Abstract for Training committee presentation at BioC2026

[Drnevich, Jenny]

Hi all,

 

I have started to jot down some ideas for an abstract submission (short talk) to give an update on the Training committee at BioC2026 – I am going and will present. It’s just bullet points now with ideas of what it should cover. Please look it over and add ideas or details. The last bit about training in the age of AI is something I’ve been following personally and think we should discuss at our next meeting what the training committee might hope to accomplish.

 

If you would like to be a co-author (or co-presenter if you are going to BioC2026), please add your name. If you do not already have a profile on https://openreview.net/, please also give your email and affiliation.

 

Deadline is nominally March 13, but it’s going to be extended one week so we have a little more time.

 

https://docs.google.com/document/d/1ZLi5R-zBVeeE6scnkq7Br6W2KzsyflVpLTk3gp7O5aU/edit?usp=sharing

 

Thanks in advance for your help!

Jenny

 

 

Jenny Drnevich, Ph.D.
Assistant Director, High Performance Computing in Biology (HPCBio)
The Roy J. Carver Biotechnology Center

University of Illinois, Urbana-Champaign

Carl R. Woese Institute for Genomic Biology
1206 W. Gregory Dr., MC-195, Rm. 2112, Urbana, IL 61801
USA
ph: 217-300-6543
e-mail: drne...@illinois.edu

 

[Kevin RUE]

Hi Jenny,

Thanks for that.

I'm already over-booked with travel plans this year, so I won't be able to attend BioC2026, but I've added my name and a couple of bullet points that you might find relevant to mention.

I noted that your list of bullet points is introduced by "In the last year" although some aspects are forward-looking, so I've allowed myself to mention things that are about to start. (also considering that they'll be well underway by July/August.

I've tried to be informative yet concise in my bullet points; happy to expand or answer any clarifying question you may have while drafting the abstract.

Best,

Kevin

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[Drnevich, Jenny]

Hi everyone,

 

Thanks for your input so far on the abstract for BioC2026. I’ve made a first pass at putting the bullet points into an abstract. I wasn’t sure how much to name names in the abstract, like for the development of the Microbiome workshop. Kevin’s fellowship and BioFAIR project are specific enough to him that I put his name in (and tagged him to please provide an overview summary!). I also ran out of steam on the AI part. I will try again tomorrow but feel free to put in your ideas for the AI or anything else.

 

Thanks for your help,

Jenny

 

Link again: https://docs.google.com/document/d/1ZLi5R-zBVeeE6scnkq7Br6W2KzsyflVpLTk3gp7O5aU/edit?usp=sharing

To view this discussion, visit https://groups.google.com/d/msgid/bioconductor-teaching/CAJ3Kd8tNna_4aBL7x6PjBNfEbSymofCFSZR3M%2BshDW2H4x2CDA%40mail.gmail.com.

[Kevin RUE]

Hi all,

Thanks again, Jenny.

I've added a brief sentence. Happy to refine/expand if needed.

PS: I'll be on leave for a few days from Friday included.

Best,

Kevin

[Robert Castelo]

Hi,

I have added a proposal of sentence of the AI part, based on my recent experience teaching about it this year. A possible take on this that I think makes sense in training, is to focus the AI part on the concept of "AI pair programming" and how to give "context" to the AI programming tool so that the suggestions it makes match the level of the learner and the training materials. I have been teaching that for Python at a very basic introductory level using GitHub Copilot, you see a practical I developed here:

https://funcompbio.github.io/practical11

one problem with developing training materials for this, is that because LLMs are non-deterministic, the interactions you make with Copilot may not match the screenshots and instructions in the training materials, and in the end, with some of the groups I had to do quite some passive-aggressive insisting on the Copilot chat to force Copilot to read the 'copilot-instructions.md' context file. these materials I developed them based on the first ~20 minutes of this video:

https://www.youtube.com/watch?v=SJqGYwRq0uc

in any case, if this is not what you were envisioning for the use of AI in training, you may disregard the proposal. unfortunately, I've been missing the last calls and I may be out-of-sync with what the committee has been discussing lately.

cheers,

robert.

To view this discussion, visit https://groups.google.com/d/msgid/bioconductor-teaching/CAJ3Kd8sjWNTYtveH6fQH-VnLB-4EtQA7s1jtsMo-w_LSvw097w%40mail.gmail.com.

-- 
Robert Castelo, PhD
Associate Professor
Dept. of Medicine and Life Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514

[Drnevich, Jenny]

Hi Kevin,

 

I added one little bit to the sentence if this is fair:

“Both of these initiatives will strengthen connections between Bioconductor and two other major bioinformatics platforms to improve the visibility, accessibility, and reuse of complementary software and training materials across life science communities”

 

Enjoy your break,

Jenny

[kevin...@gmail.com]

Oh yeah actually that’s my bad for often forgetting to mention that training materials are also part of the scope. I try too hard to concise sometimes! 

On 18 Mar 2026, at 16:34, Drnevich, Jenny <drne...@illinois.edu> wrote:



[Drnevich, Jenny]

Hi Robert,

 

That is a very good practical! This does fit within what I’ve been envisioning, but just one of the contexts. I think AI and training can be broken down several ways:

 

How to do it (like to your practical)

When to do it or not to do it (particular situations within a lesson)

Why do it or not do it (learning device vs. outcome accelerant)

 

We haven’t done much at all in recent meetings on AI but will be putting it on the next agenda. Perhaps at the next meeting we can brainstorm some goals for the committee, and plan & publicize a community-wide call to discuss the issue more broadly. I know the Carpentries have been developing workshop materials on using AI for coding – I’ll ask Toby how it is coming along and if he can give us an update soon.

 

Thanks,

Jenny

[Wes Wilson]

I am working on some materials for CYTO workshop around the Why and Why not's that could be transferable. 

More around biological insights than how / why to vibe code. I feel like the Caprentries development course has mostly been around how to vibe code. 

/ Wes

To view this discussion, visit https://groups.google.com/d/msgid/bioconductor-teaching/DS4PPF69AE895C519DA7898F385BC7C6031B24EA%40DS4PPF69AE895C5.namprd11.prod.outlook.com.

[Tim Triche]

just as an alternative perspective, Zach updated RcppML from 0.33 to 1.0 with a pile of Claude agents and a LOT of structured testing loops ( https://zdebruine.github.io/RcppML/ ). That plus one of my grad students having Claude code up a Poisson-Gamma FP/FN simulation in 5 minutes to set adaptive variant calling thresholds pushed me over the edge -- we write unit tests to ensure that the grunt workers (agents) are implementing what they say they are, and edit documentation... even Aaron Lun would have trouble keeping up with the pace of development by modern agents, and I struggle to see how any of it can be trusted without extensive unit test harnesses. Maybe that's the key for emphasis, trustworthy libraries have become even more critical now that non-humans are coding.


Timothy J. Triche, Jr., PhD
Associate Professor of Bioinformatics, Department of Epigenetics
Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI, 49503
For scheduling requests, please cc: Jennife...@vai.org
(626) 375-9663 (mobile) / (616) 234-5252 (Jennifer Brooks)
https://trichelab.vai.org/

________________________________________
From: bioconduct...@googlegroups.com <bioconduct...@googlegroups.com> on behalf of Wes Wilson <wils...@gmail.com>
Sent: Thursday, March 19, 2026 5:43 PM
To: Drnevich, Jenny
Cc: Robert Castelo; bioconductor-teaching
Subject: [External] Re: Abstract for Training committee presentation at BioC2026

I am working on some materials for CYTO workshop around the Why and Why not's that could be transferable.

More around biological insights than how / why to vibe code. I feel like the Caprentries development course has mostly been around how to vibe code.

/ Wes

On Wed, Mar 18, 2026 at 12:52 PM Drnevich, Jenny <drne...@illinois.edu<mailto:drne...@illinois.edu>> wrote:
Hi Robert,

That is a very good practical! This does fit within what I’ve been envisioning, but just one of the contexts. I think AI and training can be broken down several ways:

How to do it (like to your practical)
When to do it or not to do it (particular situations within a lesson)
Why do it or not do it (learning device vs. outcome accelerant)

We haven’t done much at all in recent meetings on AI but will be putting it on the next agenda. Perhaps at the next meeting we can brainstorm some goals for the committee, and plan & publicize a community-wide call to discuss the issue more broadly. I know the Carpentries have been developing workshop materials on using AI for coding – I’ll ask Toby how it is coming along and if he can give us an update soon.

Thanks,
Jenny

From: Robert Castelo <robert....@upf.edu<mailto:robert....@upf.edu>>
Sent: Wednesday, March 18, 2026 4:29 AM
To: Drnevich, Jenny <drne...@illinois.edu<mailto:drne...@illinois.edu>>
Cc: bioconductor-teaching <bioconduct...@googlegroups.com<mailto:bioconduct...@googlegroups.com>>
Subject: Re: Abstract for Training committee presentation at BioC2026

Hi,

I have added a proposal of sentence of the AI part, based on my recent experience teaching about it this year. A possible take on this that I think makes sense in training, is to focus the AI part on the concept of "AI pair programming" and how to give "context" to the AI programming tool so that the suggestions it makes match the level of the learner and the training materials. I have been teaching that for Python at a very basic introductory level using GitHub Copilot, you see a practical I developed here:

https://funcompbio.github.io/practical11<https://urldefense.com/v3/__https:/funcompbio.github.io/practical11__;!!DZ3fjg!8r9W3gfmICaKUhJZwBdcYli728dYRs7NFy_gpf_MUgt7dspXckohMPeoURFtv73UnYKMsja-NIvypIXUMBArelboDLs1$>

one problem with developing training materials for this, is that because LLMs are non-deterministic, the interactions you make with Copilot may not match the screenshots and instructions in the training materials, and in the end, with some of the groups I had to do quite some passive-aggressive insisting on the Copilot chat to force Copilot to read the 'copilot-instructions.md' context file. these materials I developed them based on the first ~20 minutes of this video:

https://www.youtube.com/watch?v=SJqGYwRq0uc<https://urldefense.com/v3/__https:/www.youtube.com/watch?v=SJqGYwRq0uc__;!!DZ3fjg!8r9W3gfmICaKUhJZwBdcYli728dYRs7NFy_gpf_MUgt7dspXckohMPeoURFtv73UnYKMsja-NIvypIXUMBArep8Q7AXM$>

in any case, if this is not what you were envisioning for the use of AI in training, you may disregard the proposal. unfortunately, I've been missing the last calls and I may be out-of-sync with what the committee has been discussing lately.

cheers,

robert.

On 18/3/26 10:13, Kevin RUE wrote:
Hi all,

Thanks again, Jenny.

I've added a brief sentence. Happy to refine/expand if needed.

PS: I'll be on leave for a few days from Friday included.

Best,
Kevin

On Tue, 17 Mar 2026 at 22:12, Drnevich, Jenny <drne...@illinois.edu<mailto:drne...@illinois.edu>> wrote:
Hi everyone,

Thanks for your input so far on the abstract for BioC2026. I’ve made a first pass at putting the bullet points into an abstract. I wasn’t sure how much to name names in the abstract, like for the development of the Microbiome workshop. Kevin’s fellowship and BioFAIR project are specific enough to him that I put his name in (and tagged him to please provide an overview summary!). I also ran out of steam on the AI part. I will try again tomorrow but feel free to put in your ideas for the AI or anything else.

Thanks for your help,
Jenny

Link again: https://docs.google.com/document/d/1ZLi5R-zBVeeE6scnkq7Br6W2KzsyflVpLTk3gp7O5aU/edit?usp=sharing<https://urldefense.com/v3/__https:/docs.google.com/document/d/1ZLi5R-zBVeeE6scnkq7Br6W2KzsyflVpLTk3gp7O5aU/edit?usp=sharing__;!!DZ3fjg!8r9W3gfmICaKUhJZwBdcYli728dYRs7NFy_gpf_MUgt7dspXckohMPeoURFtv73UnYKMsja-NIvypIXUMBArejnsX8Wh$>

From: bioconduct...@googlegroups.com<mailto:bioconduct...@googlegroups.com> <bioconduct...@googlegroups.com<mailto:bioconduct...@googlegroups.com>> On Behalf Of Kevin RUE
Sent: Thursday, March 12, 2026 4:28 AM
To: Drnevich, Jenny <drne...@illinois.edu<mailto:drne...@illinois.edu>>
Cc: bioconductor-teaching <bioconduct...@googlegroups.com<mailto:bioconduct...@googlegroups.com>>
Subject: Re: Abstract for Training committee presentation at BioC2026

Hi Jenny,

Thanks for that.

I'm already over-booked with travel plans this year, so I won't be able to attend BioC2026, but I've added my name and a couple of bullet points that you might find relevant to mention.
I noted that your list of bullet points is introduced by "In the last year" although some aspects are forward-looking, so I've allowed myself to mention things that are about to start. (also considering that they'll be well underway by July/August.

I've tried to be informative yet concise in my bullet points; happy to expand or answer any clarifying question you may have while drafting the abstract.

Best,
Kevin

On Wed, 11 Mar 2026 at 22:08, Drnevich, Jenny <drne...@illinois.edu<mailto:drne...@illinois.edu>> wrote:
Hi all,

I have started to jot down some ideas for an abstract submission (short talk) to give an update on the Training committee at BioC2026 – I am going and will present. It’s just bullet points now with ideas of what it should cover. Please look it over and add ideas or details. The last bit about training in the age of AI is something I’ve been following personally and think we should discuss at our next meeting what the training committee might hope to accomplish.

If you would like to be a co-author (or co-presenter if you are going to BioC2026), please add your name. If you do not already have a profile on https://openreview.net/<https://urldefense.com/v3/__https:/openreview.net/__;!!DZ3fjg!8-v_g0Tu8-0i28A15mt8Jn1REy7AvFIOV-Um7lA4fa_2Q4C4ss93TcFSJqZGArpN-nZTdDtSHLx4LUq4Zwo3qw$>, please also give your email and affiliation.

Deadline is nominally March 13, but it’s going to be extended one week so we have a little more time.

https://docs.google.com/document/d/1ZLi5R-zBVeeE6scnkq7Br6W2KzsyflVpLTk3gp7O5aU/edit?usp=sharing<https://urldefense.com/v3/__https:/docs.google.com/document/d/1ZLi5R-zBVeeE6scnkq7Br6W2KzsyflVpLTk3gp7O5aU/edit?usp=sharing__;!!DZ3fjg!8-v_g0Tu8-0i28A15mt8Jn1REy7AvFIOV-Um7lA4fa_2Q4C4ss93TcFSJqZGArpN-nZTdDtSHLx4LUq_xsCZDA$>

Thanks in advance for your help!
Jenny


Jenny Drnevich, Ph.D.
Assistant Director, High Performance Computing in Biology (HPCBio)
The Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign
Carl R. Woese Institute for Genomic Biology
1206 W. Gregory Dr., MC-195, Rm. 2112, Urbana, IL 61801
USA
ph: 217-300-6543

e-mail: drne...@illinois.edu<mailto:drne...@illinois.edu>

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Robert Castelo, PhD

Associate Professor

Dept. of Medicine and Life Sciences

Universitat Pompeu Fabra (UPF)

Barcelona Biomedical Research Park (PRBB)

Dr Aiguader 88

E-08003 Barcelona, Spain

telf: +34.933.160.514

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