Ed's Big Plans

Python Crash Course

Having completed teaching that Python Crash Course before reading week, I can say that I’m probably not going to teach it again any time soon for its time commitment! It was a good experience for me since I’ve figured out how to balance content for time and also how to talk to a crowd of heterogeneous experience levels in programming.

There’s going to be a PERL one-off course offered by BIC on this week that I think I’ll attend to figure out what the general style is for one-session courses– it was previously offered by Edgar and is offered this time by Anna and James.

I definitely need to clean up the course materials, but Andre thinks we should have my course packaged along with the Biology for Engineers course he offered. These two packages will eventually be shipped off to oGEM & iGEM HQ as per their recent interest in local workshops.

Link: Python Crash Course Materials

CS [64]83 Structural Bioinformatics

I threw up a hints page some time two weeks ago to coordinate help for assignment three for the structural bioinformatics course I’ve been auditing. I’ll probably take it down from the main menu when it becomes completely irrelevant. For the mean time, I’ll leave it up or replace it with assignment four hints when that gets underway.

I think I’ll eventually consolidate all of my one-off pages as a single page linked in the menu to reduce clutter. I’ll probably put all of my slide shows in there too.

Link: Structural Bioinformatics A3 Hints

This week is going to be crowded enough for me that I’m going to cancel this week’s class. On the bright side, the classes have gone better than I thought it would. We will continue on February 9th.

The very first class ended up being too short, with the advanced students feeling that it moved too slowly. The second and third classes ended up being just the right speed– with the exception that the example fill-in-the-blank script from the third class was too difficult.

The difficulty rose when I too quickly introduced dictionaries whose values are lists.

The fourth class held last week was excellent– I completely ditched slides that week and produced five fill-in-the-blank scripts that were just the right tempo for everyone. I had a good mix of BIC (Bioinformatics Club), iGEM and chemistry graduate students– all who attended got something out of the hour which was my objective.

We only had time for four out of the five scripts with the remaining script as a bonus that everyone could take home and try.

Now, it’s back to Structural Bioinformatics homework… It’s quite a daunting assignment to be true (having just formally shaken hands with Singular Value Decomposition), but the parts that are Python (particularly the bonus question) are familiar enough for comfort.

The first lecture of my Python Crash Course went really well! I ran it two evenings ago in the Dean’s Conference Room.

In gearing the very first lecture for absolute beginners, I had very little to cater to BIC (Bioinformatics Club) members. I however took the opportunity to discuss with them about the SOLVER group (more on that later); many of which seemed interested.

Overall there were roughly a dozen people that turned out, including Ariana, my TA partner from last term. There were about four iGEM members and six BIC members.

I also took the opportunity to poll for the kinds of things that students wanted to learn. Here are my findings.

• Object Orientation is something everyone wants to know– especially the people coming in with a Javascript, PERL, C, C++ and Scheme background; I was surprised that the C++ people didn’t get exposure to thinking in objects earlier.
• The beginners came in two groups. First, there are the ones who are happy to learn anything as long as it can be applied later.
• The second group of beginners want to data crunch PDBs, SDFs, FASTAs, Nucleotides etc.

In week two, we’ll take care of object orientation and in week three, we’ll take care of everything anyone ever needs to know about input output in order to do data crunching. I have added a link in the navigation of this blog for the Python Crash Courseware which will eventually include all the PDFs, code modules and examples used in class.

Oh right, I don’t know if I’ll get around to it– but I am missing instructions for setting environment variables in Windows. Perhaps I will add it later when I have time.

(iGEM attendees were John Heil, Danielle Nash, Tiffany and Lina; BIC members included Fiona, James and about four others whose names I have forgotten.)

Edit: Direct link to Python Crash Courseware; Direct link to Week 1: A Mad Mad Introduction, PDF.

Draft Syllabus Here (public Google doc).

I’m currently putting together the course materials for my Python Crash Course for Biologists… all that’s left is to fasten the lesson ideas into slide shows, example code and exercise materials and I’ll be ready to indicate a launch date.

I’ve heard some interest from iGem members, lab mates here at the Meiering lab and also the Waterloo Bioinformatics Club… I want to run this soon.

Andre may be doing something similar on a different topic– so it’s been very nice to have another set of eyes evaluate the syllabus.