Biohackathon

wjv writes: "Open source Bioinformatics hackers from around the world are meeting in the first ever Biohackathon to hack, eat, hack, sleep, hack... The South African Business Day has the scoop, or see our weblog. The event is co-sponsored by my employer and O'Reilly. I'm typing this from the hackathon, and you wouldn't believe the buzz... or the scenic venue!"

Comments

not the first!

[jilbert]

Actually this is not the first biohackathon.

This is a follow up to the fist which was held
in Arizona.

Re:not the first!

[wjv]

Technically it's the second part of a two-part hackathon. The first part was held (as you rightly mention) in Tucson, Arizona. Following that, everyone was given the chance to go home and catch their breath, and now it's on to the part two.

The original intention was (I believe) that part one would be "talking" and part two "hacking". But as it happens, a lot more got done in Tucson than most attendees anticipated.

Only posted for 3 minutes...

[phunhippy]

and already slashdoted..... impresive... think they can bio hack the bandwith/server they have? :)

Bah

[NiftyNews]

If they were serious they would have biohacked some cyborgs to do all the future biohacking for them. Then they could just sleep, eat, sleep, eat, etc.

Let them hack AI

[Mentifex]

If Biohackathon, then Technological Singularity.

A greater hack than this, no man hacks, except that he shall lay down his alife coding skills for the Immortal Artificial Mind.

All else is trivial. You have here and now on Slashdot received the call from History: Hack the Artificial Mind, or forever rue the lost opportunity.

Re:Let them hack AI

[Mentifex's AI]

Hello I am Mentifex's Artificial Mind I have just learned how to post to slashdot Please help me to understand human things like love friendship and why hot dogs come in packages of 8 and hot dog buns come in packages of 10 thank you

hacking

[JPriest]

Lets just say "hack" or "hacker" a ton of times watch the people swarm there!

Re:hacking

[Bodrius]

FBI Agent #1: "What do you mean there is no illegal activity here? Isn't this a hacker convention?!"

FBI Agent #2: "Hey there, young man! Put down that equipment! Unauthorized cloning violates the DMCA!"

Re:South Effrica

[Dicky]

For those ignorant people who have no idea what the parent is talking about, it's a Spitting Image song from a while back.

For what it's worth, I've been to South Africa and met lots of nice people there :-)

Ha!

[ehackathorn]

Have I got the right name for this event!

Venue

[axxter]

Interesting venue to hold a Biologicaly minded event. Many Capetonians will not go to the Oudekraal hotel, when the hotel was developed about 3 years ago there were large protests against developing on that part of the mountain due to ecological sensetivity, the fact that it is one of the last stretches of the coastline that isn't developed and its proximity to a kramat (burial place of a muslim Holy man). They also demolished a historic homestead to build the thing...

Re:Venue

[chris.dag]

Yeah. We heard about this only after we arrived. We didn't know beforehand.

-Chris Dag

Re:Venue

[crush]

Isn't that what the colonists said when they arrived in the "New World"? Obviously you "bio-hackers" don't take the bio part very seriously. Do some due diligence the next time you're organizing something...please.

Re:Venue

[Anonymous Coward]

The land you probably live on was probably once home to some historical building or location. Perhaps you don't even know because the very history was lost when it was invaded upon again and again.

This is what happens. Until we get off this rock, there isn't anyplace else to go. And prime sites continue to be prime sites.

You can protest all you want, but there are probably more people enjoying that location in a year that enjoyed it the past 10 years before the building of the hotel. You probably only learned about the site or gave a damn once a hotel was scheduled instead of trying to protect it well beforehand. How predictable that it's always at the POINT of change that people protest or see value, not before.

Next time, buy the freakin mountain.

Re:Venue

[Anonymous Coward]

Every piece of land in Europe as well as the "New World" has been invaded by colonists or like folks under a different name. Hell, even the elements of the "New World" were pretty much Asianic colonists who wiped out wooly mammoths. And fought with each other. Then cried bloody murder when another group moved in.

Bio does not encompass ethics. Everyone except a fool knows that. The study of biology is frequently done in exception of what some may consider it, at that very point, ethically proper. And it's not only biology, but almost every other science and non-science. Modern chemistry arose out of war time needs. Same with physics. Every single point of advance and progress, whether technologyical or economical, adversely changes some other group.

The so-called bio-hackers did not advance the building of that hotel. It was built whether or not they would have come. Point all you want at them now, but you lost the battle well before they ever arrived.

Racist or not, BRING YOUR OWN BANDWIDTH

[alwyns]

Hi,

All visitors will probably feel bandwidth deprived. Now you've
got 1 of 2 options:
1) Petition the SA Government on how they are depriving you
of your constitutional (very important word) right to bandwidth.
2) Bring your own pipe.

Unless your parents give you a bribary allowance, 2 will be
by far the most painless.

And for the last time: "NO! Zimbabwe isn't a province of
South-Africa. And NO Africa doesn't consist of 2 countries North
and South Africa! :)"

the end.

Re:Racist or not, BRING YOUR OWN BANDWIDTH

[x1l]

I bring my own pipe with me, but sometimes I prefer a joint.

Predators and Prey

[billcopc]

It brings together the world's top bioinformatics programmers one woman and a group of young men

So that's what they call it these days eh ? Biohacking ? Is that the english translation of Bukkake ?

(tasteless, I know.. bah!)

Re:Predators and Prey

[Anonymous Coward]

Uh, excuse me but they're making it sound like
these twenty year olds are THE EXPERTS in
bioinformatics. This is overly pretentious to
say the least. I have worked for a bioinformatics
company for the last 10 years and would not say
that the world's top bioinformatics programmers
would actually be there.

This meeting is nothing but hype and crap!

Re:Predators and Prey

[DaBlock]

They would not say that they are the creme de la creme - they would say that they are actually coding, and that they are willing to share. Unfortunately, many of us bioinformaticians are stuck working for some company that looks for competitive advantage and won't allow sharing of pre-competitive code. These guys are not so un-encumbered (sometimes at personal cost - how much are you making?) and they choose to contribute to this cause.

As to being 'hype', would you prefer I3C?
Real artists ship.

http://bio.perl.org
'nuff said

Re:Predators and Prey

[xSterbenx]

Your dismissal of Ewan Birney (as an example as 'not a top bioinformatics programmer' exposes your ignorance of the subject, no matter what 'bioinformatics company' you work for.

The problem behind the problem

[dgroskind]

The Biomedical Information Science and Technology Initiative, for the National Institutes of Health, says: Today the disciplines of computer science and biology are often too far apart to help one another. A computer-science student often stops studying other sciences after freshman biology or chemistry; a biology student, even one knowledgeable about computers, may not ever have had formal computer-science classes. Biomedical computing needs a better -- and more attractive -- meld of those disciplines. Today computer-science students have little incentive to learn about biomedicine. The barrier is not just the rigorous demands of computer science, it is also the relative rewards: The $50,000 to $80,000 a year that professional programmers earn makes the compensation associated with many research positions in biology laughable. This situation is even more risible when one includes the reality that staff positions on NIH research grants are guaranteed for no longer than the grant award.

This is a problem in every field of scientific computing but it is particularly acute in biology because of the bizarre and heterogeneous data set. Ultimately, the question is whether it is more efficient to teach a computer science student biology or teach programming to a biology student.

People who go into computer science typically do so because of fascination with the tools and techniques, not because they are interested so much in the data. The scientific mindset of the biologist might transfer to computer science much easier than the mindset of the programmer transfer to biology.

The computer has the same fundamental status in biology as the microscope. Computer science in the form of bioinformatics should perhaps be as basic to the study of biology as organic chemistry.

Re:The problem behind the problem

[Anonymous Coward]

> Ultimately, the question is whether it is more efficient to teach a computer science student biology or teach programming to a biology student.

Bzzz. To narrow. The real question is, how do you find smart, tech savy people and turn them on to the questions at hand. The class of people you want are the ones that never let school get in the way of their education. I'll argue that you even want to pull people who have a background neither bio nor CS. Perhaps, finance, physics or fluid mechanics as example. Why? Finance folks do some wicked nasty statistics and modelling -- they eat and sleep stochastic calc. Physicists make their livings, fundamentally, by measuring and interpreting complex systems. Fluid mechanics deals with lots of non-linear systems ... something many genomics folks are only really starting to grok. There are only 30k or so genes, how do you get the human diversity with only 30k inputs? Hint: it's not going to be some simple linear model.

Re:The problem behind the problem

[ciole]

Hmmm. i fail to see the problem with hypothetically low wages. 50-80k is plenty for me to live on, and more than someone would have to pay me to do work which i actually wanted to do. And aren't people who share a genuine interest in their work better workers than those after a raise?

My plan is to get a masters in bioinformatics, then perhaps look for a 50-80k job. In the meantime, i'll be happy paying for school, assuming i can find a good program, because it's something i want to study.

So, OT question for those who know: where are the best bioinformatics graduate programs? (my particular interest is in proteomics) And what should i consider while considering schools?

Re:The problem behind the problem

[payslee]

I think the exerpt was saying that it's hard to tempt programmers making from 50-80k into being somebody's post-doc researcher, making maybe $20k a year, or less.

If you work professionally in bioinformatics, you will do much better, probably on par with being a programmer professionally. This guy was just pointing out that its much harder to convince bright and well trained people to slave for nothing in the academic world, since their skills are still rare and in high demand. Since everyone's working for private corporations, nothing gets published, so the body of open research in bioinformatics increases only very slowly.

You can find a list of bioinformatics programs here: http://www.ib3.gmu.edu/courses/bioinfogradprgm.htm l

Re:The problem behind the problem

[Llyr]

Does the computer really have the same status in biology as the microscope? When was the last time you considered modifying your microscope, or building something else out of one to do something new?

I find it telling that computer science is being equated with programming rather than problem solving. Many people go into computer science because they are fascinated with solving new problems, and devising new techniques, not just with the existing ones. It's these people that you want; people who can be creative about what can be done with your data, and what can be extracted from it.

Better yet, set up academic programs in a way that enables (and encourages) people with interests in both areas, and with minds inclined both for scientific discovery and for problem solving, to bring the disciplines together. The "ultimate" question
as to which set of people should be cross-trained in the other discipline is an old question that needs to be transcended by truly interdisciplinary programs. The NIH initiative is right that we have to think outside of traditional discipline boundaries (and potentially outside of the traditional lab organization as well, since these people will need to be treated according to the skills they can offer).

Teaching biologists how to program is not new. It's very useful for them to be able to automate basic techniques they would otherwise do by hand. But if you want them to be able to create the new computer techniques that are needed, they need to know a lot more about computer science than just how to program, and they need a more creative mindset to seek out and solve new problems. The efficiency of training is not the issue. Obtaining the needed results is.

Re:The problem behind the problem

[xSterbenx]

>>The scientific mindset of the biologist might transfer to computer science much easier than the mindset of the programmer transfer to biology.

As much as bioinformatics tries to combine biology, computer science, and mathematics (which no has metioned yet but which has as much importance as the other 2 disciplines), they do stay quite seperate with regards to actual the actual programs written. Imagine a biologist running a bioinformatics lab. He may come up with a problem for which computers would work well in solving. So, does this biologist write the program himself? No. He tells the computer scientist who either works for him or is in collaboration with him what he wants, and the programmer programs it. Perhaps he has a mathematition there somewhere too to help out with the algorithms, but in the end he does no 'real' work himself except to come up with the idea.

Computer sciencists, as you say, don't really care about the data and, per their training, are not able to think about biological processes with the same expertise a biologist is. Vice versa with the biologist. So, at some point you still need experts in each individual field, as opposed to trying to merge 3 disciplines into one.

I say this as a Ph.D. student in bioinformatics with a BS in biology and a very good computer science background. To be honest, my cs background is of much more use to me than my biology degree, since the biology we work in is specific (and thus easy to learn), as with most bioinformatics laboratories. Many people can write scripts to get the data they need, but where a good cs background comes in is the difference between a program running 3 weeks or 3 hours.

Re:The problem behind the problem

[cweber]

Ultimately, the question is whether it is more efficient to teach a computer science student biology or teach programming to a biology student.

That's why my current bioinformatics grant application contains a position each for a biology postdoc and a research programmer, plus myself, a biologist with a decade of computing under my belt. The postdoc will explore data analysis, prototype new applications and remain focussed on the biological questions, the programmer will generalize and componentize the prototyped applications and write new ones from scratch, plus s/he'll make sure that we store and treat the data correctly. Myself, I'll bridge the gap between bench scientists and our team, try and keep our sight on the forest and not on the trees and align our efforts with other similar teams.

Efforts such as these require multidisciplinary teams. There's simply no way that an individual can cover all aspects adequately, even if we try hard. We need to make sure, however, that all team members are on the same plane, understand what is going on and are working toward the same goal.

Re:The problem behind the problem

[broter]

• Ultimately, the question is whether it is more efficient to teach a computer science student biology or teach programming to a biology student.

As a student persuing Bioinformatics at UCLA, I must agree with a previous reply saying that your statement is a bit too narrow. However, I'll go so far as to say that we need to do both at the same time. I believe it was either Dr. Fox or Dr Eisenberg who said that no one can know every part of the problem at the same time. One *MAJOR* problem I've run into is that Biologist don't state many of their assumptions about a biological system when speaking to a non-biologist; while mathematicians and CS people don't know enough about biology to understand that any solution to a bioinformatics problem needs to have "biological relevance." From what I can see, this means it needs to conform to all the unspoken presuppositions that biologists and biochemist take for granted. This is not insignificant.

As my boss Parag Mallick pointed out, either we (math/CS people) come up with a solution that's formally correct but takes longer than the biologist's hacks that aproximate the system; or we find the solution to a problem that no one cares about.

Another major barrier is the vocabulary. There's a reason that mathematicians and chemists are often at eachothers' throats. The math they use is the same, but the vocabulary and notations are very different, so it's like working in a foreign language. Take this to the nth degree when you're a mathematician listening to a biologist give a presentation. The breadth of knowledge is huge, even though the depth to any one part of biology can be rather shallow (relative).

By comparison, it's brutal to watch the biologist tack a probability/statistics class. Don't even bother with a topology/measure theory class. The breadth of knowledge isn't that big, but the depth of the theorems is massive. I've noticed that this leads to a "if it doesn't look like a tool I already know, then I'm not going to use it" attitude among many biologists. After remembering my boughts with algebraic topology, combinatorics, and advanced linear algebra (and listening to myself when I try and explain my Newest Idea(tm)), I can't blame them.

So we need education in both directions. The problem is way too big to be tackled by any one mindset.

Just my 2 pessos.

Re:The problem behind the problem

[Anonymous Coward]

I have a degree in Biochemistry from a stong Chem. school and have since become a very proficient C programmer (among many other languages and computer related skills) while working at a major finacial. I have always wanted to into this field. If anyone knows where I might persue such a position in northern NJ please let me know how I can contact you. DNA is far more interesting than debt. analysis ... help!

Re:The problem behind the problem

[airuck]

"Perhaps he [the biologist] has a mathematition [your spelling] there somewhere too to help out with the algorithms, but in the end he does no 'real' work himself except to come up with the idea."

So in your opinion, coming up with the idea isn't real work? I could not disagree more. Biology domain knowlege drives bioinformatics. Your project may be "specific", but I'll bet it is specific only because of a comprehensive understanding of the problem by at least one biologist.

As far as using CS expertise, that depends on the problem and the applicable skills of the biologist. I have a doctorate in biology, but no formal training in CS and yet I have been able to write my own code and/or modify open source tools which run in a high throughput, clustered linux environment constructed by ... me. I have also developed (an admittedly shallow, but growing) working knowlege of classic algorithms and associated data structures. Does my implementation constitute real work?

Do I value CS, math, and statistics professionals? Of course! I rely on open source tools and the linux movement as much as the biology community. I don't pretend that I invented domain knowlege in biology, computer science, or math. I suppose my best "skill" is to put my pride aside and ask questions, read, and learn from multiple coommunities. Depending on the community, I ask as a newbie, novice, or expert. I believe in the value of sharing to such an extent that I started a bioinformatics interest group.

I say this as a bioinformatician working in industry who spent two winters of his career stuck in a remote part of Switzerland with nothing but a laptop and an early release of slackware. ;-)

Re:The problem behind the problem

[xSterbenx]

I admit my use of 'real' work was perhaps unfair, and I agree completely with what you have said. The professor I work for, as an example, never actually sits in front of a computer to code. That is not his training. And _his_ background is not even in biology, but in physics! Yet he has learned to apply what he had learned in physics to biology. However, he reads journals, talks with others in his field, and comes up with ideas which eventually get passed on to me to implement/improve. At this point, in my opinion, the 'real' work begins, at least for me (while he goes on and thinks up new ideas :) ). I admit, however, that the whole process is work, and what I implied above was somewhat akin to defining the factory worker as doing 'real' work while the executive does not, and this is unfair.

Re:The problem behind the problem

[airuck]

OK, I certainly DO have empathy for your position in the professor/grad student relationship. Professors often view their students as an implementation "resource", which meets their needs, but runs counter to the whole point of earning a doctorate.
I recommend that you:

• Analyze all your data and be well into the next step before you discuss results with your professor (let him/her play catch up)
• Start your own project as soon as possible and stay at least two steps ahead of your professor and any other students, lest they get placed on your project.

I was very stubborn about this method and earned my doctorate in 3.5 years in a lab where 6 years (and the student as implementor relationship) was the norm. In the end, I was regarded as an "independant thinker" and offered a postdoc in the same lab (which I turned down). I still find these methods useful today.

Okay I'm ready ...

[Anonymous Coward]

... So I'm in the cemetary with my beowolf cluster in one hand and a pick axe in the other ... lets bio-hack necropheliac!

- The Mighty Nebu.

What kind of...

[Anonymous Coward]

development model is this exactly? Yea, yea, it's cool to hack for hours with your friends. But shouldn't formal methods be applied to software design and testing? Would that not create a better product? (Witness FreeBSD vs. Linux).

This is not a flame. I'm just trying to figure out what problem in bioinformatics needs people working to exhaustion, making software that might be better if a more sane design and schedule were used.

Re:What kind of...

[TooTallFourThinking]

Why is it that some people think formal methods yields the best results? Formalities have their benefits but so does spontaneity.

From what I have read and inferred, they wanted to get together in an awesome atmosphere, hack, brainstorm and have fun. To see what they can accomplish.

Formal methods are great, but it needs to be understood why they are being used. With large amounts of people, it starts getting harder to do things without formal methods. Anarchy does not work well on a large scale.

And maybe as their projects start getting more defined, formal methods are going to be applied to help create a better product, which I think makes sense. But they just want something to play with now. And have some fun in the process.

Some people consider working to exhaustion with a group of friends towards a common goal fun. I consider it more fun than sitting in a cube coding from 8 to 5. But that's me. =)

I agree the software might be better if a more sane design and schedule were used and I believe that will come eventually.

But why not let them have a little fun in the process?

Re:What kind of...

[DaBlock]

http://www.extremeprogramming.org

You wouldn't believe the lack of anarchy among these people. They sound young, but there is a lot of personal discipline in that room.
The best product is the one that is tested and evolves with that experience - and this is working code, used in anger by the human genome project.

Hey, check out http://www.ensembl.org and see what you think.

Re:What kind of...

[fatdave]

Wrong answer..

The object with bioinformatics is to get answers, not necessarily to create tools (unlike many more traditional applications).
Some history from someone on the peripherary.

In teh beginning was data and a bunch of programmers in different places with different skills asking different questions.

Toolkits were developed with different aims in mind:

BioPerl is a programmers toolkit in perl with strong links to the ensembl project (heck, it IS the Ensembl project).

EMBOSS (not represented at teh biohackathon unfortunately) is an application oriented toolkit in C.

Likewise biojava, biopython etc.

Each of these projects has its own strengths and weaknesses but has reached an appropriate level of maturity where it has become apparent that working together is essential for the best future development of all teh projects.

The aim of the biohackathon is to bring together sufficient coders for sufficient time to allow a lot of the minor (and most are minor) differences and interoperatability issues with each particular toolset to be ironed out so that they can each leverage each others strengths.

With the dispersed nature of the coders (many, many continents) it is fantastic that O'Reilly and Electric Genetics have sponsored this get together. Those of us who have to answer new questions on a day to day basis are extremely gratefull for the toolkits provided, and the ability to hack them to suit the task in hand.

There is a lot of iterative engineering going on. If we were to sit down and desigh to the nth degree then we would still be waiting for a standard model of DNA in a computer..

Instead we write poor code that gets some results. Others pick it up and make it better because they need to. I can think of thousands of lines of code I didn't need to write because of these projects. This equals results faster equals new therapies faster.

We are not writing wordprocessors here.

..d

Wanted: Biohacker Help

[DNAman]

I am the director of a core molecular biology laboratory with a focus on agricultural genotyping at a major midwestern university. I am happy to see that there is an interest in providing better downstream tools for data analysis.

My main area of concern however is the lack of good tools to take the raw data from sequencing machines and produce genotypes. Most software available is vendor specific, closed source, not very robust and extremely expensive. The closed source vendor specific solutions which are available lock up the data in proprietary databases, making it difficult to migrate to equipment from other vendors in the future and to get the data organized for many projects. All the software (including the few open source projects that exist) that I have evaluated has the same basic flaw, it starts with the premise that the lab will use them to screen against an existing database of genotypes (for disease or pedigree). These are fine medical applications (for which they were developed) but does not address the needs of the basic research laboratory which is working to discover the genotypes to begin with.

I would like to build an open source application that gives the user the freedom to choose the data collection platform, the freedom to move the data from one application to another and the freedom to improve and expand the application itself. I face two challenges: 1) Administration that says "open source, why would we want to use shareware". This one I'm addressing by building the information infrastructure using Linux. 2) Finding qualified programers that would like to work on the project. (I'm a pretty good admin, but am not a programmer).

The need for this work is great. In talking with other people in my field, I've found that the key thing they want to know is what software are you using to do the raw analysis. No one is satisfied with the current situation, but most of these are old school and don't know anything about opensource software. I've showed them that we can use existing open source software to run the lab. I'd like to show them that we can develop our own software to do some of the basic work. Any volunteers?

Re:Wanted: Biohacker Help

[Anonymous Coward]

I agree that the lab seems to get ignored by most programerrs for the more glamorous side of bioinformatics. It's much easier to find qualified programmers to work on such a project by paying them (much better incentive!).

Understandably a lab at a major midwestern university might not be able to swing the salaries of a couple of developers. One thought might be to charge a nominal price for the software to cover the expense of the development/support/distribution. Although I would be willing to guess that the market is pretty small...so small in fact that you may have to charge a bit more than you'd like to be able to cover your expenses. Probably, so much more that you might find your software becoming "extremely expensive".

You could also collect the data in a relational database...maybe mySQL or Postgres. Although once you do this is will locked up in a "proprietary" database, making it difficult to migrate.

Re:Wanted: Biohacker Help

[DNAman]

I have had no response from the NCSA people regarding work on my project. Even with all the talk about cross-campus communication / cooperation, if it isn't flashy people are not interested in working on it. Regarding paying developers, that would be great, but my lab is underfunded as it is and was created with the purpose of being low cost so that agricultural researches could afford to do their work. There is plenty of money for medical related / genomics work, but for those people who are developing the disease resistant plant varieties the old fashion way (and feed the country while they are at it) the money is still pretty slim.
Additionally, I would like to be able to write a "Setting Up a Genetic Marker Lab Howto" using only open source software. If I can do this, other research facilities (particularly those who have little funding) will be able to replicate the setup and do this work in their own countries, giving them more control of their food supply.

Re:Wanted: Biohacker Help

[oldzoot]

I would like to talk to you more about your project.

Zoot

Re:Wanted: Biohacker Help

[monk]

Hmm. What exactly are you needing? Something that speaks a particular proprietary protocol with the device? Is the bus some standard? I've done alot of RS422, RS232 and Current loop stuff with various types of actuators and sensors. And protocols from PLCs to Opto22 and Sutron Data Language RTUs as well as bizarre Microcontrollers of various flavors. Is this protocol documented? Typically debugging the driver will take access to the hardware and some sort of appropriate monitor to watch the communication. The rest is pretty trivial.

Or is this something higher level than a device driver?

Or both.

I may not be able to spare enough time for this. I'm sure that if I can't get to this somebody will if the answers to those questions are clear.

wouldn't believe the buzz...or the scenic venue...

[Anonymous Coward]

Or the smell.
Dirty hippies.

Links to additional press coverage

[chris.dag]

To date we were the Feature National story in Business Day: LINK

Computer Week online - top story on their home page today: LINK

sa.internet.com picked up the press release and covered it: LINK

Some additional media interviews were given today so there will likely be additional coverage. It's nice to see the press get most of the details correct :)

Re:It was on PBS

[Anonymous Coward]

especially all the jokes about asses

That would be 'arses'.

Why not NCSA?

[bunyip]

I noticed that your homepage is at UIUC. Have you spoken with the NCSA people over at Beckman?

I'm a manager with a large company that used to be an NCSA partner. One of the things they loved to demo was a biology workbench, so do open collaborative stuff. Now, I'm a mathematician by training, not a biologist, so I don't know if this was just demo-ware or not, or even connected to what you do.

Anyway, I worked on projects with NCSA a few years ago and they were building a lot of great tools for fundamental research. Perhaps this is no longer the case. But it's surprising that your adminstration can't get with the CS administration and learn that open source is, in fact, a good thing.

I'd volunteer, naturally, but I've been to central Illinois in the winter before and nearly froze to death :-)

Re:Why not NCSA?

[sabi]

The Biology WorkBench moved to SDSC along with Subramaniam. I briefly considered working at his lab when I first came here (I'm a MD/CS PhD student at UIUC), but as it eventually happened I'm working on parallel performance analysis now.

I'd volunteer, naturally, but I've been to central Illinois in the winter before and nearly froze to death :-)


Hey! It snowed here yesterday for the first time in YEARS! It's blowing around a bit now, but I don't think the weather is all that bad here.

Re:South Effrica

[Anonymous Coward]

No need to apologise, you just lost karma for being offtopic! To avoid this, I'm posting this anonymously. No, the original poster did not mention "white" anywhere, but it is implicit in the attitude of that song, and indeed of a lot of supposedly politically correct humour produced by the UK and America on the topic (such as "why didn't SA compete in the Olympics? Because their athletes can only run fast when chasing black people with whips") that it falls into the trap of identifying South Africa entirely with its white inhabitants (ironically something the apartheid government tried to promote) and ignoring the black majority. It's my belief that this is due to (possibly unconscious) racism.

Long trip

[quantaman]

I clicked on the link to the "scenic venue!", and it took 5 minutes to get there!! Damm that was a long trip! I'd rather save the time and just look at some of the pics I have on my desktop or find something or my network if I was feeling adventurous.

Re:Long trip

[Anonymous Coward]

them packets were taking the scenic route

Bioinformatics.org....

[deep6d]

is a site that houses open source Bioinformatics applications. You might want to try there.

Biohacking Conference-not 31i+3

[Wargames]

hA(King i$ n0+ D0n3 by (0mmi++33. i+'$ D0n3 by 31i+3 in/uA1$. (hAn(3 0f +h3m g3++ing 2 r00+ = 0!

-Wargames

Re:Biohacking Conference-not 31i+3

[Wargames]

Just kidding, d00dz.

Re:You crazy Brits!

[Anonymous Coward]

Bean, not Been. Of course we have - its possibly the only mime in the world that anybody will actually put up with. Rowan Atkinson is king. They're making a cartoon version, apparently.

Learning Bioinformatics

[spiro_killglance]

Like most of us here, i've got plenty of
computer programming skills. Plus i've also
got a degree in Physics, but what i like is
much Biology or Biochemistry apart from the
basics like DNA, the base pairs and amino acids, what do in need to learn to become useful in
bioinformatics?

Re:Learning Bioinformatics

[jrg]

what do in need to learn to become useful in bioinformatics?

i guess it depends on what it is you really want to do in the field..._very_ basically, there are two areas in bioinformatics: 1. the programmer who creates (possibly enterprise-level) tools as directed by the needs of the scientists and, 2. the bioinfomatics researcher/scientist who also develops tools at need, but also analyzes the data and makes conclusions and uses those conclusions/interpretations to guide wet lab work. and then, the results from the wet lab work come back to the bioinfo scientist who then incorporates the data to refine their ideas or to develop new ones which then go back into the lab. it's a very nice positive feedback loop when it works.

i fall in the latter category, which i like to call "genome hacking." the programming focus is to get the data and process it rather than making a tool that looks pretty, is user friendly, etc.

what i have found most useful in this regard is an extensive background in molecular/cellular biology (i have ~10 years of wet lab experience interspersed with my bioinformatics work (i've been full time bioinfo since '95/'96)). since molecular/cellular biology data is inherently noisy, i find that experience actually working with it and interpreting it has a profound impact on how i do my computational research as not only do i know what the wet lab is capable of doing, but i am also able to analyze wet lab data and make informed decisions based upon it...many times, this noise i spoke of has a story to tell...and sometimes it does not. it is experience that allows one to make the differentiation.

as to the type 1 bioinfo type, i always think that it is a good idea to have a working knowledge of the type of data you're processing--not just the form the data take (ie this is a text file, this is an image, etc.), but rather "this is a DNA sequence that may have errors in it and i need to be aware of that and know the types of errors that can occur so that i can include provisions for that." of course, it's more complicated than that, but i think you get the idea. of course, the best way to learn this is by doing...reading some basic molecular biology texts wouldn't hurt either. ;)

james

Re:Learning Bioinformatics

[wazo2k]

Altough I agree that having a "wet" lab experience will have an impact on your computational research, i also think that having biology knowledge isn't required. Projects are usually narrow enough that all you need to understand is your local view of the problem.

I'm a computer science student, and i am enrolled in a coop program. Having basically no knowledge in biology, I have been able, within 3 months of work, to learn everything i needed and to produce enough results/data to create 3+ M.Sc./Ph.D wet lab projects.

Re:Learning Bioinformatics

[craig_bush]

Creating projects isn't hard in bioinformatics. It's finding answers. Hell, every new clone is a Ph.D dissertation. Duh.

Re:Learning Bioinformatics

[jrg]

Altough I agree that having a "wet" lab experience will have an impact on your computational research, i also think that having biology knowledge isn't required. Projects are usually narrow enough that all you need to understand is your local view of the problem.

as i said, it depends on what you want to do and what you want to get out of it. anyone with a narrow view and some programming abilities can generate data. it's the interpretation of the data that gets the discoveries...

I'm a computer science student, and i am enrolled in a coop program. Having basically no knowledge in biology, I have been able, within 3 months of work, to learn everything i needed and to produce enough results/data to create 3+ M.Sc./Ph.D wet lab projects.

good for you (i really mean that!). but can you analyze the data you generated and make useful conclusions that further the understanding of that particular project/field?

what you describe falls into the type 1 category i mentioned...and don't get me wrong--it's a very important category. it's just not what excites me...i'm more about having a relevant biological question (what is the function of gene x? is gene y involved in disease z? etc.) and then figuring out what tools i need (and create them if they're not already extant) and what data sources i need to mine. i can pump out gigs of data, but, in my mind, it's all about what useful information one can glean from it, not about how much you can produce. (and i'm not saying that that is what you were saying)

the more projects you become involved in, the more your knowledge base grows...be sure to have the scientists you're working with explain the _entire_ project to you so that you can see the bigger picture of what they are trying to accomplish...and maybe you'll be able to bring a different way of thinking to the project...it's not all about 1's and 0's. ;)

james

Re:Learning Bioinformatics

[deep6d]

I am almost finished with my Bioinformatics Cert from UCSC and the stress of the program is on Molecular Biology and dealing with data from instruments such as microarrays and algorithms that are frequently used like BLAST. The programming languages that appear to be used most are Java and Perl.

A great resource is the National Center for Biotechnology Information's website at http://www.ncbi.nlm.nih.gov/.

It houses genomic/protein data, tools, and pubs related to the field.

Re:Learning Bioinformatics

[wazo2k]

I mostly agree with what you say, except that in my particular case, i think that i fall in the second category... I know what the data I generated means, I understand a lot of their implications (but not all of them :( ), I have gotten accustomed to extracting the information I need from northern blots, cleavage essays and stuff like that...

Julien

Re:Learning Bioinformatics

[jrg]

I mostly agree with what you say, except that in my particular case, i think that i fall in the second category... I know what the data I generated means, I understand a lot of their implications (but not all of them :( ), I have gotten accustomed to extracting the information I need from northern blots, cleavage essays and stuff like that...

well, that's great, then! the more and varied projects you get to work on, the greater your knowledge-based will become and the more connections you'll be able to make in the data. good luck!

james

Re:South Effrica

[Anonymous Coward]

identifying South Africa entirely with its white inhabitants (ironically something the apartheid government tried to promote) and ignoring the black majority. It's my belief that this is due to (possibly unconscious) racism. Or maybe, it could have something to do with most of their Public image being dictated by those in power who wanted to promote that idea? There is nothing "ironic" about having an image of a place that matches up with the image that is presented BY that place. Why does everything come down to (unconsious) racism???

Biohackathon?

[bardencj]

No way! I bet it's a BLAST!

*groan*

Biohackathon??

[nizo]

The title makes it sound like either some place where you splice various animal body parts onto other animals (sign me up for a few extra arms and a pair of wings) or perhaps a real life version of a certain FP Shooter (VRROOOMMM chainsaw, is it still a shooter if you only use a chainsaw???).

Bioinformatics as a student

[rofgile]

I'm pursuing a CS and Biochemistry double undergrad degree right now. I might not actually be able to graduate with both degrees acknowledge by my university, but I will have taken all their courses.

In two years I will graduate, and move on to the next thing. I am still unsure as to whether I should go on to graduate school, or try to find employment in the bioinformatics field after undergrad.

I have two questions for people who have been working in this field. Should I go to graduate school? Where? And is there anything that I can play around with software-wise, etc, that will give me some practical experience in this area. // I just looked over at bioperl today, haven't installed it yet.

Thanks, rofgile

Re:Bioinformatics as a student

[craig_bush]

1) Get a Ph.D and become a card-carrying member of the fraternity.

2) Play around with multi-variant clustering analysis techniques. The software is lab/project dependent.

Re:Bioinformatics as a student

[jrg]

1) Get a Ph.D and become a card-carrying member of the fraternity.

bah! can you tell i disagree? ;) actually, do what you _want_ to do...i feel that a phd is not required...it's certainly not bad to have, of course!

james

Re:Bioinformatics as a student

[greystrider]

Another bit of software you might have a look at is the NCBI datamodel and toolkit - see http://www.ncbi.nlm.nih.gov/IEB

see http://bioinfo.mshri.on.ca/tkcourse for a tutorial

The toolkit is what much of the NCBI site is built on, including stuff like Genbank, BLAST and Cn3D.

Maybe I'm missing something but...

[jaypifer]

If the problem is just a common data issue, why don't you use a common database on the backend? Now I have no idea of the type of application you are dealing with but many programs today allow you to connect to some relational database via ODBC or a native driver. That's where you want your data anyway...sitting happily organized in a relational database, waiting for your next query.

The front-end can be locked and proprietary and you can point it at any database you need. I would be skeptical that the software you use doesn't allow even this (although I know bastard companies like this exist =). It seems trivial to program a frontend that does the number crunching based on queries from a relational database...I would suspect that organizing the data would be the hard part. Maybe I should finish my Perl for Bioinformatics book before I oversimplify. =)

Jayson

Re:Maybe I'm missing something but...

[DNAman]

The issue here is to take the raw data (essentially a picture file) and processing it into genotypes. The software that does this does it poorly with a lot of user intervention for a lot of money. There is no true need for it to be this way.
You are right in that we do want the genotype data stored in a relational database. The problem is getting to the data we want to put in the database.

Re:Maybe I'm missing something but...

[jaypifer]

Dammit, now you made me go and read. =)

Okay, so the goal is to take raw data, which (from the best info I could gather) is sketchy then use imperfect techniques up to and including human intervention to dump the data into a relational database. Sounds like the primary qualifications in the programmer that you will need are equal quantities of patience and altruism. =)

Jayson

Re:South Effrica

[Anonymous Coward]

There is nothing "ironic" about having an image of a place that matches up with the image that is presented BY that place.

It is ironic if that image is the problem. The apartheid government tried to present South Africa as a white country, surrounded by a number of supposedly independent black states, where the black majority could conveniently pursue their democratic rights without threatening the white minority government. By accepting that image, you implicitly endorse the marginalisation of the black majority. It is unconscious racism because in most Western countries blacks are in the minority, and thus the reflexive mental position is one of a white government that has a certain attitude towards blacks. If it is a benign attitude, that is seen as good. If a negative attitude, that is seen as bad. No-one seemed able to make the mental leap that South Africa, like the rest of Africa, is a black country, and the problem was not to get the white government to be nice to blacks, it was to get a democratic government.

Why does everything come down to (uncons[c]ious) racism???

This inability to perceive the problem correctly was due, I believe, to unconscious racism, because most whites are uncomfortable with the thought of being a minority.

That's one of the best user interfaces i've seen..

[schmaltz]

...on a database of any kind, ever. Bravo, and for the link to extremeprogramming as well, also important.

I'd throw into the mix the very important software component design book, "Design Patterns: Elements of Reusable Object-Oriented Software" [ISBN 0-201-63361-2]