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ROSALIND: An Addictive Bioinformatics Learning Site

Unknown Lamer posted about 2 years ago | from the programming-is-fun-we-swear dept.

Biotech 38

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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38 comments

Better than MOOC (3, Interesting)

vlm (69642) | about 2 years ago | (#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.

Re:Better than MOOC (2)

berashith (222128) | about 2 years ago | (#41540559)

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

Re:Better than MOOC (1)

K. S. Kyosuke (729550) | about 2 years ago | (#41541003)

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

It's a good thing, then, that tech can fix that again [supermemo.com] .

Re:Better than MOOC (0)

Anonymous Coward | about 2 years ago | (#41540609)

I agree that "fix" is a bit of a stretch for any single tech, but I'd say it's evolved quite a bit. It used to be I'd go to a library to get a book about something I thought I wanted to know about. I'd get home, read the first chapter or two, realize the book was garbage, and head back to the library. And there was a good chance they didn't even have what I needed. There was no way to know, since we didn't even have reader reviews for every book.

Now I can pull up the whole of human knowledge on my phone, if I know what to say to the device. And I've learned more from online courses I picked and took for free than I did in all my years of college. So I'd say things have improved dramatically.

But yeah, there's no silver bullet that "fixes" learning for everyone.

Re:Better than MOOC (2)

Medievalist (16032) | about 2 years ago | (#41541221)

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 (1)

Anonymous Coward | about 2 years ago | (#41541683)

Then I ask you, please, ask him to divulge as much as he can and you record it and then transcribe it onto the net, somewhere. The simply fact is that we are going to lose knowledge as our older generation dies off (at one time there were more kids than grandparents so the knowledge would be passed on; this could be the first generation where this does not happen -- I know I am in the same boat with my family (parents and grandparents) and my brothers and sisters have no will/want to learn anything except what Britany is up to today).

Even if that page is just archived somewhere and not looked at again for a hundred years it would be worth it.

Re:Better than MOOC (2)

lgw (121541) | about 2 years ago | (#41542159)

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!

Re:Better than MOOC (1)

xclr8r (658786) | about 2 years ago | (#41541243)

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]

Re:Better than MOOC (1)

rs79 (71822) | about 2 years ago | (#41541553)

Disagree. It already has.

What it hasn't fixed is "schools".

Re:Better than MOOC (1)

Raenex (947668) | about 2 years ago | (#41542497)

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] .

Re:Better than MOOC (1)

vlm (69642) | about 2 years ago | (#41543099)

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 "old" definition of education or training, but it does reflect modern reality.

complaining how everything sucks

Fair enough. Four things work:
1) Smart enough to know how to learn, plus internet access = self education. Don't really need much else anymore. Not access to subscription contracted flash websites that happen to be on the internet, not filtered internet, just raw search engine and internet.
2) Printing press seems helpful especially for workbooks (I was just kidding about the whine about papyrus being invented)
3) Improved student:teacher ratio always seems to help
4) Getting the students interested in the topic via social pressure or whatever works to light a spark

Re:Better than MOOC (0)

Anonymous Coward | about 2 years ago | (#41543151)

Hey, hey, hey, what about Prezi [prezi.com] and it's GUI, er, I mean ZUI for Zooming User Interface? (jerk off gesture)

Won't *that* totally revolutionize online education because of its mystical non-linear interfacing systematicness?!?!

Re:Better than MOOC (1)

hduff (570443) | about 2 years ago | (#41543969)

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.

Re:Better than MOOC (1)

DragonWriter (970822) | about 2 years ago | (#41544461)

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.

Help! (2)

vlm (69642) | about 2 years ago | (#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...

Re:Help! (2)

Antipater (2053064) | about 2 years ago | (#41541177)

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.

Re:Help! (0)

Anonymous Coward | about 2 years ago | (#41541283)

I'm sure the second requirement could be side-stepped by using CakePHP.

Re:Help! (1)

certron (57841) | about 2 years ago | (#41541655)

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

Re:Help! (0)

Anonymous Coward | about 2 years ago | (#41542527)

just make a plugin for wordpress or joomla.. why reinvent the wheel?

Finally a challenge! (1)

Phizital1ty (1755648) | about 2 years ago | (#41540579)

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 (4, Interesting)

necro81 (917438) | about 2 years ago | (#41540637)

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 (2)

pieisgood (841871) | about 2 years ago | (#41541291)

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

Atomic-level, or close to it, at that. (1)

Impy the Impiuos Imp (442658) | about 2 years ago | (#41540891)

What if you're already addictd to biology-oriented sites?

Bioinformatics Bubble? (2)

superid (46543) | about 2 years ago | (#41540935)

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? (1)

Anonymous Coward | about 2 years ago | (#41541287)

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.

Re:Bioinformatics Bubble? (1)

Mitchell314 (1576581) | about 2 years ago | (#41541309)

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

Re:Bioinformatics Bubble? (1)

cjav (1331511) | about 2 years ago | (#41541447)

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 barriers make things a little harder. I did enroll and finish a Master in Bioinformatics program in a local prestigious University to increase my chances.

Biology professionals only want to use a computer for as long as they forcibly have to, computer science professionals have much easier ways to make their living.

Re:Bioinformatics Bubble? (4, Interesting)

rockmuelle (575982) | about 2 years ago | (#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's definitely worth listening to. I also did a talk a few years back at TEDxAustin on the topic that makes the connection between big data and sequencing ( http://bit.ly/mueller-tedxaustin [bit.ly] ). Affordable sequencing is changing biology dramatically. Going forward, it will be hard to practice some parts biology without sequencing and sequencing needs informatics to function.

Good luck!

-Chris

Re:Bioinformatics Bubble? (1)

DriedClexler (814907) | about 2 years ago | (#41543205)

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?

Re:Bioinformatics Bubble? (0)

Anonymous Coward | about 2 years ago | (#41566475)

as always,academia wants the best of everything paying the lowest.... young...know biology-statistics-programming-labtech-etc-etc.. and, of course, you need to know how to live with just a few dollars...

Re:Bioinformatics Bubble? (1)

DragonWriter (970822) | about 2 years ago | (#41544523)

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-improbable vo-tech certificate, you can probably do more with it than actually get a job in bioinformatics. And having way too many grads doesn't mean skilled and motivated people can't get a job in the field, it just means you can't coast through and get one. (Internships and networking being at least as important as the actual piece of paper here.)

Re:Bioinformatics Bubble? (1)

caseybergman (2746201) | about 2 years ago | (#41559709)

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 biology have not (and will not) go away any time soon, neither will computational techniques. The crucial thing to recognize is that there is still a relative underrepresentation of *good* computational biologists (i.e. with strong skills in biology AND computing) so I would strongly recommend this career path for your son.

For more on why I think PhD students and post-docs should train in computational biology, please see: (Top N Reasons To Do A Ph.D. or Post-Doc in Bioinformatics/Computational Biology [wordpress.com] ). Some of these should apply directly to undergraduates, and should factor into his decision making process for the long-term.

Can I get a job? (2)

gr8_phk (621180) | about 2 years ago | (#41541259)

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

can someone explain... (2)

Mr. Slippery (47854) | about 2 years ago | (#41541543)

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 [wikipedia.org] , space science [nasa.gov] , telephony [intomobile.com] , and e-commerce [trocadero.com] . What makes processing strings of ACTG different than processing other strings? Thanks.

Re:can someone explain... (0)

Anonymous Coward | about 2 years ago | (#41542967)

Because it's not just string processing. I think bioinformatics is better described as being at the intersection of biology, statistics, and computer science. The problems are highly domain specific (think mechanisms of viral infection). Understanding the problems requires a pretty in-depth understanding of the biology. Understanding how to approach the problem requires some pretty tricky statistical methods (the data is quirky). And developing tools that other scientists understand how to use takes knowledges of algorithms, computer science and the ability to communicate to other scientists (like virologists).

Re:can someone explain... (0)

Anonymous Coward | about 2 years ago | (#41543037)

For one, it's not string processing.

Re:can someone explain... (0)

Anonymous Coward | about 2 years ago | (#41547139)

Mathematics, now with computers! See what I did there?

The people in the bioinformatics biz have a rather awkward combination of skills to bring together in one brain. You need biological context, you need strong computer science skills and code-writing abilties, and you need to be able to do valid statistics. My experience so far is of good biologists with awful software engineering, and good coders who struggle with the inherent fuzziness of biological systems.

Whether these degree courses cover any of these disciplines in enough depth to push forward is another matter. My feeling is that three collaborating experts can achieve much more in terms of groundbreaking research than three jack-of-all-trades types. We need people to be able to say "why can't we use this technique I learned while solving a completely unrelated problem?".

MMORPG? (1)

Gothmolly (148874) | about 2 years ago | (#41542803)

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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