ROSALIND: An Addictive Bioinformatics Learning Site

Shipud writes "Bioinformatics science which deals with the study of methods for storing, retrieving, and analyzing molecular biology data. Byte Size Biology writes about ROSALIND, a cool concept in learning bioinformatics, similar to Project Euler. You are given problems of increasing difficulty to solve. Start with nucleotide counting (trivial) and end with genome assembly (putting it mildly, not so trivial). To solve a problem, you download a sample data set, write your code and debug it. Once you think you are ready, you have a time limit to solve and provide an answer for the actual problem dataset. If you mess up, there is a timed new dataset to download. This thing is coder-addictive. Currently in Beta, but a lot of fun and seems stable."

Comments

Better than MOOC

[vlm]

I like Euler and this looks fun. Much more interesting than massively online classes, which are a pretty boring concept, and this will probably be compared to it. But I see this as a fun project, not educational. Wedged sideways into the .edu system it would just exercise cheating ability. Big Eh.

You know what else is boring? The technological silver bullet for education. I've spent my entire life under the spell that new technology is going to revolutionize education. The filmstrip and LP vinyl record. The VCR. The computer. The computer graded standardized test. The computer again. Shitty internet videos. Online classes with 20 classmates. Online classes with 200000 classmates. They all suck. I'm sure the older /.ers will chime in about the invention of papyrus and written language.

The whole meme of "tech will fix education" is tired, obsolete, and needs to go away.

Re:Better than MOOC

[berashith]

tech has been screwing up education ever since reading and writing took the place of memorization.

Re:Better than MOOC

[Medievalist]

Now I can pull up the whole of human knowledge on my phone, if I know what to say to the device.

The only problem is you might actually think that's true!

I have books in my library that will never be on your phone, and my father has knowledge of the US Space Race in his head that wikipedia won't accept because it hasn't been published anywhere. Most of that knowledge will die with him, although of course a little bit has passed down to his grandchildren.

Re:Better than MOOC

[lgw]

Record that knowledge, but not in Wikipedia. Wikipedia isn't really that special. It's easy to put up a site to record a narrative of your life, after all. Let a future generation copypaste the text into Wikipedia, and cite your site!

Help!

[vlm]

Hey /. hive mind help me here. I've looked at the html source of euler and this new thing and they appear to be custom.

Does anyone know of a "framework" "CMS" or whatever you'd call it, specializing in what for lack of a better term I'd call "competitive problem solving koan websites"?

If not, I'm about 75% committed to writing one on github. Probably in Scala / Lift because I'm teaching myself Scala and Lift, which is a great personal project justification but a terrible architecture decision justification ... anyway...

Nice enough enduser frontend, database schema behind it to hold the goods, semi static stats and rankings pages for speed, backend for admin...

Re:Help!

[Antipater]

The problem is that creating a competitive problem-solving environment requires you to design an AI with questionable ethical constraints to run the experiments.

Also you have to learn to bake.

source for the name

[necro81]

I am going to guess this project was named for Dr. Rosalind Franklin, whose x-ray crystallography work illuminated the double-helix structure of DNA

Re:source for the name

[pieisgood]

Given they state this on their site, you're correct. http://rosalind.info/about/

Bioinformatics Bubble?

[superid]

I've been casually trying to learn some basic bioinformatics skills and have played with biopython for about a year. My son is a a senior in HS and has been thinking about a BS in Microbiology and a minor in CompSci. We've been to a couple of University open houses lately and they all are pushing bioinformatics programs. I see chatter about it online and even on TV. I even discovered that one of my cousins just got his PhD in bioinformatics. It's everywhere!

Is there a risk that 4 years from now there will be WAY too many bioinformatics grads? I'd hate to reccommend a field to my son where the employment bubble will burst soon. Any thoughts about job prospects down the road? [ mitigating factor - We're near Boston which appears to be the hub of the industry on the east coast ]

Re:Bioinformatics Bubble?

[rockmuelle]

I run a bioinformatics software company, have been in the field for over a decade, and have worked in scientific computing even longer.

I'll start with a quick answer to the bubble question: there are already too many 'bioinformatics' grads but there are not enough bioinformatics professionals (and probably never will be). There are many bioinformatics Masters programs out there that spend two years exposing students to bioinformatics toolsets and give them cursory introductions to biology, computer science, and statistics. These students graduate with trade skills that have a short shelf life and lack the proper foundations to gain new skills. In that respect, there's a bubble, unfortunately.

If you're serious about getting into bioinformatics, there are a few good routes to take, all of which will provide you with a solid foundation to have a productive career.

The first thing to decide is what type of career you want. Three common career paths are Researcher, Analyst, and Engineer. The foundational fields for all are Biology, Computer Science (all inclusive through software engineering), and Statistics. Which career path you follow determines the mix...

Researchers have Ph.D.s and tend to pursue academic or government lab careers. Many research paths do lead to industry jobs, but these tend to morph into the analyst or engineer roles (much to the dismay of the researcher, usually). Bioinformatics researchers tend to have Ph.D.s in Biology, Computer Science, Physics, Math, or Statistics. Pursing a Ph.D. in any of these areas and focusing your research on biologically relavent problems is a good starting point for a research career. However, there are currently more Ph.D.s produced than research jobs available, so after years in school, many bioinformatics-oriented Ph.D.s tend to end up in Analysis or Engineering jobs. Your day job here is mostly grant writing and running a research lab.

Bioinformatics Analysts (not really a standard term, but a useful distinction) focus on analyzing data for scientists or performing their own analyses. A strong background in statistics is essential (and, unfortunately, often missing) for this role along with a good understanding of biology. Lab skills are not essential here, though familiarity with experimental protocols is. A good way to train for this career path is to get an undergraduate degree in Math, Stats, or Physics. This provides the math background required to excel as an analyst along with exposure to 'hard science'. Along the way, look for courses and research opportunities that involve bioinformatics or even double major in Biology. Basic software skills are also needed, as most of tools are Linux-based command line applications. Your day job here is working on teams to answer key questions from experiments.

Bioinformatics engineers/developers (again, not really a standard term, but bear with me) write the software tools used by analysts and researchers and may perform research themselves. A deep understanding of algorithms and data structures, software engineering, and high performance computing is required to really excel in this field, though good programming skills and a desire to learn the science are enough to get started. The best education for this path is a Computer Science degree with a focus on bioinformatics and scientific computing (many problems that are starting to emerge in bioinformatics have good solutions from other scientific disciplines). Again, aligning additional coursework and undergraduate research with biologists is key to building a foundation. A double major in Biology would be useful, too. To fully round this out, a Masters in Statistics would make a great candidate, as long as their side projects were all biology related. Your day job here is building the tools and infrastructure to make bioinformatics function.

All three career paths can be rewarding and appeal to different mindsets.

If you haven't followed the NPR series on gene sequencing over the last few weeks, it

Can I get a job?

[gr8_phk]

As a long time software guy, will solving all or most of these problems help me change fields?

can someone explain...

[Mr. Slippery]

Can someone explain to me why "storing, retrieving, and analyzing molecular biology data" is considered to be its own field, where people actually get degrees specifically in bioinformatics, while storing, retrieving, and analyzing any other sort of data is just software engineering/computer science?

Not trying to troll or bait flames, I'm genuinely wondering if there's something I'm missing, or if there's just hype about "biochemistry, now with *computers*!" I've taken my plain vanilla CS degree to a wide array of fields including information security, space science, telephony, and e-commerce. What makes processing strings of ACTG different than processing other strings? Thanks.