Wednesday, 28 September 2016

The Life Bioinformatic with Andrew Lonsdale - Episode 0 - "You need a better microphone."

The first episode of The Life Bioinformatic begins in Sydney, 2015, at the inaugural  Australian Bioinformatics and Computational Biology Society conference, ABACBS. ABACBS 2015 was hosted at the Garvan Institute, and admittedly half way though the conference dinner, I thought it might be a good idea to start a podcast.  Initially there was scepticism that this podcast was legitimate:

AL: I'm speaking with David Ma, photographer extraordinaire, David, you've taken photos of ABACBS and COMBINE. What do these conferences and symposiums mean to you? 
[.. silence ..]  
DM: You need a better microphone I think. We have some, but I guess it's a little late now.
AL: It is! I had this idea just 20 minutes ago. 
DM: Wait, do you run a podcasts normally? 
AL: Not normally, but this could be the first episode 
DM: What's the name of your podcast? 
AL: Umm, it can be whatever you want it to be be? 
DM: OK.
Al: But my idea was the The Life Bioinformatic 
DM: Oh yeah, I love that movie by Wes Anderson, the Life Aquatic. 
AL: Exactly, I'm running for a pun on that, do you think that would work? 
DM: I don't know if it's well known enough.

David was right (possibly on both counts) - the sound quality was such that almost none of it is really suitable for a podcast, and has sat on my phone for the better part of a year. 

But with AB3ACBS 2016 just five weeks away and abstract submissions due this Friday 30th of September (http://www.abacbs.org/conference), it seemed as good a time as any to go through it to see if there was anything worth salvaging. I've transcribed the best into this article. I was, and hopefully you will be too, pleasantly surprised by the genuine enthusiasm that came through for the ABACBS conference, despite the late hour and ample amount hospitality being enjoyed at time of recording. 

Although it was the inaugural conference under the umbrella of the newly formed society, it directly led from the great success of the Australian Bioinformatics Conference (ABiC) the year before.  With the new name, and newish society, I started the podcast by asking simple question: 

What does ABACBS mean to you?

Names have been suppressed to protect the innocent (and those who made some terrible jokes). Responses covered three basic themes:  jokes about the ABACBS acronym, Professor David Lovell and his entertaining role as host of the lightning talks, and a genuine appreciation and enthusiasm for the bioinformatics and computational biology community in Australia:
  • "You know it's uh.. just a conference where you've got come and make things count...you know, ABACBS... get. it... like an abacus and you count things?" [Mild laughter in background].
  • I get to see David Lovell once a year.
  • I get to meet other bioinformaticians and hang out with them which is always fun. 
  • Ummmm......bioinformatics....David Lovell being silly...I dunno.
  • Well i thought its going to be about different tools and just learning tools and and just using tools, and bioinformaticy tools, all about tools you know?
  • It means the state of affairs of bioinformatics in Australia.
  • Well firstly, COMBINE beforehand, great, lots of good free food, then ABABCS, also lot a great good free food, uh, some great poster presentations, some great tips and you get to hang out with gods of bioinformatics.
  • Its great opportunity to see my past colleagues, my present colleagues, who knows about the future!
  • Well obviously its a place where Australian bioinformaticians come together, and for me personally its really important thats its accessible to students.
  • What I've enjoyed the most is the chance to meet people I've wanted to to meet for quite a while.
  • ABiC last year was fantastic, and I don't think we could beat it, so at best we've tried to emulate it in a different place.
  • Its a coming together of bioinformatics communities, and that community is so essential because its really open and collaborative environment.
  • It means everything. 
  • Well, its abacus with a SNP. 
  • So its really about bringing the bioinformatics community together, and exchanging ideas and providing feedback to each other and support, and just developing the community. 
  • It signifies a community of people who share a common love of bioinformatics and computational biology, good spirit, good conversations, intellectual generosity, bring on 2016 I say!

The full transcript (which should never see the light of day!) contained more gold, and I might be able to put together a shortened version if I ever get time (read: never) so instead I've produced this word cloud to summarise what ABACBS means to those in attendance last year:



That's it for episode 0 of the podcast, and in Brisbane in November, the Life Bioinformatic will be back for episode 1... this time with a better microphone!


Monday, 15 February 2016

I'm retiring (from #sideprojects (for a while (probably)))


Despite the excessive parenthesis, this post is meant to be a definitive statement that I can refer back to whenever something interesting (non-research) comes up in the next year or so.

With the long preparation and eventual publication of Ten Simple Rules for a Bioinformatics Journal Club,  ABACBS due for an AGM soon where a new student representative will be elected, and an ever decreasing amount of time left of PhD scholarship, it's an apt time for me to retire from the fun and rewarding world of #sideprojects.

Last year was a particularly busy year for #sideprojects, continuing some degree of involvement in various groups (such as BGSA, ABACBS, Parkville Bioinformatics Journal Club, and of course COMBINE), co-chairing the EMBL Australia PhD Symposium (EAPS15), and teaching a number of Software Carpentry and  Data Carpentry workshops.

Many have asked how I can keep up all my research and still do a plethora of these community-centric things.

The simple answer of course is that I don't.

I've felt, and in discussions with others have formed the opinion, that there always is a balance; at the end of a research degree, there is the conventional wisdom that you need some degree of extra-curricular activities to avoid being a one dimensional at the completion of your degree. Having those 'other' things on your resume are valued, but without any novel research to complement it, you can risk being one dimensional the other way.

So to reduce this risk, it is time for a Sweeping Public Statement: I'm out.

I'm retired from #sideprojects. I keep telling people this, in the hopes that the repetition and public accountability will make it true.

Another piece conventional wisdom is that learning to say "No" to opportunities is also an important skill for a researcher and so far this year I've been keeping track of the great opportunities that I just don't have time for. By noting them down, I've found it's a great way to imagine what time I could have lost to them!

So from now until the end of my PhD, I'll do less not PhD, and more PhD. That there will be the occasional relapse, I do not doubt*, but the intention is very much to say "No", especially to myself.

With regards to COMBINE (the student sub-committee of ABACBS, and the ISCB Regional Student Group for Australia) this is actually a very easy decision, because of the safe hands it is in. The great work of the current president (@hdashnow) and the rest of the committee of COMBINE (past and present: Westa Domanava, Scott Ritchie, Thomas Coudrat, Jane Hawkey, Zoe Dyson, Tim Rice, Kian Ho, Ben Goudey, Karin Klotzbuecher and many more) over the last few years means that COMBINE looks set to make great strides in its goals of world domination a national network of students and ECRS, and I feel I can stop active involvement with full confidence that things will continue.

It's also true that what started out as attempts to build up a network of peers developed quickly into simply friends, and I'm sure those friendships will continue. I really enjoy all these activities, and post-PhD look forward to a nice balance of both research, teaching and community involvement then, but for now, it's time to go to the mattresses on research.

No more #sideproject ideas or trips to teach SWC/DC**.

People in bioinformatics and computational biology often know me for my other activities rather than my research. It's time to change that.



* Because, of course, who are we kidding? Plus I'm sure a few more of these will get written in idle moments. 

** I enjoy teaching SWC and DC, and in terms of time commitment, can be relatively minor when familiar with the materials. I don't intend to teach anymore this year, though if a combination of travel to a conference and an adjacent workshop came up I might consider it, and there a few workshops in planning that I'll help get off the ground for COMBINE.***

*** Yes this is a weasel-ing out of the entire point of this post, but, see *.