Software Carpentry

Helping scientists make better software since 1997

Archive for July 2009


Today (Thursday) was the second-to-last of the course. It’s been a long haul, but we hope a rewarding one. In the morning, the students had an hour-long overview of results from empirical studies of real-world software engineering; in the afternoon, we looked at how traditional and agile development processes are responses to those facts. Tomorrow morning, we’ll spend an hour talking about what’s gone right and what’s gone wrong, then head out for a farewell lunch.

And in late-breaking news, one of the students, Mark Tovey, has started a blog on open source cognitive science. Thinking about it now, we should have required all of the students to start and maintain blogs during the course; here’s hoping some will do it now of their own accord (hint, hint).

Written by Greg Wilson

2009/07/31 at 00:23

Posted in Alberta, Toronto, Version 3

A Good Afternoon

Yesterday afternoon, the students and ninety other guests were treated to six engaging talks about Science 2.0 from Titus Brown, Cameron Neylon, Victoria Stodden, David Rich, Michael Nielsen, and Jon Udell. We’ll post slides and video here as soon as we get them; until then, you can catch up on what happened in the FriendFeed room or by reading Steve Easterbrook’s real-time blog of the event.

Our thanks once again to everyone who made the day possible:


Written by Greg Wilson

2009/07/31 at 00:20

Every Day Is a Big Day…

…but today is bigger than most: after lectures yesterday on server-side web programming and building GUIs, students will spend this morning exploring ways to apply what they’ve learned in the course to their own research problems.  This afternoon, we have a stellar line up of speakers from 1:00 to 6:00 pm at the MaRS Centre to talk about how the web is changing the way science is done. We’ll post video of the talks as soon as we can, but if you’d like to follow along in real time, we are:

Written by Greg Wilson

2009/07/29 at 09:45

Posted in Alberta, Toronto, Version 3

Day 11 and Day 12

Yesterday (Monday) morning we covered the basics of handling binary data, including bit twiddling and the use of Python’s struct module to pack and unpack binary representations of objects.  The afternoon was a lightning introduction to how the web works: a simple socket example (just to show students the plumbing) was followed by a description of HTTP’s requests and responses, then a look at urllib.  Today is going to be devoted to the absolute bare bones of server-side programming, with GUI programming using Tkinter as a follow-up.  “Fast paced” doesn’t even touch it, but I hope students will come away with an idea of what’s possible, and where to look for more information.

Written by Greg Wilson

2009/07/28 at 09:59

Posted in Alberta, Toronto, Version 3

Where This Course Came From

I have created an Listmania list for the books that most directly influenced this course.  Some topics aren’t directly represented—there’s nothing devoted to handling XML or binary data, for example, or on big-Oh complexity or web programming—but I hope what’s there will be of use.

Written by Greg Wilson

2009/07/27 at 16:27

Posted in Content

Martin Fenner on SciBarCamp

Nature‘s Martin Fenner has blogged a summary of what he heard and saw at SciBarCamp’09 in Palo Alto a couple of weeks ago.  Cameron Neylon was there too—in fact, I’d be willing to bet that a healthy number of attendees posted their experiences in some form or another.  Maybe the next challenge for scientific publishing is something that will aggregate and summarize disparate reports of such events?

What I’m most interested in, though, is figuring out what’s needed to make that kind of reporting happen. Mark Tovey has been reporting on the Software Carpentry course in near-real time at FriendFeed, but there have been very few comments or contributions from other students.  Is his record complete enough that no one can think of anything to add?  As quickly as he types, that still seems unlikely, and even if it was true, I’d expect people to have questions or to want to add more detail. Is it the classroom setting, and all the behavioral baggage that brings with it?  I had the students in my software engineering class last term write up lectures as wiki pages to earn 10% of their course grade; perhaps that kind of stick has to accompany the carrot of social good?

Written by Greg Wilson

2009/07/26 at 15:54

Posted in Community, Noticed

Day 10 Done — and With It, Week 2

XML in the morning, regular expressions in the afternoon—it’s been a long week, but a productive one (I hope).  We’re going to shuffle some of the material around so that we can do binary data processing, web client and server programming, and GUI programming next week.  The highlight, of course, will be the guest speakers on Wednesday afternoon.  I hope the students have a restful weekend; I’m looking forward to the last lap.

Written by Greg Wilson

2009/07/24 at 21:45

Posted in Alberta, Toronto, Version 3

Day 9

I meant to write this post yesterday, but we’re watching Torchwood: Children of Earth, and, well, you know how it goes.  We spent two sessions looking at the basics of SQL and relational databases, which almost every scientist is going to encounter at some point in their career. The morning exercises were obviously too easy—students completed them in a little over and hour—but the afternoon seemed to go at the right pace. This morning we’re going to look at XML, and this afternoon at text processing with regular expressions.

Written by Greg Wilson

2009/07/24 at 12:57

Posted in Alberta, Toronto, Version 3

Day 8: Getting It Right

This morning’s lecture was a high-level look at software testing, with a long-ish detour into exceptions; this afternoon was an introduction to Python’s unittest framework, with some handwaving about testing that functions throw the right kinds of exceptions, replacing files and other slow objects with mock equivalents, and how you decide what tests to write first. It felt like it went better than yesterday’s lectures on object-oriented programming, which I think left some students a little bewildered. We’re spending tomorrow looking at databases, which means I have to brush up on my SQL tonight…

Written by Greg Wilson

2009/07/22 at 20:01

Posted in Alberta, Toronto, Version 3

Day 7: Lots More Objects

We took a detour from the notes yesterday morning and built some classes to represent matrices. One reason was to show students how to break a problem down into pieces and solve them one by one; another was to introduce the notions of encapsulation, polymorphism, and inheritance.  Aran Donohue (one of the TAs here in Toronto) thinks that inheritance is over-taught, and taught too early—he may be right, but it’s also hard to avoid, since so many libraries and frameworks (and tutorials, but that’s a circular argument) expect familiarity with it.

We looked at operator overloading and (very briefly) at design patterns in the afternoon, then did a modeling exercise. What classes would you create if you were writing a program to simulate solar systems? What would those classes’ responsibilities be, and which classes would collaborate with which others? The most creative solution included Santa Claus; the most complete took collisions and explosions into account.

Day 8 will be quality assurance and unit testing. By the time we’re done, we’ll be halfway through…

Written by Greg Wilson

2009/07/22 at 12:58

Posted in Alberta, Toronto, Version 3


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