

Ask HN: How can a Web Developer get into Bioinformatics? - bioweek

I've been doing web application development (and general programming) for almost 10 years now.  I've also done a lot database design, working with very large databases, and optimizing queries, etc.  But I have no biology experience.<p>I've always wanted to work with new biological technologies, for example figuring out what genes do, or how proteins fold, or anything cool like that where I can increase the world's knowledge.<p>It seems to me that a good programmer would be useful for these types of jobs.  Does anyone have advice for how to enact this career shift?
======
rglullis
That's exactly what happened to me, but I have to say that it was more of an
accident than a planned move.

I was looking for a job where they'd hire people with Python skills and that
could provide sponsorship for a H1B. The intersection of these requirements
proved to be quite small, but I was fortunate to find a research lab
affiliated to Harvard Medical that did just that.

My first project has less to do with bioinformatics and more with secure
manipulation of patients' EMR. It's funded by the CDC and all of the code is
GPL.

I think the other project I'm getting involved is more according to what you
are looking for: Galaxy (<http://galaxy.psu.edu/>) is a really cool system
where you can process and share huge amounts of data. It's also an open source
project(<http://bitbucket.org/galaxy/galaxy-central/wiki/Home>), and Penn
State is hiring.

~~~
Gmo
We started using Galaxy a couple of months ago in my company. I'm not involved
in the projects using it but I've seen a demo and it seemed like a cool
software, although it has its glitches, according to my colleagues :)

------
gintas
Bioinformatics is cool, but it's basically less sexy than you might think.
There are various directions to work on, but the kind of work is essentially
statistics and pattern matching. If you want to figure out what genes do or
how proteins fold in general, go read a textbook. Spending a year on a single
gene processing gigabytes of dirty data may not be as sexy as you might think.
Or it might be if that's your cup of tea, but as I said, in the end, it's
mostly statistics.

~~~
indigoviolet
That's a very poor representation of bioinformatics. There's certainly a lot
of data munging and cleaning (like in any field with lots of data), but
bioinformatics/computational biology is not about dumb pattern matching or
just writing code. Biologists can code just fine (I got a job at Facebook off
a PhD in computational biology).

It's all about data mining and machine learning on biological data, to gain
real insight about the functioning of an organism, often then doing the
experiments to test that insight. I've seen lots of computer scientists and
programmers jump in and flounder, because they're under the misconception that
all it takes is the application of canned algorithms to a new data set. You
need to understand biology (genomics, molecular biology, genetics, structural
biology), first and foremost. Then you need to understand a significant amount
of statistics, information theory, and computer science.

This isn't meant to discourage you, but you're not going to get far beyond
doing more web programming for biology websites if you don't teach yourself
some of these areas.

------
nvn1
Coming from having done a Bioinformatics PhD and Post-Doc, I reckon getting in
touch speculatively with people in Bioinformatics should work. You might get a
lot of knock-backs but there's definitely a need for people with IT skills and
a genuine interest in Biology. I'd also say that a strong grounding in
statistics would be the biggest selling point - probably greater than a
knowledge of biology. Good luck, I hope it works out for you.

~~~
stevenbedrick
I'll second the "strong grounding in statistics" point. Most computational
bioinformatics ultimately boils down to statistics in some form or another...

------
tjr
A few years ago, I was talking with the director for bioinformatics and such
at a reasonably large medical research university. He told me they really
don't hire "pure" computer science people any more, because there are
increasingly academic programs combining CS with biology, and they much prefer
to hire people who are skilled in both arenas.

That said, I agree with you; it ought to be possible for a good programmer to
get into the field and be useful. But gaining more experience/knowledge about
the biology side of things may be an important ingredient.

------
tom
What you're describing is the life I left to start my latest co. I worked at a
big research university having not had bio since college .. years ago. The key
is to find ways you can help, find someone who needs what you have to offer,
and work like crazy to get them to like you. Not that I did this, I kinda fell
into it, but I watched others do it with much success. That said, as others
have mentioned, statistics, statistics, and then when you need break, some
more statistics. Learn Python and bioPython, learn NCBI Blast, and WU BLAST
inside and out (read the papers), know some bio basics, and prepare to take a
pay cut.

Also, if you find a group you're interested in, who's work you like and can
get to interview, or at least a meeting / talk with anyone, read every paper
to come out of their lab since the dawn of time. These papers can be hard to
grok, and down right painful to read. Read them, and read them again. Show
interest in their work and they will like you. It's ok to not get it all. It's
ok, to not truly understand what they're trying to do. Trust me, some
reviewers don't seem to read the entire papers either ...

If you have any further q's, you can derive my email quite easily from my
profile. Ping me. Also, where do you live? If you're in the Boston area, we
can talk in person. I know a LOT of people in this space and we were always
looking for great software engineers who had a thirst for biology.

------
blaser
You can get into bioinformatics without a background in biology, but you'll
need some math. Assuming you have basic calculus & some statistics, I'd
recommend looking at the Univeristy of Illinois at Chicago's online
certificate in bioinformatics (<http://proteomics.bioengr.uic.edu/online/>).
You take an intro course and then choose two more from among computational
genomics, molecular modeling and biostatistics. It's a great program. They
also have a masters of engineering degree with a bioinformatics
specialization, again completely online.

If you're looking for something more immediate, get a hold of a couple books
and familiarize yourself with the basics. Mount's Bioinformatics is great, and
it's the text for the intro class at UIC. Other good ones are Bioinformatics
Algorithms, Python for Bioinformatics, and the O'Reilly books on Perl for
Bioinformatics.

Finally, hook up with a bio professor who needs some tech help and volunteer.
You'll learn a ton.

------
mitalia
There are definitely opportunities for someone with your skills to ease into
bioinformatics. Having conducted a job search not long ago, they are
unfortunately a bit hard to find at times, depending on where you're located.
In general, I think you'd have good luck starting with some of the less
science-heavy bioinformatics work. For example, I'm at The Center for
Biomedical Informatics in The Children's Hospital of Philadelphia Research
Institute. Our group spends a lot of time meeting with researchers,
understanding what they need, and building (or buying) systems that solve some
of those problems. The team I am part of is much more focused on biomedical
informatics than pure bioinformatics (though we have people who do "pure"
bioinformatics as well). Our setup really makes things interesting. Many of
the "big questions" in bioinformatics are real tough problems to crack (such
as protein folding). But there is practically an unlimited need for people to
have many smaller problems solved (with great impact). Simple things like
integrating research data into a database-backed web-app can give a clinician
the tools he or she needs to conduct their research more efficiently and
uncover new hypotheses. Plus, we get to work on things that directly impact
the health of kids. Many times, we're working directly with a physician who is
conducting research into a particular disease. They literally will be seeing
kids early in the day, and having a meeting with us about UI design later in
the day.

We are actually hiring for two positions right now:

Senior Data Integration Analyst:
[http://www.chop.edu.apply2jobs.com/index.cfm?fuseaction=mExt...](http://www.chop.edu.apply2jobs.com/index.cfm?fuseaction=mExternal.showJob&RID=18950&CurrentPage=1)

Analyst/Programmer
[http://www.chop.edu.apply2jobs.com/index.cfm?fuseaction=mExt...](http://www.chop.edu.apply2jobs.com/index.cfm?fuseaction=mExternal.showJob&RID=19225&CurrentPage=1)

We're always looking for the right kind of people and I maintain that hacker
news readers are a good pool to draw from. Don't let the corporate sound of
those descriptions fool you, we're a pretty entrepreneurial group. If by any
chance you're within easy travel distance from Philly, or even if you just
want to chat more about bioinformatics, feel free to email me at italiam [at]
email.chop.edu.

------
falsestprophet
You may not have luck finding work in the field without knowledge of biology
or chemistry or statistics or maths. There are many graduate programs that
focus on retraining software developers as bioinformatics researchers. Also
consider cheminformatics.

Please send me an email [1] if you want to learn more. The lab I work in is
always looking for eager new students.

[1]
[http://mailhide.recaptcha.net/d?k=01kUsXu40I09lRKAR_qd4ZFQ==...](http://mailhide.recaptcha.net/d?k=01kUsXu40I09lRKAR_qd4ZFQ==&c=pXDlSPqQSGfB5pER_vq03GfJUpP23WF3nSjrNoljyrY=)

------
jergason
I am in an undergraduate-level bioinformatics course right now, and can echo
what was said about statistics. The biology isn't too tough to pick up, but I
am weak in stats and that is my greatest difficulty with this class. That
said, I am enjoying it immensely. The book we use is a good overview of the
subject - [http://www.amazon.com/Bioinformatics-Molecular-Evolution-
Pau...](http://www.amazon.com/Bioinformatics-Molecular-Evolution-Paul-
Higgs/dp/1405106832) -Bioinformatics and Molecular Evolution. Most of the
tools that bioinformaticians use are buggy, horribly designed and very
unfriendly to the average user. One way to get involved is just improving the
usability and stability of the tools. There are plenty of command line tools
that you can add a GUI to if that is your thing:

<http://bio-bwa.sourceforge.net/>

<http://abacus.gene.ucl.ac.uk/software/paml.html>

<http://samtools.sourceforge.net/>

You don't need to know too much to contribute. If you are in Utah and
interested I could get you some contacts with professors.

------
abyssknight
I have a friend who is doing his master's thesis in Bioinformatics. If you
like running batch jobs that can run days and fail in the middle, then its a
great discipline for you! All kidding aside, the local University might be a
good place to start. Often working as a grad student you can learn the books
as well as get practical knowledge when working with a mentor. If you're near
Orlando, FL I can get you in touch with my friend at UCF.

~~~
khafra
I keep finding interesting things out about central florida--does Tampa Bay
have anything interesting in that area?

~~~
abyssknight
I'm not familiar with USF's program. You might be able to contact their people
and see though.

------
gurraman
I had the exact same desire about a year ago; I was bored with web development
and wanted to learn a new discipline (I never went through with my plans
though, so I have no real advice for you). My planned route was to get a
formal education at the university. I'm sure there are self-taught
bioinformaticians out there, but my perception of the field was that it would
be very useful to take at-least a few courses to get into it.

------
caffeine
If you're contacting people about this (and you should), try to do some
reading beforehand. In particular this bit:

 _I've always wanted to work with new biological technologies, for example
figuring out what genes do, or how proteins fold, or anything cool like that
where I can increase the world's knowledge._

What about Bioinformatics interests you? More specifically: exactly what part
of the world's knowledge would you like to increase and why?

I think a good, detailed answer to that question (and decent coding skills) is
the most useful thing for you right now.

Maybe this is useful?

[http://ocw.mit.edu/OcwWeb/Electrical-Engineering-and-
Compute...](http://ocw.mit.edu/OcwWeb/Electrical-Engineering-and-Computer-
Science/6-092January--IAP--2005/CourseHome/index.htm)

And here are links to courses (and therefore course notes) at Stanford:

[http://www-helix.stanford.edu/people/altman/bioinformatics.h...](http://www-
helix.stanford.edu/people/altman/bioinformatics.html#three)

------
ben1040
Another possible angle is high performance computing as it relates to
biological data.

Today's DNA sequencing instruments can kick out tens of millions of data
points. These can be mapped back to where they belong on a genome and then
from that data, variations can be calculated. Want to find out what mutations
a cancer patient might have? This is how.

This would be a perfect place for someone who might be interested in cloud
computing, for example.

I work in the field myself, and on my team there is a mix of pure CS people
and computational biologists. In my experience there are plenty of
opportunities for good developers to get in the door and make huge
contributions without necessarily having to have all the comp bio experience.

And, for what it's worth, data visualization is always a problem and the field
will always need sharp web guys to develop good tools to view what's going on.
This gets especially important now that the volume of data that you're trying
to get answers out of is so ridiculously huge.

------
twharris
You don't need courses solely in bioinformatics. You need a solid foundation
in molecular biology and genetics. These will give you the requisite
background to speak intelligently about the issues. You can take additional
courses in (or read independently) about bioinformatics concurrently.

------
fkirigin
Depending on the project, there is a good deal of statistics, as well as
biology knowledge.

As far as getting involved, I would check out current literature in the
general area of "Bioinformatics". Also consider searching for publications in
Systems Biology, Computational Biology, Functional Genomics. Usually there are
good articles coming out of Genome Biology, BMC Bioinformatics, BMC Genomics,
as well as Nature, Cell, etc.

I recently began a position as a Bioinformatics Software Engineer, after
spending 8 years on Wall St building trading and financial analysis
applications, which was somewhat of a switch (though my bachelor's is in
Chemistry). Spending time reading the current literature has helped me get
involved/engaged.

------
phren0logy
There are plenty of approaches that are helpful for programmers in both Web
and Bioinformatics domains. Seriously.

Check out Programming Collective Intelligence, and I bet it will give you some
ideas.

~~~
jamongkad
You would be referring to the book written by Toby Sagaran would you? If it is
I second your notion, an excellent book btw. Really got me into algorithms and
the like.

------
Mongoose
There are a lot of bioinformatics positions out there that don't require much
biology out of the box. Many universities have bioinformatics departments with
lots of programming positions. I worked for the past year as a student
programmer helping develop and maintain the data entry website for a set of
international clinical trials. My superior was a seasoned Unix/Perl hacker who
found a niche coordinating the development of clinical studies websites.

------
whichdokta
<http://www.tcoffee.org/Courses/Exercises/index.html>

<http://www.larrygonick.com/html/pub/books/sci3.html>

Don't laugh, excellent books!

------
mcgin
Might be worth checking out these guys - <http://diybio.org/>

See if theres a local group and go along and talk to a few people. I'm sure
they'll have some stuff you can get your hands dirty on that will at least get
you some experience in the field

------
jeldred
There are many current opportunities in bioinformatics. The discussion in this
thread seems to have some valid commentary. One place to check out might be

<http://genome.wustl.edu/careers/>

We are hiring. jeldred@genome.wustl.edu

------
sganesh
Some of these jobs look like a good place to start in the field..
<http://www.bioinformatics.org/jobs/> The best way to get in is to find what
these companies are looking for and start honing your skills in that
direction.

------
joebottherobot
I made a similar plunge several years ago. My best advice is to look for a
position in a research group that does both wet-lab experiments and
computation. They may be very interested in your web background.

------
ximeng
[http://arcanius.silverfir.net/blog/clinical-research-
experie...](http://arcanius.silverfir.net/blog/clinical-research-experience-
for-engineers)

Maybe this guy can help.

------
gms
Maybe read a textbook on bioinformatics, implement a couple of non-trivial
programs/algorithms, and put them on your resume?

------
socram2k
Do you need biology knowledge? I have studied in school a little about
genetics, Mendel's laws and things like that...

------
Mz
Pick up a copy of "What color is your parachute?" Read up on the advice on
informational interviews. Do your best to find some contacts in this field and
see if they will agree to an informational interview. (Rule #1: You are NOT
networking at this point. There can be no intent to finagle a job this way.)

Someone higher up than me at my company (not a bioinformatics thing) told me
that I might qualify for some positions that it doesn't look like I would
because I have a strong-ish math background and they basically look for that
and do the other training in house because they simply can't find people who
already do what they need done. So you might find that some jobs in bio-
informatics follow a similar pattern. This information is unlikely to be
public knowledge or advertised openly in job descriptions. You will need the
inside scoop and that's where an informational interview would come in very
handy.

Good luck with this.

~~~
dlnovell
That book is absolutely amazing. It's almost a secret weapon for finding work
in that it's completely indirect. If you talk to enough people who do the kind
of work you want to do, eventually someone will see potential in you and not
necessarily offer you a job, but KNOW someone that might. Just talk to
everyone that's willing to give you the time, be honest and enthusiastic about
what you want to do (and having enough background knowledge to sound competent
sure helps), and eventually you'll make the right contact. It's almost
certainly not going to be a quick process, but it's an incredibly powerful
one.

------
kapauldo
do a search of recently awarded government grants on bioinformatics,
particularly small business grants (SBIR). awards are all public, so you
should have no problem finding them. contact those folks and just tell them
honestly what you are interested in doing (be sure to read their awards first
so you have some idea what work they're doing). everyone respects people who
are trying to learn new skills, and i think you'll get a lot of warm
receptions.

~~~
bioweek
That sounds like a good idea. I'll give that a try.

~~~
blaser
The results of a search like that would make a great post. Please share what
you find.

