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Biotech Education Science

ROSALIND: An Addictive Bioinformatics Learning Site 38

Posted by Unknown Lamer
from the programming-is-fun-we-swear dept.
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."
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ROSALIND: An Addictive Bioinformatics Learning Site

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  • Better than MOOC (Score:4, Interesting)

    by vlm (69642) on Wednesday October 03, 2012 @01:34PM (#41540429)

    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.

    • by berashith (222128)

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

    • by xclr8r (658786)
      Tech applied incorrectly screws up education but if you really watch the model that Khan is putting forth it shows the granular focus you can give a student to help him/her overcome a concept. At least watch the video for his discussion of analytics that can be provided. http://www.youtube.com/watch?feature=player_embedded&v=gM95HHI4gLk [youtube.com]
    • by rs79 (71822)

      Disagree. It already has.

      What it hasn't fixed is "schools".

    • by Raenex (947668)

      But I see this as a fun project, not educational.

      Why isn't it educational? Are you seriously claiming you can work your way through those problems without having learned about bioinformatics?

      They all suck. [..] The whole meme of "tech will fix education" is tired, obsolete, and needs to go away.

      What needs to go away are people constantly complaining how everything sucks while ignoring all the positives [slashdot.org].

      • by vlm (69642)

        Why isn't it educational?... without having learned ....

        Modern education means you'll pay some at least semi-crooked corporation as much money as they figure they can get you to borrow, in exchange for a sheet of paper you can show to someone who knows nothing about anything other than that a piece of paper qualifies you to have a job. Currently it ranks right up there with "I watched an old episode of NOVA on PBS" and "I have a certificate/associates degree" hard to say which of three three prioritizes lower.

        I know it doesn't have much to do with the "real" or

    • by hduff (570443)

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

      It started after WW2 when "overhead projectors" were going to revolutionize education.

      • It started after WW2 when "overhead projectors" were going to revolutionize education.

        It started (or, at least, had already started) thousands of years ago when making marks on clay tablets was going to revolutionize education, and has continued since. And, you know, the whole time technology has been revolutionizing education. Though, usually, it takes people quite a while from the introduction of a technology in education to develop the practices that actually allow it to revolutionize education.

  • by vlm (69642) on Wednesday October 03, 2012 @01:48PM (#41540551)

    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...

    • 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.

      • by certron (57841)

        Had I the mod points, you would certainly be getting one. Look at me still posting when there's lurking to do...

  • As a computer information technology major, I have been looking for other programming challenges since my C# programming has been wrapping up this semester. About to start this right now!
  • source for the name (Score:5, Interesting)

    by necro81 (917438) on Wednesday October 03, 2012 @01:53PM (#41540637) Journal
    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
  • What if you're already addictd to biology-oriented sites?

  • by superid (46543) on Wednesday October 03, 2012 @02:15PM (#41540935) Homepage

    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 ]

    • by Anonymous Coward

      I am currently completing my MS in CS at a top-10 US engineering school. A BS in Microbiology and minor in CS is an outstanding choice and will be in great demand for the indefinite future. I enjoy pure CS/software engineering and make 6 figures, but bioinformatics is even more marketable.

      Bioinformatics is hardly on the bubble at this point and in any case, would only 'burst' if we somehow fixed healthcare for good.

    • In my experience, there's been a huge push for bioinformatics because the demand is fairly high. I'm planning on going the bioinformatics/biomathematics route myself, and I doubt there will be a bubble. Mostly because the #1 way to turn a sparkly-eyed undergrad off is with a heavy dose of mathematics. :P
    • by cjav (1331511)
      This is how I see it.

      I graduated in 2003 from a small university in latin america. BS in Biology with a twist at the end toward bioinformatics. In my almost 10 years of experience in the field, I found that people with the very odd mix of skills combining biology and computer science are quite hard to find. If you have both sets of skills, you won't have a hard time finding a job. Not even is as me, you move to a highly competitive area like US North East( DC area ), where in my case language and cultural
    • by rockmuelle (575982) on Wednesday October 03, 2012 @03:59PM (#41542125)

      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

      • I think you may be able to answer this question then: are the problems hard enough that someone solving them quickly could have applications for current research? Do the problems increase in difficulty up to research level?

        I remember that there was a similar effort in gamification that led to an video game player "winning" a game that thereby produced a solution to a protein folding problem. Can something similar happen here?

    • My son is a a senior in HS and has been thinking about a BS in Microbiology and a minor in CompSci.

      I'm not in either field (but I know quite a few people who are quite well), but I get the impression that Biochemistry is both more valuable in the job market, and more relevant to bioinformatics, than Microbiology as a degree.

      Is there a risk that 4 years from now there will be WAY too many bioinformatics grads?

      Sure, there's a risk. But if you get a degree in bioinformatics rather than some weird and highly-i

    • rockmuelle's reply is excellent, and gives a fairly accurate assessment of the field.

      My view is that Bioinformatics/Computational Biology is not a bubble, simply because these disciplines do not reflect a *job market* but rather a shift in how all of biology will be done in the future. Just as molecular approaches transformed the way biology is done during the 1970s-1990s, computational approaches will likewise transform how biology is done in the 21st century. And just as molecular techniques in biolo
  • by gr8_phk (621180) on Wednesday October 03, 2012 @02:42PM (#41541259)
    As a long time software guy, will solving all or most of these problems help me change fields?
  • 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

  • So you took biology, and made it into a series of quest arcs? Of course you're getting adoption from nerds.

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