On to Omicia!

I’ve dropped a few hints about where I’m headed, recently.  I left a pretty awesome lab at the CMMT last week to join a small company that most people have probably never heard of.  Yes, I still owe the Kobor Lab a final blog post, and have 2 publications in preparation going at the moment, so I guess I haven’t completely left yet, but as of tomorrow morning, I’ll be starting my new role with Omicia.  They’re a small company in the Bay Area, but they have a disproportionate passion for their work and some pretty cool ideas and connections. (Shoutout to the Yandell lab.  Yes, I’d like a few VAAST stickers, but I’m hoping to meet @zevkronenberg in person to ask for them one day…)

For the moment, I’m still in Vancouver, where I’ll stay until we find a place to live in the Oakland Area, but things are officially in motion.

Ironically, it’s been a long road to get here, since I first met up with Omicia about 3 years ago.  Somehow, it just took a long time for the stars to align… but here we are, and the real journey is about to begin.

Frontiers in Science Latex missing packages.

I’m working on a manuscript to be sent in to a frontiers journal, and discovered a few missing dependencies for LaTeX, so I figured I’d share them here.

If you find you’re missing chngpage.sty, install texlive-latex-extra

if you find you’re missing lineno.sty, install texlive-humanities

On a Mac, that’s:

sudo port -v install texlive-humanities texlive-latex-extra

Happy compiling.

What’s the point of doing a PhD? (reply to Kathy Weston)

I wanted to comment on a blog post called “What’s the point of doing a PhD” on Blue Skies and Bench Space, by Kathy Weston.  Right off the top, I want to admit that I’ve not followed the blog in the past, and my comments aren’t to say that Kathy doesn’t have a point, but that what she’s proposing is only a partial solution – or rather, it feels to me like it’s only half the picture.

Warning, I’ve not edited this yet – it’s probably pretty edgy.

I believe Kathy is responding to a report (Alberts et al) that proposes such things as cutting the numbers of postdocs, creating more staff scientist positions and making sure that non-academic PhD options are seen as successful careers.  Those are the usual talking points of academics on this subject, so I don’t see much new there.  Personally, I suspect that the systemic failures of the research community are small part of a far broader culture war in which research is seen as an “optional” part of the economy rather than a driver, which results in endless budget cuts, leading to our current system, rather than as an issue on it’s own.  However, that’s another post for another time.

Originally, I’d written out a point-by-point rebuttal of the whole thing, but I realized I can sum it up in one nice little package:  Please read all of Kathy’s criteria for who should get a PhD.  Maybe read it twice, then think about what she’s selecting for… could it possibly be academics?

Advice to undergrads could be summarized as: prepare for a career of 80 hour workweeks (aka, the academic lifestyle) and if you don’t know for sure why you’re getting your PhD (aka, to become an academic), don’t do it!   Frankly,  there are lots of reasons to get a PhD that don’t involve becoming an academic.  There’s nothing wrong with that path, but a PhD leads to many MANY 9-5 jobs, if that’s what you want, or sales jobs, or research jobs, or entrepreneurial jobs.  Heck, my entire life story could be summed up as “I don’t know why I need to know that, but it’s cool, so I’ll go learn it!”, which is probably why I was so upset with Kathy’s article in the first place.

Lets summarize the advice to PhD students: If you don’t know why you need to learn a specific skill, don’t do a post doc! I’m going to gloss over the rest of that section – I really don’t think I need a committee of external adjudicators to tell me if they think my dreams are firmly grounded, and if your dream isn’t to be an academic, why should you walk away from a postdoc?

Advice to postdocs: “This is your last chance to become an academic, so think hard about it!”  Meh – Academics R Us.  (Repeat ad nauseum for N-plex postdoc positions.)

Everything else is just a rehash of the tenure track, with some insults thrown in:  “Don’t hire mediocre people” is just the salt in the wound.  No one wants to hire mediocre people, but people who are brilliant at one thing are often horribly bad at another.  Maybe the job is a bad fit.  Maybe the environment is a bad fit.  Is there a ruler by which we can judge another person’s mediocrity?  Perhaps Kathy’s post is mediocre, in my opinion, but there are likely thousands of people who think it’s great – should I tell others not to hire Kathy?  NO!

I think this whole discussion needs to be re-framed into something more constructive.  We can’t keep the mediocre people of out science – and we shouldn’t even try.  We shouldn’t tell people they can’t get a PhD, or discourage them.  What we should be doing is three-fold:

First, we should take a long hard look at the academic system and ask ourselves why we allow Investigators to exploit young students in the name of research.  Budget cuts aren’t going to come to a sudden halt, and exploitation is only going to get worse as long as we continue to have a reward-based system that requires more papers with less money.  It can’t be done indefinitely.

Second, we should start giving students the tools to ask the right questions from early on in their careers.  I’d highlight organizations like UBC’s Student Biotechology Network, which exist with this goal as their main function.  Educate students to be aware of the fact that >90% of the jobs that will exist, once they’re done their degrees, will be non-academic.  A dose of accurate statistics never hurts your odds in preparing for the future.

Finally, we can also stop this whole non-sense that academia is the goal of the academic process!  Seriously, people.  Not everyone wants to be a prof, so we should stop up-selling it.  Tenure is not a golden apple, or the pot at the end of the rainbow.  It’s a career, and we don’t all need to idolize it.  Just like we’re not all going to be CEOs (and wouldn’t all want to be), we’re not all going to be professors emeritus!

If you’re an Investigator, and you want to do your students a favour, help organize events where they get to see the other (fantastic!) career options out there.  Help make the contacts that will help them find jobs.  Help your students ask the right questions… and then ask them yourself, why did you hire 8 post-docs?  Is it because they are cheap trained labour, or are you actually invested in their careers too?

Lets not kid ourselves – part of it is the system.  The other part of it is people who are exploiting the system.

A few open bioinformatics positions.

Occasionally, I get emailed information about open positions at bioinformatics companies, so I thought I’d pass along a couple today.

First and foremost, if anyone is interested, the company I’m looking forward to starting with next week is hiring, so I’ll pass along that link:  http://www.omicia.com/jobs/ There are software engineer, bioinformatics and data scientist positions available, so I suggest checking them out.

Second, for those who are a little further in their career, I understand that Caprion is looking for a director of bioinformatics as well as a biostatistician (http://www.caprion.com/en/caprion/career.php).  It’s a little far outside my field, given that it’s mostly proteomics work, but I’ve heard good things about Caprion, and they’re in Montreal, which is a pretty awesome place with excellent poutine.  (I’ve only spent two days there, so yes, the poutine does stand out, along with the excellent smoked meat sandwiches and a very crowded hostel… maybe it’s best if you don’t ask my advice on Montreal.)

Otherwise, I’ve also been passed a description from what appears to be a startup company looking for an “important position” with the following description:

Experience in genomic research relating to the development of novel computational approaches and tools. Preference may be given to candidates with expertise in one or more of the following areas: Modeling and network analysis; Molecular pathways; Systems biology; Comparative genomics; Quantitative genetics / Genomics (QTL / eQTL). Knowledge and ability of applying bioinformatics programming languages to develop and/or improve computational analysis tools (i.e. algorithms, statistical analysis).

If you’re interested, I can cheerfully pass contact information along to the right people.