Thread Reply:* Here you are! You can set your time zone up on the top left 🙂 All things equal I would have a slight preference for Wednesday as I work from home that day so zooms are a little easier-- but I’ve marked off all my availability!
*Thread Reply:* Hey both 🙂 I selected the slots you were both free. So Wed - Fri afternoon 🙂 Really looking forward to this project
*Thread Reply:* How about Wednesday 9/22 at 9AM Chicago/ 2PM GMT?
*Thread Reply:* Works for me!
*Thread Reply:* Topic: SPAAM Blog Time: Sep 22, 2021 02:00 PM London
Join Zoom Meeting https://york-ac-uk.zoom.us/j/95063756661?pwd=RmhQcGRWZ0hrVzkwYnRTelZwOGFOQT09
Meeting ID: 950 6375 6661 Passcode: 4Vw93jrn
*Thread Reply:* Sent you both google calendar invites (York email for you @Ele as I guess York still uses google stuff? And Shreya's gmail)
*Thread Reply:* Hmm am having same problem with zoom link!
*Thread Reply:* @Shreya do you have a Chicago zoom thingy?
*Thread Reply:* Or we can meet on jitsi
*Thread Reply:* I do have zoom! Hang on let me send a link
Markdown tips: https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet
By the way, the SPAAM blog could also eventually lead to a publication in JOSE (the Journal of Open Source Education) - https://jose.theoj.org/
*Thread Reply:* I’ve actually never used Zenodo, so the nuance here is a bit lost on me at this stage, but I think it makes sense!
*Thread Reply:* Ok. The auto thing is each time you make a 'release' of a repository, it would autoamtically upload the whole repository to Zenodo where it gets converted to an unmodifiable 'blob' file which is permanent so to say.
But the auto-method includes the entire changelog of the repository, rather just the 'latest' changes, so to say.
*Thread Reply:* But regardless, we can go through it toether 😉
*Thread Reply:* Could also try OSF.io instead 🤔
Potential crowdsourced blog idea
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*Thread Reply:* If some one points me to how exactly the blog summary can be contributed, I can do this over the weekend!
*Thread Reply:* :partyparrot::poopparty::partydino: THANK YOU Kevin!! Whatever’s easiest for you! Probably the easiest would be writing it in a google doc and sharing it with me and @Ele at shreya23@uchicago.edu and eg715@york.ac.uk … BUT if there is a different format you prefer, we’ll work with that!
*Thread Reply:* @Gunnar Neumann, @Pooja Swali, @Åshild (Ash), @Meriam Guellil - I've paraphrased your comments as part of a blog post draft and credited you all+your institutions.
If you'd like to make any edits or changes please go ahead - you all have more experience in the field than I! If you'd rather have your quotation removed just say, no issue.
https://docs.google.com/document/d/1Vl1RAAtiNZzDPx1n1SC3aOQKg2pFHmKqMolRY7RBAIA/edit?usp=sharing
*Thread Reply:* I am fine with the quote. Maybe something to mention in other major factors influencing the effectiveness is fragment length. If you have a library with very small fragments you are just going to need a lot more sequencing because barely any reads will be assigned using most taxonomic identifiers. Min read length for classification is around 30-35bp usually, although there are exceptions. But then you could argue how accurate these exceptions are when they are based on fragments under 30bp. Anyways always good to have a look at your libraries first.
*Thread Reply:* Very good point! I've added the following: Similarly, libraries with a shorter overall fragment length profile will benefit from additional sequencing. The inherent challenge of identifying the origin of shorter DNA sequences will limit confidence in taxonomic or genome assignment. Libraries with median fragment lengths closer to the 30-35bp range - the typical (but not universal) minimum length cut-off - may require additional allocated reads.
*Thread Reply:* Hi @Kevin Daly, sorry for the late reaction and thanks to @Shreya for the reminder! quote looks good to me, i didnt contribute much to the conversation anyways. also text looks very good. thanks for writing this up!!
*Thread Reply:* @Shreya - is there interest in moving ahead with this?
*Thread Reply:* yes! @Ele and I were just talking about how great your post is!! Stay tuned (I’m about to leave for a conference) and thank you again for writing it up!!
trying to keep all mentions of me as blog editor in this channel so I don’t lose them! @James Fellows Yates, @Nikolay Oskolkov, edit: @Maria Lopopolo, this sounds like a great three-person blog post!
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*Thread Reply:* @Maria Lopopolo, are you finding the results of this discussion to be helpful? If so do you feel like writing a blog post summarizing what you’ve found? cc @Ele
*Thread Reply:* ah yes, going to be honest i 100% have not had time to read the thread and just saw my tag
*Thread Reply:* And who is still working out what all of that means lol 😆