why research blogging has mattered to me

A little while back I had the honor of speaking on a 'careers in bioinformatics' panel put on by my former graduate program at the University of British Columbia.  Other panelists included Inanc Birol,  Bioinformatics Group Leader, Michael Smith Genome Sciences Centre (who good-naturedly called postdocs the 'burger flippers' of science), Phil Hieter, Professor of Medical Genetics, University of British Columbia, and Anthony Fejes, Co-founder, Zymeworks and PhD candidate at UBC.  Blogging came up a few times in the discussion as Anthony and I have both been at it for a while now and have seen a clear positive impact on our careers from it.  Anthony's blog has become so popular that he has started to get invited to conferences solely because the organizers want him to blog about them..   My blog hasn't achieved the audience that fejes.ca enjoys but it has managed to connect me with some excellent people that I wouldn't normally have met and through them with opportunities I never would have discovered.  I think its worth jotting down a couple examples.

Blogging got me to Sci Foo.  While its hard to say exactly why you get invited I have a pretty solid guess that my writing here about semantic social tagging is what caught the attention of Timo Hannay and resulted in my trip to the GooglePlex.  Had I waited for my work on tagging to be published through a traditional journal this never would have happened.

Blogging connected me with Barend Mons and what would become the Concept Web Alliance.  Barend picked up on the same set of posts (mainly the big one that turned into a lovely rejected paper) and eventually invited me to do a postdoc in his group.  Babies and geography aside I would probably be working with him now.  Though I didn't end up working with him in Leiden, he did invite me to the first Concept Web Alliance meeting where I met Andrew Su, who would become my employer nearly a year later..

Blogging got me a better Gene Wiki network visualization!  A while ago I posted a Gene Wiki hairball picture illustrating the hyperlink network emerging from the articles in the gene wiki.  This post was picked up and used as an example of what not to do when visualizing large networks by Martin Krzywinski - author of the popular Circos visualization system and the up and coming hive plot paradigm.  After discovering our ahem 'connection', we've been working with Martin to build something more beautiful and more informative.  Posts to come about that one..

In short, sharing ideas openly here in i9606 has been one of the best parts of my experience in science and one I hope to continue for many years to come.

I was wrong - 2008

I’ve been thinking a little bit about how to finish 2008 and start 2009 here on i9606 and the things that spring first to mind are mistakes made in my thinking this past year. Maybe this is because mistakes are where learning happens or maybe its simply because I tend to be self-critical in my self reflection. In any case, here are just two of the many things I got wrong this past year with a few thoughts on why.

• I really thought I was going to graduate in 2008, but I was wrong. 
  

I think that this happened for two reasons, first, I got distracted by a side-project and second, I didn’t have a clear idea of what really constitutes a dissertation. In hindsight, when the project that was supposed to take two weeks reached, maybe 5 weeks, I should have dropped it and moved on – well before it had a chance to eat up seven more months of effort. I think that if I had a clearer vision of the end goal, of the dissertation in this case, I might have made better decisions regarding the use of my time in the short term.  

• I wrote in a comment in a post by Timo Hannay that I would continue to blog even if no one ever read my posts, that the most important audience for these words is my future self rather than friends and unknown others, but, once again, I was wrong. 
  

At the time, I was reacting against the apparently popular desire to bottle up the blog form, especially in scientific contexts, into something overly specific, to classify it as science writing for a popular or otherwise uninformed audience. To me it never really felt like that. It has always been an intensely personal platform without any higher purpose beyond myself and I always considered my audience likley to be better informed than me. I confess. I write here exclusively for my own benefit and believe that most other writers do the same. Though there are a few others, the main reason I started to write here and still do is to attract feedback on my ideas. I am after that most precious resource, the attention of informed and intelligent colleagues. Without occasional comments, I suppose that I would eventually give it up and move things over to a private journal. So, thanks everyone for all of your responses in 2009, I really appreciate them and will do my best to reciprocate where I can. (The consequences of this need for feedback and the pattern of seeking it in public, digital space are, I believe, interesting and wide-reaching, but that is food for another post.)

What mistakes did you make in 2008?

Happy 2009 everyone!

another year older -My 2008 Research In Progress seminar

I just finished giving my annual Research in Progress seminar for the iCAPTURE Heart and Lung research institute where I "work".  In the talk, titled "The social construction of a semantic web for the life sciences" which might someday be the title of my thesis, I describe results from comparisons of different approaches to the indexing problem (like MEDLINE versus Connotea ..) and use those results to motivate the Entity Describer project.  I also spent a short digression on my experiences with "publishing" the ideas for that project on my blog and encouraging the younger grad students to do the same thing with their work.

I think that, in general, the talk was well received, but we will see if it actually produces any new users ;) !

On the Entity Describer front, I should point out that we have a couple new people working on various aspects of it and that their work will be described on the ED developer blog.  (Throw out a comment for our most active contributer Paul!).  I will continue to write about the project here, but it is my hope that the other site will be a better source for more technical commentary as the project unfolds over time.

Feelin groovy today (despite the ongoing onslaught of "Junuary" in YVR.

shameless self promotion

Euan Adie invited me to write a guest post for Nascent, how cool is that!  

I wasn't sure how to work in the acknowledgements for a little piece of writing like that, so thanks once more to Eddie Kawas, without his capable coding ED and the iHOPerator would never have existed.  Thanks also to Adrian Png and Byron Kuo for starting to explore the other side of the ED project.

Looking at the article, I realize I didn't actually talk specifically about science..  hmm, maybe next time.  At least I had some geeky gene examples!

New Look , New Order

Thanks to the-blogger-templates, i9606 has a new look. How do you like it?

Some of you have been complaining that my posts have been a bit off-topic and random lately. If you are not interested in the full i9606 experience, but would like to stay abreast on my thoughts on specific topics like the Semantic Web or the related E.D. project, I invite you to sign up for the topic-specific feeds visible in the right column. Thanks to Clarius for describing how to make this easy.

This restructuring has come to pass because lately I've felt the need to write about non work-related things. This is partly because my main current collaborator is a little less interested in pre-publishing unfinished work than I am (and I still am, despite the failure from last year), but mostly its because I find myself viewing and using i9606 as a general purpose platform for communicating with friends, family, and my future self.

I suppose I could start a separate blog (which I did at one point), but, given that the content from this one can so easily be modularly syndicated it just doesn't seem necessary. Perhaps one day I will try to create a more specific, professional blog (like bokardo) but I'm not there yet. Right now, this is just me talking...

2007 done 2008 already begun

T'is the season for reflections on the past and plans for the future, here are some of both.

In 2007 I started this blog and posted in it 47 times. Its been the most positive new thing in my worklife this year by far and, in 2008, I intend to increase that number slightly but mainly I hope to improve the quality of the posts by reading more often before I write.

From a quick sample, it looks like about 25 email messages a day made it in through my spam filter and that I sent out around 10 - meaning I read more than 9,000 and sent more than 3000 in the year. In 2008 I'm hoping to slowly wean my way off the email habit by taking better advantage of iChat for short, personal communications and better advantage of my time in general by simply ignoring it for longer periods of time.

Academically speaking, it was a bit of a funny year. I had two overwhelmingly positive meetings with my thesis committee, in stark contrast to previous encounters with them, yet I had the least successful publishing year in quite a while. Which is worse, having your committee disapprove of your work or your reviewers?? Hopefully I will solve this personal conundrum this year by graduating..

I've never been a particularly quantitative person, so thats it for the numbers for the year.

all the best for 2008!