Gender differences in UC Davis VetMed students (1952–2011)

Sometimes I find myself walking down corridors on campus where you can see the graduation photos for past years of the UC Davis School of Veterinary Medicine. I'm struck by how much the gender balance has changed. In 1952, the oldest year for which a photo is shown, there are no women at all. I'm sure this is probably true of many other academic departments from this era, particularly in STEM subjects.

Fast forward 50 years or so, and the situation is very different. The latest graduation photo, from 2011, shows that 102 of the 125 students are women. Quite a reversal. I wonder how many other departments or schools have seen such a dramatic switch.

Here is how the gender balance has changed over time.

Don't make me angry, you wouldn't like me when I'm angry

Ever wonder what happens if you make a Caenorhabditis elegans nematode angry? Well you shouldn’t make a nematode angry, you wouldn’t like them if they are angry. Especially if they have harnessed the power of gamma radiation:

Before & after comparison:

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First nematode image taken from uu.nl. Green bean taken from my kitchen.

Some brief thoughts on developing and supporting command-line bioinformatics tools

A student from a class I teach emailed me recently to ask for help with a bioinformatics problem. Our email exchange prompted him to ask:

…given that so many of the command line tools are in such a difficult state to use, why would biologists start using the command line? The bioinformatics community ought to be not only supply more free easy-to-use tools, but more such tools that work via the command line. Command line tools should be installable without having to compile the program, for example

I sympathize with the frustration of everyone who’s tried, and subsequently failed, to install and/or correctly use a piece of command-line driven bioinformatics software. I especially think that lack of documentation — not to mention good documentation — is a huge issue. However, I also sympathize with the people who have to write, release, and support bioinformatics code. It can be a thankless task. This was my reply to the student:

I agree with just about everything you have said, but bear in mind:

1. Writing code is fun; writing documentation (let alone ‘good’ documentation) is a pain and often receives no reward or thanks (not that this is an excuse to not write documentation).
2. So much software becomes obsolete so quickly, it can be hard to be motivated to spend a lot of time making something easy (or easier) to use when it you know that it will be supplanted by someone else’s tool in 12 months time
3. Providing ‘free’ tools is always good, but sometime has to pay for it somewhere (at least in time spent working on code, writing documentation, fixing bugs etc).
4. Providing tools that don’t require compilation means someone would have to make software available for every different flavor of Unix and Linux (not to mention Windows). It can be hard enough to make pre-compiled code work on one distribution of Linux. Software might never be released if someone had to first compile it for multiple systems. In this sense, it is a good thing that source code can be provided so at least you can try to compile yourself.
5. A lot of software development doesn’t result in much of the way of publication success. People sometimes try publishing papers on major updates to their software and are rejected by journals (for lack of novelty). Without a good reward in the form of the currency that scientists need (e.g. publications) it is sometimes hard to encourage someone to spend any more time than is necessary to work on code.
6. People that use freely developed software are often bad at not citing it properly and/or not including full command-line examples of how they used it (both of which can end up hurting the original developer through lack of acknowledgement). It is great when people decide to blog about how something worked, or share a post on forums like SeqAnswers.
7. Many users never bother to contact the developer to see if things could be changed/improved. Some developers are working in the dark as to what people actually need from software. In this sense, improving code and documentation is a two-way street.
8. To a degree, the nature of the command-line means that command-line tools will always be more user-unfriendly than a nice, shiny GUI. But at the same time, the nature of command-line tools means that they will always be more powerful than a GUI.

My memories of Simon Chan

I still feel in a complete state of shock that Simon Chan, my friend and colleague, is no longer with us. For most of the last four years I’ve been collaborating with Simon and his lab on a number of research projects and I came to know him well. What started as a professional relationship, developed into a friendship, and I would always look forward to our regular weekly meeting with Simon. It seems so hard to believe that these meetings will never happen again.

Over the last few days I have been humbled and amazed by the realization of just how many other people have been touched by Simon’s kindness, warmth, and by his inspirational personality. At the time of writing, there have now been 146 comments left behind on this blog post, which first announced the tragic news of Simon’s passing. Without exception, every single comment reveals a story of someone who’s life has been made better from having met Simon. These are not just comments from people who have known Simon for a long time. In many instances, people have shared their experience of meeting Simon just once, but revealing how strong an impact he still managed to have on them. A second memorial page adds another fifty or so comments that shed more light on what an amazing person Simon was.

Much has already been said about Simon’s scientific achievements, about his sweet and kind personality, and about his infectious positive energy which always left you coming out of meetings with him in a ‘we can do this!’ frame of mind. In this blog post, I wanted to briefly touch on two of his other qualities: his love of music, and his love of food.

Music

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From our last practice session together, Dec 16 2010

I didn’t know Simon very well until he was invited to join the band that I was in (a UC Davis-based band that would play infrequent gigs at work-related functions). Simon could play saxophone, ukulele, and bass guitar and was very talented at all three instruments. It was the last of these instruments, the bass, that he played in our band. I’ve played in a few other bands and you sometimes play with musicians who, when learning songs for the first time, need to see the printed music in order to read every bar of every chord. More commonly, you’ll play with people who at least need to glance at the chord changes from time to time, or at the very least have to ask what key a song is in. Simon was not one of these people. He had a fantastic ear for music and could easily pick up any song and jam along effortlessly as soon as he heard a few notes. Whenever we’d have to stop playing mid-practice because one of us had screwed things up, you can bet that it was never Simon.

This was not the only reason why it was great to play alongside Simon in the band. He really loved to play music and was comfortable playing just about any genre of music. The majority of our band’s output mostly consisted of rock-based cover songs from the 50’s through to the 80’s. But Simon was just as happy when playing on some of our more jazz-inspired numbers as he was when playing on some of the grungier rock songs in our repertoire.

Within the band, we were all huge aficionados of the ‘mockumentary’ film This is Spinal Tap and given any chance at all, we would happily spend a lot of our practice time quoting from the film (what we would call STRs: Spinal Tap References). When Simon first joined, I knew he was a huge fan of jazz and wasn’t sure whether he would be irritated by our devotion to Spinal Tap and to the many, many STRs. I was overjoyed to discover that he loved the film too and was just as happy making people laugh with a well-timed STR.

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From our last gig together, Dec 17 2010

Food

To say that Simon loved food, and loved trying new food, is something of a huge understatement. Simon lived for new culinary experiences. After being able to explore the gastronomic diversity of a city like Los Angeles (where he did his post-doc) he must have found Davis somewhat limiting. But that did not stop himself from trying just about everything that Davis, and the surrounding region, had to offer.

There were many conversations between us that would begin with me asking him ‘Have you tried new restaurant ‘X’ in Davis?’ and the answer was invariably ‘yes’. Occasionally I would try a new place in Davis in the week that it had opened, and this would give me the false confidence that I could approach Simon to tell him of a place that he had not yet tried. Invariably, however, he would have already been there and would be able to offer thoughtful commentary on their menu. If you ever ate with Simon at a place that he liked (e.g. Hometown Chinese in Davis), then it was common to realize that he was on first name terms with the owners. I can only imagine that Simon has made firm friendships with restauranteurs around the world.

For my 40th birthday I organized a quiz which Simon attended. One of the questions was based on guessing how many different eateries in Davis I had frequented (researched using the Davis Wiki restaurants page). The day after my birthday, Simon sent me an email to reveal that he had eaten at 97 of the 126 Davis restaurants on the list, with the exceptions — mostly chain fast-food restaurants — being through choice. The same email went on to reveal the total number of restaurants that Simon had eaten at since he first started logging such activities (I think this may have begun while he was in Los Angeles). Simon’s list featured a jaw-dropping 1,338 different restaurants! This was a man that loved his food.

As soon as Simon heard that I had to go to Vancouver to renew a visa, his first piece of advice was to check out a particular restaurant in China Town for their braised pork in soy sauce. When Simon recommends a place, you can’t really ignore that advice. I found the restaurant, ordered the pork, and it was indeed excellent.

Simon didn’t just love trying out new restaurants, he loved trying out different and unusual ingredients. He once shared details with me of The Omnivores Hundred: a list of one hundred different items that “every good omnivore should have tried at least once in their life”. This list includes relatively benign items such as ‘Eggs benedict’ and ‘Polenta’, but also includes such…shall we say interesting, delicacies as Brawn, Sweetbreads, and Roadkill. As of April 2009, Simon had tried 81 things off of this list, and I imagine he ticked off a few more in the years since then.

I once remarked to Simon that my wife and I often tried to host a traditional Burns Night Supper in Davis, but that it was really hard to find Haggis here. The next time I saw Simon, he produced a tin of haggis for me which he had found for us somewhere in the Bay Area. That was exactly the sort of person Simon was: always generous, always thinking of others…and probably always thinking of food!

Goodbye

Simon has been taken from us all far too soon and it still doesn’t seem real that he won’t be around to tell us of amazing new eateries he’s discovered, or regale us with tales of strange foods from far away lands. I’d like to extend my sincerest condolences to Simon’s family. At the same time, I’d like to thank them all for helping make Simon the wonderful person that he was. Like so many others, my life has been enriched for knowing Simon and I will treasure the memories that I have of him.

Farewell Simon. In music, in food, and in life, you always went up to 11 (STR).

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Simon Chan 1974-2012