Presentation submission for BioC2021 by March 16th!

[Drnevich, Jenny]

Hi all,

 

One thing we forgot to talk about yesterday – doing some sort of presentation at BioC2021. The deadline for submissions has been extended to March 16^th ( https://bioc2021.bioconductor.org/submissions/).  Do we think we will have the Intro to R workshop in good enough shape to present part of it as a long workshop (1.5 – 2 hrs)? That could be a good way to test it out and get lots of feedback. I remember that there often were short talks on a topic with “come to our workshop to learn more” and or we could possibly also put in for a Birds of a Feather for after the workshop to discuss teaching/training issues? I would be happy to take the lead on doing the submission depending on what every thinks we can do.

 

Best,

Jenny

 

 

Jenny Drnevich, Ph.D.
Functional Genomics Bioinformatics Specialist
High Performance Computing in Biology (HPCBio)
and The Roy J. Carver Biotechnology Center

University of Illinois, Urbana-Champaign

2112 IGB
1206 W. Gregory Dr.
Urbana, IL 61801
USA
ph: 217-300-6543
fax: 217-265-5066
e-mail: drne...@illinois.edu

 

[Laurent Gatto]

Hi Jenny, 

I think it would certainly be a great idea to submit something, but not sure if a workshop is appropriate, unless you think of running a short intro to R. However, a birth-of-a-feather session would be great to gather feedback. A short talk to talk about the committee and our efforts would be great too.

Laurent 

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[Robert Castelo]

+1 !!

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[Charlotte Soneson]

Thanks Jenny - I agree that we should do something. Maybe one possibility could be a “joint material development session” or something like that, where we invite people to contribute to/comment on the developed material, start drawing up new possible lessons (or find a group of like-minded to do it with), or discuss what lessons might be useful? I guess this could qualify as a birds-of-a-feather session, or even a long workshop? I also agree that it could probably be useful to submit a similar short talk as for EuroBioc, to make more people aware of the efforts.

Charlotte

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[Toby Hodges]

Hi Charlotte,

If you decide to run such a development session, you may find these recommendations for organising/running a lesson development sprint useful, and any feedback you can provide would be appreciated! 

https://github.com/tobyhodges/lesson-sprint-recommendations

Thanks,

Toby

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[Charlotte Soneson]

Hi all,

as anticipated in the call this week, the next Bioconductor teaching committee meeting (on April 12) will take place at 5pm CEST instead of the usual time, in order to accommodate the BiocSwirl presenters’ timezone a bit better. We’ll send out a reminder as usual just before the meeting.

Charlotte

[Charlotte Soneson]

Thanks Toby, this looks very helpful!

For anyone interested in contributing, we are planning a brief call to outline the submission to BioC2021 on Friday, March 12 at 4pm CET. We’ll use the regular jitsi channel (https://meet.jit.si/BioconductorTeaching). 

Charlotte

[Charlotte Soneson]

Hi everyone,

from the meeting today, the suggestion was to submit two abstracts to BioC2021:

- a short talk aimed at giving an overview of who we are and what we do (similar to the one from EuroBioc last year)

- a long workshop structured according to the ‘lesson development sprint’/‘joint material development session’ mentioned below (with an initial introduction of the guiding principles and the practicalities of lesson development). 

We started drafting the abstracts in this google doc (also linked from the usual agenda): https://docs.google.com/document/d/1j3uz_lWYisb7JgReeQyNHqelyn2PVKvO6z-whEI5jnc/edit?usp=sharing 

Contributions and suggestions are welcome - note that the deadline for submission is on Tuesday (March 16), so please make sure to provide any comments before lunchtime on Tuesday. 

Charlotte

[Drnevich, Jenny]

Hi everyone,

 

I have a draft of the Workshop submission syllabus (html attached). Location on github:

 

https://github.com/jdrnevich/BuildACarpentriesWorkshop/blob/master/vignettes/CarpentriesWorkshopSyllabus.Rmd

 

Feel free to edit heavily if you can – it is really rough shape right now and I realized how much work we will need to do not only on developing this “lesson sprint” workshop but also the main Introduction to R workshop. In skimming through the Curriculum Development handbook, the Chapter on Curriculum structure lays out episodes vs. lessons vs. curriculum (https://cdh.carpentries.org/our-curriculum-structure.html). If the Introduction to R is going to be an entire curriculum, then most of our efforts so far have been more focused on the data import, cleaning and visualization. I tried to broaden this out to include a standard data organization and management section. It shouldn’t be that hard to modify these concepts from the Ecology or Genomics curricula to fit our -omics based data set.

 

Having never submitted to run a BioC workshop before, I am not sure how acceptable this rough syllabus will be. Anyone with experience, please chime in with what area needs to be the main focus for improvement before the submission deadline in approximately 24 hours from now (for me).

 

Thanks,

Jenny

To view this discussion on the web, visit https://groups.google.com/d/msgid/bioconductor-teaching/AC57EB7F-00A9-444E-A542-AEE848BE0A69%40gmail.com.

[Charlotte Soneson]

Hi everyone,

sorry for the delay on this - as agreed in the last meeting, I have started a google doc to formulate the plans (learning outcomes, contents, etc) for the BiocProject and RNA-seq lessons: https://docs.google.com/document/d/1wMrkyTh5ItNflp7YZuVQ7dBwkdi3ije-5cOh9qRGPbU/edit?usp=sharing 

Feel free to add any thoughts, comments, objections, ideas, etc - I think we can keep the discussions in the document, and when we agree on the plan we’ll move things to GitHub and start writing. 

Happy Easter

Charlotte

[Charlotte Soneson]

Hi all,

just a quick reminder of the bioc-teaching call on Monday (April 12). Note that, as previously announced, this meeting will exceptionally take place at 5-6pm CEST to accommodate our guests from California. After a couple of short updates on current work in progress, the main agenda item will be a presentation and discussion from the BiocSwirl team (https://github.com/biocswirl-dev-team/BiocSwirl). The Jitsi link for the meeting is https://meet.jit.si/BioconductorTeaching. 

Hope to see you on Monday,

Charlotte & Laurent

[Charlotte Soneson]

Hi everyone,

a quick reminder of the bioc-teaching call on Monday (May 10), now back at the usual time at 2pm CEST. Please add any item that you would like to discuss to the agenda in the google doc; currently the plan is to review our BioC2021 contributions and discuss the current draft plans for the project and RNA-seq lessons. 

Jitsi link: https://meet.jit.si/BioconductorTeaching 

See you on Monday,

Charlotte & Laurent

[Charlotte Soneson]

Hi everyone, 

on Monday (June 14) we’ll have our next bioc-teaching call (2pm CEST). We’ll continue working on the lessons that are under development, and plan for the BioC2021 workshop. If you have additional topics that you would like to cover, please feel free to add them to the agenda google doc!

Jitsi link:  https://meet.jit.si/BioconductorTeaching 

See you on Monday,

Charlotte & Laurent

[Charlotte Soneson]

Hi everyone,

a quick reminder that we’re meeting tomorrow (Mon June 28), 5-6pm CEST, to continue working on the material for BioC2021.

Jitsi link: https://meet.jit.si/BioconductorTeaching 

Charlotte 

[Charlotte Soneson]

Hi all,

just a reminder of our meeting on Monday, July 12, on the usual time (2-3pm CEST).

Jitsi link: https://meet.jit.si/BioconductorTeaching 

Charlotte

[Charlotte Soneson]

Dear all,

this is a reminder of our bioconductor-teaching group call on Monday, August 9, 2-3pm CEST. We’ll debrief after the conference workshop and plan how to move forward; if you have additional topics to discuss, plese feel free to bring them as well!

The jitsi link is https://meet.jit.si/BioconductorTeaching

See you on Monday

Charlotte & Laurent 

[Charlotte Soneson]

Hi all,

quick reminder about the next Bioconductor teaching group call on Monday, September 13, at 2pm CEST. The jitsi link as usual is https://meet.jit.si/BioconductorTeaching

Cheers,

Charlotte & Laurent

[Charlotte Soneson]

Hi everyone - quick reminder of the bioc-teaching call on Monday, October 11, at 2pm CEST. Please add any items you'd like to discuss to the agenda. As discussed last time, I made an attempt to create a list of the different types of educational material within the Bioconductor ecosystem (added to the agenda document) - feel free to add/modify! 

Jitsi link as usual: https://meet.jit.si/BioconductorTeaching

See you on Monday!

Charlotte & Laurent

[Charlotte Soneson]

Hi all,

just a reminder about our next bioconductor-teaching group call on Monday, November 8, 2-3pm CET. 

The jitsi link as usual is https://meet.jit.si/BioconductorTeaching

See you on Monday,

Charlotte & Laurent

On 8 Aug 2021, at 09:24, Charlotte Soneson <charlott...@gmail.com> wrote:

[Charlotte Soneson]

Hi all,

quick reminder of the Bioc teaching group call on Monday, December 13, 2-3pm CET. 

jitsi link: https://meet.jit.si/BioconductorTeaching

Charlotte & Laurent

On 8 Aug 2021, at 09:24, Charlotte Soneson <charlott...@gmail.com> wrote:

[Charlotte Soneson]

Happy New Year! Quick reminder about the bioc-teaching group call on Monday, January 10, 2-3pm CET. 

Jitsi link as usual: https://meet.jit.si/BioconductorTeaching

See you on Monday,

Charlotte & Laurent

On 8 Aug 2021, at 09:24, Charlotte Soneson <charlott...@gmail.com> wrote:

[Kevin RUE]

Hi all,

Unfortunately, an important one-off meeting out of my control clashes with this teaching call. Sorry that I'll miss it.

Best

Kevin

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[Marco Chiapello]

Hello everyone,

today I teach a workshop, so I will not be able to attend the meeting.

Cheers,

M

[Charlotte Soneson]

Hi all,

quick reminder about the bioc-teaching group call on Monday, Feb 14, 2-3pm CET.
Jitsi link: https://meet.jit.si/BioconductorTeaching

See you next week,

Charlotte & Laurent

> On 8 Aug 2021, at 09:24, Charlotte Soneson <charlott...@gmail.com> wrote:
>

[Charlotte Soneson]

Reminder about the bioc-teaching call on Monday, March 14 at 2pm CET (and a note that Europe has not yet changed to summer time).

Jitsi link: https://meet.jit.si/BioconductorTeaching
See you on Monday,
Charlotte & Laurent

[Charlotte Soneson]

Hi everyone,

a quick reminder about the bioc-teaching group call on Monday, April 11, 2-3pm CEST.
Jitsi link: https://meet.jit.si/BioconductorTeaching

Hope to see you there
Charlotte & Laurent

[Charlotte Soneson]

Hi all,

quick reminder about the bioconductor-teaching group call on Monday, May 9, 2-3pm CEST.

Jitsi link: https://meet.jit.si/BioconductorTeaching

See you on Monday,
Charlotte & Laurent

> On 8 Aug 2021, at 09:24, Charlotte Soneson <charlott...@gmail.com> wrote:
>

[Robert Castelo]

I'm teaching at that time, I'm sorry I'm missing the last calls, somehow
lately I'm unlucky with my agenda and these calls. I hope I have a
better luck next time.

have a nice weekend,

robert.

--
Robert Castelo, PhD
Associate Professor

Dept. of Medicine and Life Sciences

[Susan Holmes]

Hi there,

For once I am on the right side of the world for this to work,

look forward to touching base today.

Susan

[Charlotte Soneson]

Hi all,

I totally forgot to send an early reminder of the bioc-teaching call today, sorry! As decided during the May meeting, we're exceptionally meeting two weeks later than usual this month - today (Jun 27) at 2pm CEST.

Jitsi link as usual: https://meet.jit.si/BioconductorTeaching

Charlotte & Laurent

> On 8 Aug 2021, at 09:24, Charlotte Soneson <charlott...@gmail.com> wrote:
>

[Susan Holmes]

Sorry I will miss this because I will be traveling at that time, please update us afterwards, especially about the "education week".

Thanks

Susan

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[Marco Chiapello]

Hello everyone,

sorry but I have conflicting meeting today I can not attend the bioc-teaching call today.

Cheers,

M

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[Charlotte Soneson]

Hi everyone,

a quick reminder about the bioc-teaching call on Monday, July 11, 2-3pm CEST.

Agenda document: https://docs.google.com/document/d/1s2QMk5XA-uhBVprAO3ZDk1Yfv1cnUWLp9zdvYq9Feu4/edit?usp=sharing

[Kevin RUE]

Apologies for missing that meeting: i'm on annual leave and travelling from today to Monday included.

Best

Kevin

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[Charlotte Soneson]

Hi all,

just a quick reminder of the bioc-teaching call on Monday, August 8, 2-3pm CEST.
I will be on vacation and will likely not be able to join the call, but I have added my thoughts and comments to the agenda document and will follow up afterwards.

jitsi link: https://meet.jit.si/BioconductorTeaching

Charlotte & Laurent

[Charlotte Soneson]

Hi everyone,

a quick reminder of the bioc-teaching call on Monday, September 19, 2-3pm CEST. We will summarize and discuss takeaways from the recent teaching week and Carpentries course, and plan how to move ahead.

The jitsi link is https://meet.jit.si/BioconductorTeaching

See you on Monday,
Charlotte & Laurent

[Frederick Tan]

Hi everyone,

. Would it be possible to push the start of this meeting back by one hour to 3pm CEST?  The current time can work but an hour later makes morning drop-off routines a little less hectic for the EST (sorry PST! :))

. ... and thank you Charlotte and Laurent for the great discussion today and continuing this effort!

Sincerely,

Frederick Tan

[Drnevich, Jenny]

I second moving the meeting time to 3pm CEST! (US CST myself, and it is always difficult to make it so early for me on a Monday).

 

Thanks,

Jenny

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[Vincent Carey]

sorry to be a pest   is there a slack channel?   google doc w notes?

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[Drnevich, Jenny]

Hi Vince,

 

All the information is on here: https://bioconductor.org/help/education-training/

[Toby Hodges]

15:00 CEST/13:00 UTC is fine for me. Happy to move to make the meeting more accommodating for those in the west.

Cheers,

Toby

To view this discussion on the web, visit https://groups.google.com/d/msgid/bioconductor-teaching/DM5PR11MB00277B51D55D6B2D057720DCB24D9%40DM5PR11MB0027.namprd11.prod.outlook.com.

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[Robert Castelo]

Fine with me too!!!

cheers,

robert.

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[Susan Holmes]

It would definitely help for those on PST ( as I may be next month), this month was just inability to do minus one on my own

time zone ;).

Best wishes

Susan

Susan Holmes, Professor, 

Statistics  Department,

John Henry Samter Fellow in Undergraduate Education,

102, Sequoia Hall,  

390 Jane Stanford Way,

Stanford

@SherlockpHolmes

http://www-stat.stanford.edu/~susan/

With Wolfgang Huber, the book is here: http://bios221.stanford.edu/book/

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[Kevin RUE]

I only miss occurrences that clash with all-day teaching, so there's no problem moving the time for me.

Best

kevin

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[Laurent Gatto]

Dear all, 

Thank you all for supporting the requested change. Our meeting will start at 3 pm CEST from now on.

Our next meeting will be on Mon 10 Oct (at 3 pm CEST).

Best wishes,

Laurent 

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[Charlotte Soneson]

Hi everyone,

here's a reminder about the bioc-teaching call on Monday, November 14, 3-4pm CET.
The jitsi link as usual: https://meet.jit.si/BioconductorTeaching

See you on Monday,
Charlotte & Laurent

[Susan Holmes]

Sorry I have to miss the meeting, I am afraid I will be travelling at exactly that time.

Best wishes, Susan

Susan Holmes, Professor, 

Statistics  Department,

John Henry Samter Fellow in Undergraduate Education,

102, Sequoia Hall,  

390 Jane Stanford Way,

Stanford

@SherlockpHolmes

http://www-stat.stanford.edu/~susan/

With Wolfgang Huber, the book is here: http://bios221.stanford.edu/book/

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[Charlotte Soneson]

Hi all,

a reminder about the teaching committee meeting on Monday, December 12, 3-4pm CET.
Jitsi link: https://meet.jit.si/BioconductorTeaching

Charlotte & Laurent

[Kevin RUE]

Hi all,

I might be able to join but I cannot guarantee it, as I'll be running between places that day.

Best wishes

Kevin

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[Charlotte Soneson]

Dear all,

the bioc-teaching group call this month will take place on Monday, January 16, 3-4pm CET. Apologies again for not realising during the last meeting that this is a US holiday - if you have comments but are not able to attend on Monday, please feel free to add them to the minutes document: https://docs.google.com/document/d/1s2QMk5XA-uhBVprAO3ZDk1Yfv1cnUWLp9zdvYq9Feu4/edit?usp=sharing

The jitsi link is https://meet.jit.si/BioconductorTeaching

[Charlotte Soneson]

Hi,

quick reminder about the bioconductor-teaching call on Monday, February 13, 3-4pm CET.

Minutes/agenda: https://docs.google.com/document/d/1s2QMk5XA-uhBVprAO3ZDk1Yfv1cnUWLp9zdvYq9Feu4/edit?usp=sharing
Jitsi link: https://meet.jit.si/BioconductorTeaching

See you on Monday,
Charlotte & Laurent

[Charlotte Soneson]

Hi,

a reminder about the bioc-teaching call on Monday, March 13, 3-4pm CET (please check the time, as we are in the period where some parts of the world are in daylight saving time and others are not).
I made an attempt at formulating some questions and key points for the bioc-rnaseq lesson (which we discussed in our planning meeting two weeks ago). I added them to the bioc-rnaseq planning document (https://docs.google.com/document/d/1YDKTeDX3z9W6eGbWaTQAUb_hs0iUC9saGvkO_Po5tfA/edit?usp=sharing) to make it easier to get an overview and discuss - please feel free to add yours there too, or edit these.

Minutes/agenda: https://docs.google.com/document/d/1s2QMk5XA-uhBVprAO3ZDk1Yfv1cnUWLp9zdvYq9Feu4/edit?usp=sharing
Jitsi link: https://meet.jit.si/BioconductorTeaching

See you on Monday,
Charlotte & Laurent

[Charlotte Soneson]

Hi,

quick reminder about the bioc-teaching call on Monday, April 3, 3-4pm CEST (as discussed last month, we moved the meeting a week earlier so it wouldn't fall on Easter Monday).

jitsi link: https://meet.jit.si/BioconductorTeaching

[Charlotte Soneson]

Hi all,

a reminder about the Bioconductor teaching group call on Monday, May 8, at 3pm CEST.

[Charlotte Soneson]

Hi all,
a quick reminder about the bioc-teaching call on Monday, June 12, at 3pm CEST.
Jitsi link: https://meet.jit.si/BioconductorTeaching

[Charlotte Soneson]

Hi all,

a quick reminder about the bioc-teaching call on Monday, July 10, 3-4pm CEST.

[Charlotte Soneson]

Hi all,
quick reminder about the bioconductor-teaching call on Monday, August 14, 3-4pm CEST.

[Charlotte Soneson]

Dear all,

a quick reminder of the bioconductor-teaching group call on Monday, September 11, 3-4 pm CEST.

[Charlotte Soneson]

Dear all,

a quick reminder of the bioc-teaching group call on Monday, October 9, 3-4pm CEST.

[Charlotte Soneson]

Hi all,

a reminder that the next bioc-teaching call is scheduled for Monday, November 13, 3-4pm CET.
jitsi link: https://meet.jit.si/BioconductorTeaching

Best,
Charlotte & Laurent

[Charlotte Soneson]

Hi,
quick reminder about the bioc-teaching call on Monday, Dec 11 at 3pm CET.

[Charlotte Soneson]

Hi all,
happy new year!
A quick reminder about the Bioc-teaching meeting on Monday, January 8, 3-4pm CET.
Jitsi link: https://meet.jit.si/BioconductorTeaching
See you on Monday,
Charlotte and Laurent

[Charlotte Soneson]

Hi all,

a quick reminder about the bioconductor-teaching group call on Monday, February 12, 3-4pm CET.

Jitsi link: https://meet.jit.si/BioconductorTeaching

See you on Monday,

Charlotte & Laurent

[Charlotte Soneson]

Hi all,

a quick reminder of the bioconductor-teaching group call on Monday, March 11, 3-4pm CET. US (and perhaps also other) participants - please take note that Europe has not yet changed to summer time, so this month's meeting will be at a different time than usual for you.

Jitsi link: https://meet.jit.si/BioconductorTeaching

See you on Monday,
Charlotte & Laurent

> On 8 Aug 2021, at 09:24, Charlotte Soneson <charlott...@gmail.com> wrote:
>
> Dear all,
>

> this is a reminder of our bioconductor-teaching group call on Monday, August 9, 2-3pm CEST. We’ll debrief after the conference workshop and plan how to move forward; if you have additional topics to discuss, plese feel free to bring them as well!
>
> The jitsi link is https://meet.jit.si/BioconductorTeaching
>
> See you on Monday
> Charlotte & Laurent
>
>> On 11 Jun 2021, at 10:53, Charlotte Soneson <charlott...@gmail.com> wrote:
>>
>> Hi everyone,
>>
>> on Monday (June 14) we’ll have our next bioc-teaching call (2pm CEST). We’ll continue working on the lessons that are under development, and plan for the BioC2021 workshop. If you have additional topics that you would like to cover, please feel free to add them to the agenda google doc!

>> Jitsi link: https://meet.jit.si/BioconductorTeaching
>> See you on Monday,
>> Charlotte & Laurent
>>

>>> On 7 May 2021, at 11:31, Charlotte Soneson <charlott...@gmail.com> wrote:
>>>
>>> Hi everyone,
>>>
>>> a quick reminder of the bioc-teaching call on Monday (May 10), now back at the usual time at 2pm CEST. Please add any item that you would like to discuss to the agenda in the google doc; currently the plan is to review our BioC2021 contributions and discuss the current draft plans for the project and RNA-seq lessons.

[Charlotte Soneson]

Hello,
a quick reminder about the bioc-teaching call on Monday, April 8, 3-4pm CEST.