Some blog updates

Yes, I’ve had a few minutes of time that I dedicated to my blog last night.  I’ve made great progress on my thesis, so I didn’t mind spending a few minutes in the evening writing, coding or learning a bit more about wordpress.  Frankly, I think my blog needed a few cosmetic updates anyhow.

First, I’ve customized the menu above.  Turns out it’s not hard to do in word press.  Once that was done, I wrote a new about page, added a couple links and then realized that the links on the right were redundant, so they’re gone now.  Yay progress.

The font size for the main text has been shrunk.  If it’s too small for anyone, let me know.  I had always felt it was a bit too large, so I’m glad it wasn’t too hard to do.

I also added a link to my old blog, but then discovered that wordpress offers a half-assed method of importing from blogger.  Unfortunately, none of the comments made it over, but the nearly 400 blog entries from my old blog did (albeit with some funky extra “>” characters).  However, that makes my old blog pretty much obsolete, so if I ever get the comments to move over, I’ll take down the website and the new button as well. At any rate, you can use the search bar on the right to go through all of my blog posts from 2006 till now (minus the ones at Nature blogs, of course).

That means that my site now spans just over 5 years, covering some 555 posts (including this one) and 106 categories.   That’s an average of about 111 posts a year, or about 2 posts a week.  I’m sure my conference blogging skews that number, but it’s not insignificant.  Wow.  I certainly hadn’t thought I’d been blogging that much…!

Finally, I’ve also changed my blog’s perma-links from the ugly /?p=XXX format to one that reflects the date and title of the post.  The old format should also work if you’re linking here from an old URL, but it won’t be how I refer to posts from now on.  Just thought you should know.

So, no major changes, but a lot of little details.  I hope they make my blog a bit more usable and readable… and perhaps just a little more professional looking.  If there’s anything I’ve missed that would be useful, don’t hesitate to let me know.

Is blogging revolutionizing science communication?

There’s been a lot of talk about blogging changing the nature of science communication recently that I think is completely missing the mark.  And, given that I see this really often, I thought I’d comment on it quickly.   (aka, this is a short, and not particularly well researched post… but deal with it.  I’m on “vacation” this week.)

Two of the articles/posts that are still on my desktop (that discuss this topic, albeit in the context of changing the presentation of science, not really in science communication) are:

But  I’ve come across a ton of them, and they all say (emphatically) that blogging has changed the way we communicate in science.  Well Yes and No.

Yes, it has changed the way scientists communicate between themselves.  I don’t run to the journal stacks anymore when I want to know what’s going on in someone’s lab, I run to the lab blog.  Or I check the twitter feed… or I’ll look for someone else blogging about the research.  You learn a lot that way, and it is actually representative of what’s going on in the world – and the researcher’s opinions on a much broader set of topics.  That is to say, it’s not a static picture of what small set of experiments worked in the lab in 1997.

On the other hand, I don’t think that there are nearly enough bloggers making science accessible for lay people.  We haven’t made science more easily understood by those outside of our fields – we’ve just make it easier for scientists inside our own field to find and compare information.

I know there are a few good blogs out there trying to make research easier to understand, but they are few and far between.  I, personally, haven’t written an article trying to explain what I do for a non-scientist in well over a year.

So, yes, blogging has changed science communication, but as far as I can tell, we’ve only changed it for the scientists.

11 tips for blogging talks and conferences

While I’m still not quite recovered from the jet-lag from the flight home, I thought I’d take a quick shot at answering a question I was asked frequently last week:  “How do you blog a scientific conference?”  So I thought I’d take a stab at some of the key points in case anyone else has any interest in trying.

  1. Focus! The hardest thing about blogging a conference is the amount of attention it takes.  If you are easily distracted, you’ll miss things – and it can be really hard to get back into a talk once you’ve missed a couple of key points.  Checking your email, twitter or surfing the web are all bad ideas.
  2. Listen! The speaker is really the best source for getting the key points.  If they’re doing a good job, then you don’t even need to see the slides – they’ll summarize the main points and make your job easy.
  3. Know your limits. If you don’t understand something, you’re not going to be able to summarize and explain it.  Frankly, product talks are pretty much impossible to blog – just point to the catalog.
  4. Read the slides.  A really bad speaker can make it hard to blog their talk, but fortunately, that’s what slides are for: summarizing the presenter’s points.  If you can’t follow along with what they’re saying, you can always interpret the slides for yourself.
  5. Know what to omit.  A really good speaker can be incredibly distracting, wandering away from the main point of the talk to tell stories or insert asides.  You don’t need to write down everything, especially if you can’t reproduce it well.  Capturing speakers jokes can be next to impossible.
  6. Think! It may sound odd, but the process of writing notes is about what you think is important.  You have to carefully interpret what the speaker is saying and decide what is that you feel is central to the arguments.  Blindly copying things frequently fails to tell the story well.
  7. Don’t guess! It’s easy to miss something (and yes, you will miss things), but how you handle the things you miss is important.  If you can’t remember a number or an exact phrasing, just summarize it – if you guess about the value or quote someone incorrectly, it can really upset both the speaker who’s work you’ve misrepresented or the audience, who may rely on what you’ve told them.  If you’re not sure on a point, be clear about that as well.  It’s better to err on the side of caution.
  8. Keep your thoughts separate. This can be challenging.  With all that’s going on, it’s easy to mix up your opinions with the speaker’s points, since your notes are really just your interpretation of what you’re hearing.   However, to preserve the integrity of the speaker’s points, you need to ensure that they don’t get confused.  I use a system of brackets to do so but any other clearly marked system will work as well.
  9. Type fast! This should be obvious.  The faster you can type, the more complete your notes will be.  Conference blogging is not for slow typers.
  10. Use the right tools. I blog directly in my blog’s editor, but you can use any other system that works for you.  The most challenging part is to make sure you have autosave on, and that it works well.  There’s nothing worse than losing something you’ve written – especially since you can’t go back to ask a speaker to do their first 10 slides over if something goes wrong.
  11. Practice! This isn’t a skill you develop overnight – the more you do this, the easier it becomes.  Start with a single talk and learn from your mistakes.

So, there you have it.  The top 11 tips I’d give for anyone who would like to blog a talk – or even a whole conference.   And, of course, don’t forget to enjoy the talks.  If you’re not getting something out of listening to someone else speaking, why are you taking notes on it? (-:

CPHx: Apologies


Yes, there are no notes for the second talk, by Dr. Søren Johannes Sørensen from the University of Copenhagen.

I had difficulty with my web server going off line temporarily (I’ll be looking into that this evening) and ended up spending the few minutes setting up an alternate location to blog.  I’ll hold that as a standby in case of further issues, although it appears the problems have now been resolved.

In any case, the talk mainly focussed on determining how to measure diversity – and where to draw the line in quantifying diversity.  It was a challenging talk to blog, in any case, as it was full of graphics showing that diversity can be measured differently and has subtle effects, depending on where you place your thresholds

In any case, I’m glad to have the technical issues strike at the beginning – with luck, the rest of the conference will go smoothly.


Most enlightened blogging policy…

I really have to hand it to the Copenhagenomics foundation – they have an incredibly enlightened blogging policy, in three different directions.

  1. They encourage blogging and twittering – the best way to open communications and conversations in the science community and to give people who can’t attend an opportunity to participate in the discussion.
  2. They’ve invited a blogger to ensure that the science does become recorded.  It’s not enough to assume that having an open blogging policy will push the discussion out into the internet, you need to ensure it gets there. (In full disclosure mode, I’m the blogger they’ve invited, so I guess it’ll be my fault if the conference doesn’t get a lot of followers. doh!)
  3. They’ve prepared the speakers by ensuring they’re all familiar with the blogging/tweeting policy.  With an open default position, it’s up to the speakers to restrict where they don’t want the blogging to cover, rather than to open it up. This makes much more sense, as science should be an open endeavour rather than peeking out from closed doors.

I encourage anyone who’s interested in hosting a conference to follow the CPHx lead.  Here’s the post on their web page about their “sharing is caring” policy.

Oh, and by the way, if you’re reading my blog over the next few days and happen to catch the occasional “ø” instead of an apostrophe, it’s because I’ve gone native with a Danish keyboard, thanks to the great people at CLCbio.  My own laptop will be visiting the apple repair store next week, when I get back to Vancouver.

blogging as practice for thesis writing…

I’ve been telling all of the students around me that they should try their hand at blogging – in fact, I’ve been telling everyone around me that blogging is definitely something you should try if you have a chance. I know that not everyone has a lot to say, but that it’s a great habit to be in. It’s a great way to practice organized writing (without 140 character limits), putting your views out where others can see it, defending your ideas and, of course, it’s great practice at organizing your thoughts. In other words, it’s a microcosm of your final 6-9 months of your graduate studies.

Indeed, I had no idea how much that advice was actually worth till I sat down yesterday afternoon, and started writing out some parts of my thesis. (Yes, I’m now actually writing my thesis!) The brilliant thing was, after spending so much time writing on my blog, the thesis seems SO much easier than the ones I’ve done in the past. (This is actually my 4th thesis.) The text just flowed, which makes the whole process rather fun.. (Yes, thesis and fun in one sentence!)

When I sat down and organized my thoughts on a subject, things just came together and I knew what I wanted to say and how to say it, which I can only ascribe to the endless practice of writing on my blog. Yes, the style is a bit different and less reflective, but other than minor stylistic changes, the process is almost identical.

So, for anyone who’s going to eventually have to write a thesis, I’ll make a suggestion: start practicing for it by starting a blog, even if no one reads it. Keeping your writing skills in shape is invaluable.

My lesson learned.

One shouldn’t often engage in a war of words with people who comment on blogs on the Internet.  It’s rarely productive.  In this case, there are a few points I could clarify by responding to a comment with a particularly ugly tone, especially given that it was written by someone with an illustrious career in a field related to my own.  They’ve held the position of chair and vice chair of multiple departments, have been a professor since before I was born and have hundreds of publications…  And yet, this individual has chosen to send me a message with the identity “fuckhead” – accusing me of intimidating a junior grad student.  Instead of using his real name, I’ll use the moniker “fuckhead” that he chose for himself, and I’ll post fuckhead’s comments below, interspersed with my reply.

I do need to acknowledge that my tone in my “Advice to graduate students” was somewhat condescending, due to some rather unfortunate word choices on my part.  I have since edited the post for tone, but not for content.  That said, fuckhead’s comment (and unfortunate choice of moniker) was still inappropriate and deserves a reply – and yes, it is a great cathartic release to reply to a negative comment once in a while.

“Coming on the heels of the previous “why I have not graduated yet” post, this is telling”.

Oddly enough, the point of my post on why I haven’t graduated yet was because I’m unable to find any clear signals in the noise in my data set, while my point on advice to other graduate students was about respecting your colleagues, even if it wasn’t necessarily obvious in my first released version of the post.  Putting the two together might allow for a few interesting conclusions – although I would suggest that it is not the ones that are suggested in the comment.

“It’s one thing to intimidate a student out of the way (rather simple, actually, if you have the slightest clue what you are doing), but what you espouse here will poison you. So you’ve been working on the topic for a while, and some meatball comes along and asks you about the topic, and your reaction is ‘get bent’? What will you tell people when they ask what you spent X years of your life on in graduate school? ‘Get bent’?”

It should be clear right away that fuckhead really doesn’t know me well.  I run a blog to share information and help other people, I have more than 200 posts (answering questions) on, all of the code I’ve written towards my thesis has been available freely on source forge for 3 years, I’ve dedicated countless hours to helping other bioinformaticians online and always make time to help out my fellow students. (My resume is online somewhere, if you want more than that.) I probably have told a few people to “get bent”, as it were, but in this case, I most certainly didn’t.

It’s rather telling to me that fuckhead didn’t take the time to find out who I am before jumping to the conclusion that I’m obstructive and surly towards my colleagues.  I can be gruff when people don’t take the time to think through their questions, but I always take the time to listen to my colleagues and help them find the information they need.  If my tone is a bit gruff sometimes, we all have off days – and it’s an inherent danger of insufficient blog editing as well.

“Do you think that you are going to cure cancer, or are you trying to make a little tiny dent in the vast universe of ignorance that surrounds humankind?”

Wow… leading question.  While I do joke that my job is to “cure cancer”, I’m fully aware that expectations for graduate students are low and making a “little tiny dent in the vast universe of ignorance” is where the bar is normally set.  In case it wasn’t clear, no one expects me to cure cancer while working on my doctorate.

That said, who’s to say that neither myself nor the incoming graduate student can’t be the one who does find an important cure? Why hobble myself by agreeing to do no more than meet your base expectations.? Fuckhead doesn’t say why he thinks I shouldn’t have big goals – or why he thinks I’m incapable of meeting them.  Nor does he explicitly state his underlying assumption, which is clear here.  To paraphrase: “You’re just a lowly graduate student, and thus you aren’t the one doing the important work.”

For the record, I like to think big – and I like to achieve my goals.

“And if you are after the latter, why not start off with the ignorant student that approached you?”

Ironically, since fuckhead’s main point is that he thinks I’m intimidating junior colleagues, his tone is oddly lacking in self reflection.  The implication that I haven’t helped the graduate student already is plain – and plain wrong.  However, that is between myself and the student, and we are in the process of establishing a better relation on stronger co-operation where my time is respected and the students needs are better met.  After all, that is the goal:  By getting the student to ask more focused questions, he’ll get better answers.

Further, given that I am fuckhead’s junior colleague, I have to ask why he chose to respond to my post with such venom.  He could have taken the time to set me straight by leading me to see his point, rather than writing a biting comment that chastises me for being rude to those who have less experience than I.

Irony, anyone?

“If you have lots of good ideas, some dolt stealing one of them won’t hurt you.”

I’m not afraid of people stealing my work, but one should recall the context of my comments.  Frankly, I am a strong believer in open source and collaborative work and if you want to see the code I’m working on this week, all you have to do is download my work from source forge.

Unfortunately, in academia, one generally doesn’t release data until it’s published – that is the default position – and one I have openly questioned in the past.  But, if I want someone’s unpublished results, I go to them with the respect for the work that went into it.  It is as simple as that.

Besides, as someone with an entrepreneurial past, I’m well aware of the value of ideas. One does not disclose the “secret sauce” to competitors without an NDA (non-disclosure agreement), but when it comes to investors, you have to respect their time and effort and be aware that your idea has no value until you’ve done something with it – and even then, it’s still not the idea itself that has value.

However, the proof is in the pudding, as they say.  If I were afraid of people stealing my ideas, would I be blogging them?

“If you don’t have lots of good ideas, how the hell will you survive on your own as a researcher?”

I haven’t the foggiest clue.  I’ve never found myself lacking in ideas, although I’m shying away from the academic career path for this very reason.  I know the value of sharing ideas and of working in a group to combine and improve ideas.  Unfortunately, I don’t see that kind of environment being created in academia where professors competing for a small pool of grant money hoard their findings so that others will be less effective in competing with them.

If there’s one thing that I hate, it is wasting time reinventing the wheel.  Unfortunately, that appears to be an inherent part of the academic process.  (I’m not talking about independently confirming results, which is an inherent and important part of the scientific method.)

To wrap things up, yes, I’ll go quietly back into my little bubble of the universe in which I will quietly battle the raging sea of ignorance around me, but I can’t promise that I’ll stay there.  However, even as I fade quietly back into obscurity, I do plan to learn from my mistakes and to let others learn from them as well.

The hard lesson I learned today was to watch my own tone when communicating on the Internet, to keep myself from unintentionally sounding arrogant and condescending.  I’d be happy to pass the same lesson on to you, fuckhead.

New developments…

I’ve not been blogging lately because I have managed to convince myself that blogging was taking time away from other things I need to be doing, which I feel I need to focus on.  The most important thing at the moment is to get a paper done, which will be the backbone of my thesis.  Clearly, it is high priority, however, it’s becoming harder and harder not to talk about things that are going on, so I thought I’d interrupt my “non-blogging” with a few quick updates.  I have a whole list of topics I’m dying to write about, but just haven’t found the time to work on yet, but trust me, they will get done.  Moving along….

First, I’m INCREDIBLY happy that I’ve been invited to attend and blog the Copenhagenomics 2011 conference (June 9/10, 2011).  I’m not being paid, but the organizers are supporting my travel and hotel (and presumably waiving the conference fee), so that I can do it.  That means, of course, that I’ll be working hard to match or exceed what I was able to do for AGBT 2011. And, of course, I’ll be taking a few days to see some of Denmark and presumably do some photography.  Travel, photography, science and blogging!  What a week that’ll be!

Anyhow, this invitation came just before the wonderful editorial in Nature Methods, in which social media is discussed as a positive scientific communication for conference organizers.  I have much to say on this issue, but I don’t want to get into it at the moment.  It will have to wait till I’m a few figures further in my paper, but needless to say, I believe very strongly in it and think that conferences can get a lot of value out of supporting bloggers.

Moving along (again), I will also be traveling in June to give an invited talk, which will be my first outside of Vancouver. Details have not been arranged yet, but once things are settled down, I’ll definitely share some more information.

And, a little closer to home, I’ve been invited to sit on a panel for VanBug (the Vancouver Bioinformatics Users Group) on their “Careers in Bioinformatics” night (April 14th).  Apparently, my bioinformatics start-up credentials are still good and I’ve been told I’m an interesting speaker.  (In case you’re wondering, I will do my best to avoid suggesting a career as a permanent graduate student…) Of course, I’m looking forward to sitting on a panel with the other speakers: Dr. Inanc Birol, Dr. Ben Good and Dr. Phil Hieter – all of whom are better speakers than I am.  I’ve had the opportunity to interact with all of them at one point or another and found them to be fascinating people. In fact, I took my very first genomics course with Dr. Hieter nearly a decade ago, in an interesting twist of fate.  (You can find the poster for the event here.)

Even with just the few things I’ve mentioned above, the next few months should be busy, but I’m really excited.  Not only can I start to see the proverbial light at the end of the tunnel for grad school, I’m really starting to get excited about what comes after that.  It’s hard to not want to work, when you can see the results taking shape infront of your eyes.  If only there were a few more hours in the day!


AGBT – page views

In case anyone was wondering what traffic to my blog looks like during AGBT season, I think this image is relatively informative.   I don’t have the ones from the last couple year’s AGBT conferences, but it looks about the same.  Fortunately, my computer seems to be coping with the load – and my wife hasn’t emailed me to say that its fan is whining yet.. (Yes, every time you view my blog, you’re actually visiting my living room.)

Graph shows jan 19 – Feb 4, 2001.  Y-axis is page views.

New Years Resolutions

My resolutions this year break into two categories: tasks and self-improvement. The tasks are pretty obvious, they’re the things that I need to accomplish this year:


  • Finish papers
  • Mine my database
  • Write my thesis
  • Get a Job

The resolutions are things I’d like to do better in the new year, and areas in which I can improve.


  • Discuss more about my work on my blog – eg, visualisation projects
  • Read at least one paper a day – including “days off”.
  • No hesitation in learning new things – learning curves aren’t that bad and usually pay off in the end.
  • Remember to say no to new tasks that will slow me down from my goals
  • No procrastination (eg, youtube)
  • Be friendlier with people who distract me from my goals – they aren’t aware of their time draining ways.

All in all, I’m aiming to be more productive, and more verbal about my productivity. Both of those will help my with my job search, which, by the way, will begin today! Happy 2011, everyone.