schedule alterations

[smcclatchy]

The following table references chapters from The Bioconductor 2018 Workshop Compilation.
You can see the workshop schedule that I developed on the workshop website. Please comment on which topics you might want to skip, others you might want to add in that aren't there yet, or things that you'd like to spend more or less time on.

Level	Chapter	Activity	Time	Teach this?
100	2.2	Introduction to R	45m	no; R is _a__ prerequisite
100	2.3	Introduction to Bioconductor	60m	yes
201	7.2-7.8	RNA-seq data analysis with DESeq2	120m	yes, and Martin recommends this one as opposed to limma, etc
LUNCH
102	4.4-4.19	Solving common bioinformatic challenges using GenomicRanges	60m for Workflows only; allocated 75m	yes
COFFEE
101	3.4	Introduction to Bioconductor annotation resources	unspecified; allocated 45m	yes
103	5.3-5.10	Public data resources and Bioconductor	75m, but only allocated 60m	yes
103	5.11	Microbiome data	15m	no
103	5.12	Pharmacogenomics	20m	no
200	6.4-6.7	RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR	60m	no
210	9.4-9.13	Functional enrichment analysis of high-throughput omics data	75m	no, but Martin says this is a good option

[omsai]

Thanks for putting this together @smcclatchy! It's great seeing how useful the BiocWorkshops are toward making the 1-day Carpentries workshop.

The end of 2.3 introduces DESeq2 analysis but our schedule doesn't get to DESeq2 until the very end with 7.x. In the original schedule, 2.x and 7.x were taught back-to-back.

We definitely should choose between 6.x and 7.x because edgeR and DESeq2 both do differential gene expression and probably only want to teach one of them. Looking through the lessons, 7.x teaches scientific concepts and data exploration using high level tools, and 6.x has more typical processing steps and I think broader appeal.

We might reorder to have differential expression (6.x or 7.x) after the intro because I seems to have less cognitive load than GenomicRanges (4.x) and follow up with annotation and public resources (3.x, 5.3-5.10). It's not that GenomicRanges is really harder, there's just more things to cover.

One might trim down the teaching material by identifying more parts to be packaged as optional "Challenges" because I get the sense that at least some of the modules were taught by executing code blocks in Markdown documents, which is not the Carpentries style of typing every word out; students running code blocks risk not understanding what's going on. Would it be too early to decide who teaches which section for the October workshops? I have this inefficient habit of working through the workshop exercises fully to feel out the hot spots and don't think we individually would have the bandwidth to do all the sections so we could each pick our piece to closely examine.

[smcclatchy]

I've heard back from Martin Morgan with his recommendations for Bioconductor teaching @jethrojohnson @asliuyar @omsai @dmgatti

Hi Susan -- glad to hear that there is enthusiasm. I'd aim for about four topics of those workshops, maximum -- 4 x 1.5 hour sessions, with breaks and lunch.

Is 100 relevant (personally I think almost always yes, participants sometimes think we spend too much time here). 200 / 201 / 202 have a similar flavor; choose one? (I'd do 201) 101 / 103 are complementary; maybe combine selectively? 210 looks good

I'd be tempted find some domain-specific material from http://bioconductor.org/packages/release/BiocViews.html#___Workflow especially the methylation or ChIP-seq workflows but these might require some fairly heavy effort to get into shape for the available time.

Martin

[smcclatchy]

Hi @jethrojohnson @asliuyar @omsai @dmgatti

You can sign up to teach at the Fri Oct 12 Bar Harbor Bioconductor Workshop

OR

Wed Oct 17 Farmington Bioconductor Workshop

You can also re-arrange, add, or delete topics to the instructor sign-up sheet, and I'll update the workshop website accordingly. I'll also find helpers.

[omsai]

@smcclatchy I've signed up for Bioconductor Farmington for the topics I'm most familiar; I can add myself to 1 more slot if need be. Also if you need more instructors for the prerequisite R workshop the 2 days before, I can teach that Monday October 15 afternoon.

[smcclatchy]

Great, thank @omsai There is one other person who might be interested in teaching Bioconductor in Farmington, but he only just went through Carpentry instructor training last week. I have selected only experienced Carpentry instructors to teach Bioconductor because I know all of you will be able to handle putting together disparate training materials and adapting to situations on the fly as needed. If we need another person though, I can ask Diogo if he would take a teaching slot. He might also be a good alternative in case @jethrojohnson isn't available or doesn't want to teach a specific segment.