greenelab / GCB535

Materials for GCB535 at Penn.
BSD 3-Clause "New" or "Revised" License
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Timing/pacing of course #30

Closed cgreene closed 8 years ago

cgreene commented 8 years ago
cgreene commented 8 years ago

@bvoight What do you think about starting with browser-based methods. UCSC (and motifs? didn't notice programming there but might have missed it - @ksiewert ). Then progressing through Unix & ChIP-Seq. Then we could hit R/Python and the modules that use them.

cgreene commented 8 years ago

Also - if TAs have any records of what assignments were the most trouble to people based on inference from office hours ( @alexamlie @ksiewert ) that'd be great. Doesn't look like the students provided specifics.

bvoight commented 8 years ago

UCSC doesn't use much programming; motifs etc. uses bedtools as the main thing. So, I think the'd need to know some UNIX before they ran with this. -BV


Benjamin F. Voight, Ph.D. Assistant Professor, Departments of Pharmacology and Genetics The University of Pennsylvania - Perelman School of Medicine Tel: (215) 746-8083; Email: bvoight@upenn.edu; Twitter: @bvoight28 https://twitter.com/bvoight28 http://coruscant.itmat.upenn.edu

On Mon, Jun 20, 2016 at 10:41 AM, Casey Greene notifications@github.com wrote:

@bvoight https://github.com/bvoight What do you think about starting with browser-based methods. UCSC (and motifs? didn't notice programming there but might have missed it - @ksiewert https://github.com/ksiewert ). Then progressing through Unix & ChIP-Seq. Then we could hit R/Python and the modules that use them.

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cgreene commented 8 years ago
cgreene commented 8 years ago

ENCODE ipynbs aren't loading for me right now - I think they might just depend UNIX/Databases but not sure.

ksiewert commented 8 years ago

The hardest assignments were definitely the the bioconductor ones, so we ended giving them an extra class to do them (11 and 12 I think were the numbers). Are the ENCODE ipynbs loading now? I updated new versions.

cgreene commented 8 years ago

@ksiewert : Might be the github interface. I still get failure to load on chrome. Any luck for you?

ksiewert commented 8 years ago

Yeah, ENCODE 1 isn't working for me on the github interface, but ENCODE 2 is. Let me e-mail you the .ipynb notebook file, and maybe you can try uploading it? Might be a jupyter for linux issue?

cgreene commented 8 years ago

I think it's probably just timing out in the rendering. I can clone the repo and see it, so I'm not too worried.

On Wed, Jul 6, 2016 at 3:24 PM ksiewert notifications@github.com wrote:

Yeah, ENCODE 1 isn't working for me on the github interface, but ENCODE 2 is. Let me e-mail you the .ipynb notebook file, and maybe you can try uploading it? Might be a jupyter for linux issue?

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cgreene commented 8 years ago

The course has been reorganized to address these concerns. Closed by #59