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Feedback

Trainers

  • Adrian Baez-Ortega
  • Tomás Di Domenico
  • Mareike Herzog
  • Mukarram Hossain
  • Maire Lawlor
  • Sergio Martinez Cuesta
  • Anne Pajon
  • Cristian Riccio

Present at the meeting after training on 22-23 September 2016

Discussion

  • convert to python 3
  • split course into beginner/intermediate/advance
  • other python libraries to cover like pandas
  • course feedbacks

Convert to Python 3 — for sure

  • BioPython, pandas all migrated
  • anaconda is 3 by default

Add linux command introduction — basic command and tree representation; it is essential to run python from a script on the command line

Better introduction — on why we use python in a notebook, on the command line and in file explaining how we run things

Contents to drop

  • file I/O should stay but remove reading XML/PDB format only keep delimited files and maybe JSON
  • drop system call
  • drop exceptions

Contents to add

  • way of searching into python library documentation for string
  • independent learners
  • bonus exercise — use pandas to parse this file to keep them busy
  • add BioPython exercise for the reverse complement function by writing second function using BioPython doing the same thing

Contents to re-arrange

  • restructure the second day
  • section 4 (1) file then (2) command line
  • move functions before section 2

How to better stimulate the learner

  • better explanation on how to solve each exercises by splitting problems into smaller chunks
    • (1) explain how to solve an exercise by starting with a blank page and comments to divide the problem in small chunks
    • (2) search for solution on internet either on forum or in python library
    • (3) program together using functions to solve exercises
  • better manage expectations by being clearer on objectives
  • build connected exercises not disconnected ones, build upon learning — start simple and increase complexity
  • write code in group of 2 or 3; one function each to solve one bigger problem; explain and make them sure to write together a bigger program; then exchange code and progress to next level
  • bring your questions

Actions

Meeting once a month — to get running.

Next course — December 16

  • Keep exercises for sure
  • Minimize the lecture part
  • Make them search for solution
  • Assignment — like workshop couple of urls
  • Create 3 levels of exercises beginner/intermediate/advance

Checklists for December course

  • Anne to re-organize course and add BioPython exercise
  • Tomás to convert code to Python 3
  • Christian to correct typos

Christian sent his feedback by email — exceptions and reading PDB and XML files is too advanced for a beginner course. There are a few typos in the course that I can correct if somebody tells me how.