Monday, June 18, 2012

Class picture

Here we are, standing in front of the AIMS building. Emma, the lead tutor, is on the left (right behind me). The other tutor, Fadoua, was away for the photo, unfortunately.

Classes end today. It's been quite a ride. I have learned a lot about computational neuroscience, and how to teach it. Thanks to all 15 students who worked hard to do the assignments I gave them. I hope they got the message that the brain is a network of neurons, and that our behaviour -- though complex -- is the result of interactions between billions of neurons. And that mathematical and computational models can be used to study those dynamics.

I finished off with the same thing I said on day 1: The brain is a complex mapping between sensory input, and motor output.

Sunday, June 17, 2012

Mystery fruit

Oh look, a pear as part of our breakfast.

Guess again.

Apparently, it's guava. I expect I've had it before, but never in this form. You eat the seeds too; they're very crunchy. The guava has a slightly sweet, and slightly tart, refreshing taste. I liked it... so I had a second.

Saturday, June 16, 2012

Shark siren

I heard a long wailing sound, and thought that it might be the fabled shark siren I've heard about. In the mountain next to the beach there is an official "shark spotter" who radios down to the beach when they see the ominous shadow of a shark. The siren means that a shark has been spotted.

Ordinarily, the waves are littered with surfers. But when I arrived at the beach, this is what I saw.

No surfing
Sure enough, that sound was the shark siren, initiated by a helicopter that had flown over and observed a dark figure in the water. After about 30 minutes with no further sightings, the beach was declared safe once again (I guess "safe" is a relative term).

It didn't take much coaxing for these eager surfers to jump back in.

I guess I would compare it to Canadians going outback camping... where bears live.

Friday, June 15, 2012

Words for names

Not surprisingly, names are quite different here than in Canada.  In particular, I've noticed that some people have names that are words. Adjectives and nouns for positive attributes, to be more precise. For example, I chatted with "Marvellous" at dinner yesterday. Another student is named "Fortunate". And I was just having breakfast with "Trust".

Of course, that does occur in the west sometimes. For example, "Charity", "Faith", "Hope".

I asked Trust about such names, and he told me that it's common practice in Nigeria and Zimbabwe.  He is from Zimbabwe. And sure enough, Marvellous is from Nigeria.

Fortunate is from South Africa, which is -- unfortunately -- a counter-example.

Thursday, June 14, 2012

Happy birthday to me

Today I get to open the present that was stashed in my bag. And... it IS cocaine.  Just kidding. This is what I got.

Front of the shirt
Back of the shirt
It's a running shirt. Which is perfect because I only brought one, and it's always stinky because I'm running quite a bit (or "hiking" might be more accurate, depending on the slope). I'll wear my new shirt for my run tomorrow.

Thank you Trish and family. It feels great to know I'm so loved.

As I mentioned, my birthday is not on the AIMS birthday calendar. I am a little relieved that no one has made a fuss.

Wednesday, June 13, 2012


One of the tutors here, Emma, organized a trip to see a rugby game. It was at Newlands Stadium, home of the South African team, Springbok (have you seen Invictus?).

The match was between the hometown Stormers (in blue) and the Cheetahs (in white), part of the Super Rugby league. I really don't understand the rules of the game. I guess I understand the general play, but I usually can't figure out what happened when play stops, eg. for a penalty. But one thing that transcends the rules... how tough the sport it. These guys run into each other, and they're big.

We joked that one of us visitors would stand up and yell "TOUCHDOWN!"

The Cheetahs almost made a come-back in the second half, but the Stormers won 16-14.


There was a fight during the match. Here it is.

Tuesday, June 12, 2012

Nots frum hom

In the days leading up to my departure, I could tell that something was up. Hush-hush talk between Addie, Heather and Trish. And sure enough, there was a mysterious envelope in my backpack as I got ready to leave.

They had written me lots of notes, more than one per day. Every morning, I pull one or two out and read them. Here is a sampling of the ones I've read so far.

Multi-coloured typesetting. I love the creativity. 
Addie's note, with her trademark monkey sticker. She's right, I miss her.
My collection of read notes (so far).
And today I pulled out one from Trish. Thank you Heather, Addie and Trish for your thoughtfulness. I am blessed.

My birthday is in a couple days, and I also found a wrapped gift in my bag with instructions not to open it until May 14 (I had to lie at the airport when asked if I packed everything myself... I hope it's not a parcel of cocaine).

More running sights

The hills beside Muizenberg are a treasure trove of things to see. I ran up to Muizernberg peak again yesterday, and here's what I saw.

I kept noticing scurrying on the rocks, and it didn't take me long to see that some species of geckos lived in the neighbourhood. This was a good morning to sun themselves on the rocks.
Some sort of gecko (yes, this is the best shot I got)
Many people pray and worship on in the hills. It's common to hear chanting and observe people in a trance-like state. I tried to be discrete as I took a quick picture of this man praying.
Man praying and chanting
He was chanting loudly, repeating the word "baba" throughout. It seems to mean "father" in many languages (such as Turkish), though Google translate says it means "baby" in Afrikaans. In any case, I'm pretty sure he's not referring to the Baba I know.

Finally, my reward for the 490m climb. A 360o panorama from the top of Muizenberg peak. (click on it to see a larger version)

Monday, June 11, 2012

She arrives in one week

In exactly one week, I'll be at the Cape Town airport to pick up Trish. She'll be dead tired, I'm sure (two overnight flights in a row).

It's exciting knowing that I'll be able to share some of my discoveries and experiences with her. Usually when I go away, it's to a conference, and Trish stays home to look after the kids. This time, my mum has agreed to take care of our kids for about 10 days while Trish comes to Cape Town. I'm so excited!

One week.

Saturday, June 9, 2012

People from different countries

Cape Town has lots of different races. Whites, blacks, browns. The one notable exception is Asians... I don't see many of them here. Of course, I haven't done a systematic study; this is just what I've noticed.

A colleague was talking about Madagascar, and I thought I misheard him when he said "Malagasi". He did in fact say Malagasi... that's what you call people from Madagascar. And their names tend to be VERY long. For example, "Randriafanomezantsoa".

Someone from Botswana was also at the table. "Motswana" is the word for people from Botswana, where their language is Setswana.


It's also feels different having so many countries on one continent. I'm not sure why. I live in North America, where there are only 2 countries (excluding Mexico). So, if you're not from Canada, then you're either American or from overseas (I don't actually encounter many people from Mexico or other Central American countries). Here, all the students are from Africa, but from many different countries: Botswana, Ghana, Ethiopia, Sudan, Madagascar, Rwanda, Malawi, Nigeria, ...

Friday, June 8, 2012

13 days away

I've been away from home for 13 days now. This is easily the longest I've ever gone without seeing my kids in person. It feels weird, especially when I can see what they're up to on my wife's blog.

My lecture tomorrow has been moved into the morning slot so I can go with some colleagues to Stellenbosch.

Thursday, June 7, 2012

Interesting meals

I've had some interesting meals since arriving here (meals are supplied for us). One breakfast was pieces of liver in a gravy, dumped on a piece of French bread. And the dinner I just ate was tripe, cow stomach in a spicy gravy (along with potatoes, etc.). According to my colleague, it's a local dish.

I ate them, though a certain amount of concentration was required, reminding myself that it's perfectly good food. They tasted fine, but I'm not used to those types of meals.

Wednesday, June 6, 2012


There is a tradition here at AIMS, as I'm told. I've witnessed it twice so far. Birthdays are not just politely acknowledged by friends. They are celebrated by the whole community. Here's how it goes.

First of all, there is a Google calendar that has birthdays on it.

During dinner in the dining hall, someone will clang their glass to get everyone's attention. Then they inform us that it's someone's birthday today, and that we should stick around after dinner for cake and celebration.

He said "cake", so I stuck around.

After dinner, out comes the goodies. But they're not distributed yet. The birthday person (today it was Stanley) sits in a chair and everyone gathers around. There is a "sharing" time when a few people tell stories, or express their gratitude to the guest of honour. Sometimes it's a bit of a roast, but all in good fun. Lots of laughing.

Then we sing Happy Birthday in about 3 different languages.

The birthday person often says a few words, and then they hand out the cake and icecream. Since the kitchen is closed at this point, we have to make do with cake on napkins, and icecream in plastic cups... no spoons.

The students and postdocs have an awesome time celebrating together... it's great to see.

The big question for me... my birthday is coming up in 8 days (May 14). But it's not in the Google calendar. What's going to happen?

Tuesday, June 5, 2012

Teaching African students

I've now taught for one week. It's about time I commented on what it's like teaching here in South Africa.

I have 14 students in my class, and they're all from South Africa. AIMS Cape Town takes students from all across the African continent, but also has a class allotted for South African students; that's the class I'm teaching.

For the most part, the students apply themselves to their studies in a serious way. For example, it's Saturday evening as I write this in my office, and I've had a number of students drop by asking questions about the assignment I gave them (the computer lab is just down the hall).

One thing I noticed is that many students seem to find some of the programming tasks difficult to understand. It's not that they can't program, but rather that they find it hard to map the task I give them onto a program. For example, I supplied them with a program that takes input X and computes output Y. The assignment asks the students to produce a plot of X vs. Y for a variety of X-values. Some needed that explained, in considerable detail.

Of course, it might be the case that my Waterloo students are exactly the same. But I don't hang out in the computer lab at Waterloo, so I'm not around for them to ask.

Part of the issue could be that they're learning a new programming language. Though I expect it's probably got a lot to do with the fact that these are math students, and not computer science students.

Our progress is slower than I anticipated, but not much slower. I think they're understanding the basics of how a neuron works, though. And that's my goal, at this point.

Day-trip to Cape Town

I hopped on the train and headed for Cape Town this morning. The train fare was a whole 22 Rand, return. That's about CDN$2.80 (Canadian dollars). Moreover, that was the first class fare (though there's not much "first class" about it... just less crammed, and probably safer for tourists).

Luckily, it was a beautiful day. Here are some photos I took.

Cape Town has palm trees.
Table Mountain, as seen from downtown Cape Town.
Under construction!
I saw species of birds I didn't recognize.
(It's an Egyptian Goose, thanks Jan G.)
I walked to a touristy area called the Waterfront. Lots of knick-knack stores that sell elephant trinkets, etc. There's also a rather large mall, very much like a North American mall.

I was watching some boats manoeuvre in the harbour, and I noticed a line of bubbles coming my way. Sure enough, I saw a big seal gracefully swoop by under the water.

After the Waterfront, I headed to the Iziko South African Museum and accompanying Planetarium. At the front desk, I was afraid to ask how much it cost. He said admission to the museum was R20, but for R25 you could also see the planetarium. For those keeping score, that's about CDN$2.50 for the museum, and an extra 65 cents to see the planetarium. That's crazy cheap, especially considering how big this museum is. In North America, I would expect to pay at least $20.

Here is a tiny sampling of the sights.

Blue whale skeleton
When I saw this cute little primate, I immediately heard a tiny voice with an English accent, "Please, sir... might I bother you for another crust of bread for me mate?"
All-in-all, the trip was a great success. The only hiccup was being honked at while crossing the road. The walk sign turned green, so I started walking. However, the walk signs around here only stay green for about 4 seconds, then flashes red. I was half-way across the road when a van stopped beside me, honking. I looked up and saw the flashing red. But it was green when I started. Frick, you'd have to be in starting-blocks to make it across in time. I was pissed, but wasn't about to raise a scene. I was probably in the wrong... somehow.

Monday, June 4, 2012


I went for a run today (May 4) up in the hills beside Muizenberg. As usual, I took my iPhone for reasons thrice:
  1. tracked my route via GPS
  2. listened to an audiobook
  3. had a camera to record the scenery
Here are some of the pictures I took. First is this panorama. Click on it to see it in full (it'll take you to the 360 Panorama page where you can really appreciate it.

I came across this rocky outcrop. There is a cave underneath it. These HUGE rocks are held up by the smallest contact points.

When reviewing the pictures after I got back I noticed something. Is it just me, or does this rock look just like Africa?

Hence, Africa is fractal. QED.

Sunday, June 3, 2012

African observations

Here are a few things that are different here than back home in Canada.
  1. There are no screens on windows (OK, it's like that in Vancouver).
  2. Cars drive on the left side of the road. That's why I almost get hit every time I try to cross the road.
  3. Drainage pipes run along the outsides of the buildings (see photo).
  4. The milk for cereal is heated.
  5. A barbecue is called a "braai" (pronounced "bri", as in "Brian"). And they rarely use propane, but rather briquettes and wood.
  6. No salad dressing.
  7. LOTS of French.
  8. There are far more Blackberries here than iPhones. That's good to see, being a Waterloo home-owner.
More later.

Saturday, June 2, 2012

Pull back on the reins

I use Matlab for my research and teaching at Waterloo.  However, AIMS encourages the use of open-source software, and that's not Matlab.

The students have been learning SciPy, a python-based scientific programming language. I decided I would use that for my computational neuroscience course. I've been wanting to learn Python for a while, anyway.

Over the past few months, I've been working on converting my basic neuroscience code from Matlab to SciPy. It's not easy. The hardest part is that in Matlab the basic data type is the matrix. But in SciPy there are different, but similar, data types. For example, if I create an array with 2 rows and 3 columns, I can store it as an "ndarray", or a "matrix". The problem is that how you can use the data depends on which type it's stored as. In particular, a plot can look totally different, even though the underlying data is the same... the data type can drastically alter how the data is interpreted. I find that annoying.

On the first day of lectures here, the instructor of the other course, Raouf Ghomrasni, said he is going to use Scilab. He said it's a free Matlab work-alike... I immediately started salivating.

Later that day, I downloaded Scilab, and found it to be excellent. In in that few hours of exposure, I decided to abandon all my SciPy preparation, and instead teach the course using Scilab.

I must admit, I feel a bit bad for the students. They know SciPy, and yet we're thrusting ANOTHER language on them. But I can make myself feel better when I consider that:
  1. Matlab is one of the most common scientific programming languages, so learning it would be an asset to these budding scientists.
  2. The students would likely stumble over the same SciPy ndarray/matrix issues I was having.
  3. Using Scilab will save me a lot of time in the long run. I'll be teaching a course on computational neuroscience at Waterloo in the fall, and I'll use Matlab for that. Investing in a Matlab-like language now will transfer more easily to that course.
So there.