Anyone have experience in the bioinformatics field comment on what type of programming jobs are available?
So far during my coop terms (similar to paid internships), it's been database joins, queries and number crunching.
Is there more to the field than that?
I expect bioinformatics to be big as the biotech bubble expands in Silicon Valley and synthetic biology matures. See the results of a "bioinformatics future" Google search.
According to the wikipedia article, the major research areas in the field are as follows:
Lots of database querying and number crunching, but that's by no means the extent of it.
see: NCBI, the National Center for Biotechnology Information in Bethesda, Maryland. I don't know if they are hiring now, but there are lots of other Biotech firms in the area just north of DC.
Download and play with their Genome Workbench. If you want you can look at the source for all of it too.
One of my family members has gone quite far in the field of being a bio statistician. At the higher levels, it becomes a managerial role. The technical knowledge you gain in your first several years in the field will inform your leadership decisions later on. (Assuming you stick with it.)
It seems to be valuable to develop a business-process specialty that is related to the field. For example, being on the team that works through the FDA (or other similar regulatory) approval process for your firm's products. Knowing exactly what kind of bio informatics projects are necessary to achieve a tangible business result would greatly increase your value to your firm.
I'm doing algorithm implementations at the moment. We're still building much of the very basic toolchain in a consistent manner because many of the important algorithms are originally only published as a proof of concept (if at all!) and every facility/enterprise implements their own version. Therefore, working with string algorithms and index data structures is still very big at the moment: implementation of high-performance algorithms. The next step, just started, will be the move to new computation platforms, such as GPGPUs and Cell processors. Fast sequencing of genomes is still one of the major cost factors. However, I expect this particular problem will be solved in a relatively short time (say, 5 years).
After that, much of the research (and therefore the work) will be focused on higher-level understanding. Virtually everything is needed here. There are so many different approaches to many of the problems that virtually any programming job will be needed. Some of the more interesting approaches will also require very good understanding of different fields in mathematics such as linear (and quadratic) optimization, semantic web, pattern recognition etc.
Database programming will of course remain important because of the sheer amount of data. The same is true for networking. Much of the basic work will also include web programming because the easiest and fastest way to access the data in an orderly fashion will be using web interfaces. Now comes a secret: All current bioinformatics web applications suck big time. If you're good in web programming, there are opportunities galore. Heck, the commercial marketing of bioinformatics web applications hasn't even begun. Most of these softwares are developed by researchers (not web professionals) for free.
Incidentally, the same is true for every single lab software that I have ever seen/used. If you don't like web programming and databases but like to do smart client application, pick a tool of your choice, make the UI better and sell it. I might be biased but I've never seen a surrounding with so many bad user interfaces and so much room for improvement.
Bad tools are one of the bottlenecks in today's research.
Is there more to the field than that?
You betcha.
My answer is more related to the future of Medical software, but I see it as so closely related to bioinformatics, as to find it difficult to make a distinction. Three areas to look into.
FDA Software 510k Process. http://www.fda.gov/cdrh/ode/guidance/337.html This will show you the documentation, requirements for the FDA Clearance. To Konrad's point, Web/Internet software in this field is in such a state of infancy, the FDA is still trying to figure out what Software As A Service really means. I am going through this process right now.
Microsoft is really pushing for enhancing Medical User Interfaces (specifically Silverlight), and has been working with the British National Health System to do it. http://www.mscui.net/
I highly recommend learning more about Microsoft HealthVault and Google Health.
There is a bunch more out there, and who knows where it will lead. But, I think those are three key areas.
Best wishes!
Roughly speaking there are two kinds of jobs that get lumped together as "Bioinformatics". The most common sort is the kind you seem to have encountered in your co-ops, frequently involving creating web front ends to big databases of biological data. In many ways these jobs aren't much different then writing database applications to track widget production, except that some people find biology inherently more interesting then widgets. The other type of job might be more accurately described as computational biology. Those jobs involve the creation of sophisticated mathematical/statistical models and novel algorithms to analyze biological processes. There aren't as many of jobs of the 2nd sort, and they tend to require a Ph.D. or at least an M.S. Geographically they are most common in the major biotech centers: San Francisco, So. Cal., Boston, and Cambridge (UK).
Medical Informatics contains very disparate positions too. A lot of it is concerned with the management of medical records, so you are back to database work, but it also includes whizzy stuff like tele-surgery and robotic surgery.
If you're a student and want to play with some component-wrapped sequence analysis tools, you might look at the Pipeline Pilot Student Edition. It'd free and wraps some of the more common BioPerl and java-based bioinformatics tools. It's pretty good for prototyping things.
There's a lot more to the field than the grunt work of running algorithms for biologists, but you might have to go to graduate school to experience it. There's some very interesting work being done on:
That's a list of scientifically interesting things that need some amount of software. If you're more of an engineer and want to do work more focused on software engineering, you could try and think about things like:
The problem is that you kind of need to be a scientist to be doing some of the scientifically interesting things, and developing scientific credibility takes a while. Doing software engineering work in this field can be fun and rewarding, but it can be frustrating too as the field is moving as we discover new and better ways to do things, and it's hard to hit a moving target. Sometimes that frustration is interesting though. :)
Bioinformatics can mean different things to different people and organizations, so watch out. I wouldn't call "database joins, queries and number crunching" bioinformatics, but there are probably others that would, depending on the data.
There are plenty of software development opportunities in the world of biotech. Some aren't that different than software development jobs in other fields, others will require specialized knowledge (biology) and perhaps an advanced degree. Depends on the needs of the employer.
The problem with bioinformatics is that it may be not worthy enough for a computer scientist to enter the field.
Most of the people working in bioinformatics are biologists and they are PhD students, or have the low salary of a PhD/postdoc student: for example, in Italy/Spain it is around 1000 euros per month.
If you are a good programmer, you will probably be able to obtain a job position for a higher salary easily. It takes a lot of effort to enter in the field of bioinformatics seriously, that you will probably do better to spend that time to learn some programming language or library and become a guru in it. If you have a background in computer science, it will take you a lot of time to learn what a cell is, how DNA works, what are proteins, how do all the complicated techniques like microarrays, etc. work, and all of that for a low salary. Is it worth it?