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2017 03 16

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Leighton Pritchard edited this page Mar 27, 2017 · 5 revisions

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Presentation 16th March 2017

Day one of the first run of the course. At the end of each session, students were asked to give one thing they liked or a positive item of feedback on a green sticky note, and one thing they didn't like or a negative item of feedback on a red sticky note.

Session 01: Peter Cock, covering platform and introduction

This session was run using MobaXterm on the Windows desktops to access a shared Linux server running as a VM. This worked reasonably well although with Jupyter Notebook accessed via Firefox over X-Windows, scrolling was painfully slow. Also in a couple of cases Firefox browser and/or X Windows appeared to hang.

Feedback

Red Stickies

  • Maybe a higher number of exercises or examples would help
  • Functions are a bit overwhelming... Maybe take more time to explain
  • Time planning (it is a bit rushed)
  • Printed material
  • It would be good if programs ran quicker, but not much that you could do about that
  • Too less background on the topic for someone starting from scratch
  • Went through some command functions too fast for a total beginner + would like to do more examples typing out myself
  • As a physicist/chemist, I struggled to follow the biology (had to Google a lot of terms)
  • Can explain codes a little bit more
  • More information on the genome annotation would be appreciated
  • A bit slow running the programs
  • Server is slow AF
  • It's great that you show us Jupyter but you could run Python code locally as well (to avoid the necessity of scrolling)
  • Too complex for beginner
  • Everything not in detail
Green Stickies
  • Artemis
  • Interactive
  • Friendly demonstrators
  • Course was easy to follow and explained simply
  • Demonstrators were patient
  • Very helpful making sure everyone on track
  • Started out nice and slow/simple
  • Really good ratio of tutors to students
  • Course is well-organised, I love that you are already giving us the code so we can focus on learning how it works
  • Explanations are great, clear, and easy to follow
  • No software issues
  • It's well explained, basic concepts
  • Things were explained well and there were enough people to help
  • It's been very clear and dynamic
  • Very didactic in general
  • Good examples to cover through course
  • Good number of exercises and things for us to try out
  • Good overview of the programs
  • Artemis
  • Interactive
  • Help provided quickly

Session 02: Leighton Pritchard, covering sequence databases

Presented lessons:

  • 01: BLAST at NCBI
  • 02: BLAST in terminal
These lessons suffered heavily in pacing and understandability because of the server issues. We didn't get to the notebook BLAST, which might be an issue in the morning session on the second day. What I got through I felt OK with at the time. [LP]
  • 06: UniProt in browser
  • 07: UniProt in notebook
This felt like the most successful explanation of the day - once the graphical output was demonstrated, and the efficiency with which you can get from a UniProt query to a manuscript-ready summary image was shown. [LP]
  • 08: KEGG in browser
  • 09: KEGG in notebook
Both KEGG lessons were a bit undercooked, and had too many examples without an obvious 'hook' - again, until the graphics came up again. But that was a bit too little too late. The examples felt too systematic as I was delivering them. [LP]

In general, I think I'd like to rework these lessons and give a bit more motivating structure to link exercises, rather than just have apparently unconnected exercises - maybe linking in to previously published papers would help.

Feedback

Red Stickies

  • Encumbered second session
  • Too quick
  • A basic dictionary would be useful, and a slower pace for some steps
  • Too many information in a go and command based
  • A bit fast sometimes because the browser is slow
  • Too much info together
  • Too fast for learning programming (using command)
  • A little bit fast on certain topics
  • It was a bit rushed
  • Was losing concentration near the end - an extra break would have been good
Green Stickies
  • Friendly and helpful demonstrators
  • Interesting content
  • Interesting
  • Very helpful information about UniProt and KEGG
  • KEGG
  • KEGG
  • How it works, really clear and useful
  • Well done each database for their function/use
  • Uniprot & KEGG, Browser and notebook
  • Awesome presentation
  • Great material coverage
  • The GitHub cloud is very useful - please keep it online as I will use it to revise
  • Demonstrators were helpful and very good at explaining things
  • Helpful when asking for help
  • Good explanations but difficult to follow at same time as doing something on the computer
  • Course well laid out
  • Many interesting info
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