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.

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.

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

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.

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

[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

[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: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!

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

[oldzoot]

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

Zoot

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 :)

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 :-)

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.

Bioinformatics.org....

[deep6d]

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

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: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.

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

[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.

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

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: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

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]