Thanks, Ryan. I generally attend all AWG Microbe and its subgroup meetings. I’m not sure it’s ready for a full presentation, but I can certainly discuss how this was done in an upcoming AWG meeting—it shouldn’t take more than 10–15 minutes.
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Thank you for the information Dirk.
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Dear all,
I have uploaded the data to the oral subgroup folder under the folder name MGnify_data. Please let me know if you are able to access it on the drive.
Best regards,
Anupam
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I noticed the subgroup is identifying oral microbiome datasets through MGnify. One idea that came to mind was creating a standardized metadata layer and quality scoring pipeline across the studies so they’re easier to search, compare, and reuse for downstream ML analyses. I’d be happy to work on something like this if it’s useful.
here’s my mail hitaeshi25sehgal@gmail.com. Looking forward to collaborate!
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Hi Anupam, I saw your work on identifying the oral microbiome datasets through the MGnify API. Really nice work! My background is in AI, bioinformatics, and research data engineering, and I think there are some interesting extensions we could explore, like metadata standardization, quality scoring, semantic dataset retrieval, or an ML-assisted dataset explorer. If you’re looking for contributors, I’d be happy to help.
Hi Hitaeshi,
Great from you reaching out. We need more initiatives like yours.
I am on holiday now until august 17th. But reachable.
Could you resume what you want in an email directed to me, neefsdirk@gmail.com.
I will forward it to Nick and Jon.
Our next meeting will be in september but we can always anticipate on your initiative.
Regards,
Dirk
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Thank you very much, Dirk! I really appreciate your encouragement. I’ll send you a short proposal by email outlining the idea, the motivation, and how I’d be happy to contribute. Looking forward to collaborating with you, Nick, and Jon.
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Dear @lilmisscupcake,
Certainly, we can meet and discuss this. The vacation period is currently underway, but I would be happy to meet with you and see what can be done.
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Hi Anupam! Just following up, since it’s been a little while. Would love to find a time to chat about the metadata/quality-scoring idea if you’re free, happy to work around your schedule. Let me know if there’s anything else you’d need from me before we sync up!
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Hello @DirkNeefs and Oral Microbiome Subgroup colleagues,
I am Lissandra Kruse Fuganti, a master’s student in Applied Computing at UEPG, Brazil, and a Microbes AWG member. I would like to participate in the Oral Microbiome Subgroup and contribute remotely through Python, public-dataset discovery, metadata organization, quality checks or reproducible notebooks. I am still learning microbiome analysis and would appreciate guidance and a small initial task.
Could suitable analyses be carried out in Kaggle Notebooks? Are there public datasets, an existing pipeline or example notebooks you recommend, and specific software, memory or storage requirements? I would only use data approved for that platform and follow the group’s sharing rules.
I have difficulty speaking English and following live English conversations. Would it be possible to contribute mainly through written, asynchronous communication, with instructions and feedback in the forum, chat or email? Written communication is easier for me.
Please let me know the current joining steps and where a new computational contributor could be most useful.
Thank you!
Lissandra Kruse Fuganti
UEPG, Brazil
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