Slashdot Mirror
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!"
Fist Sport!
"Why did they cancel my favorite Sci-Fi show? I downloaded ALL the episodes!"
No I've never met a nice South African
Which is not suprising, man.
'cos they're a load of racist bastards
With no sense of humor.
"Why did they cancel my favorite Sci-Fi show? I downloaded ALL the episodes!"
Metallica - Fight Fire With Fire
Do unto others as they have done unto you
But what in the hell is this world coming to?
Blow the universe into nothingness
Nuclear warfare shall lay us to rest
chorus:
Fight fire with fire
Ending is near
Fight fire with fire
Bursting with fear
We shall die
Time is like a fuse, short and burning fast
Armageddon is here, like said in the past
chorus
Soon to fill our lungs the hot winds of death
The gods are laughing, so take your last breath
chorus
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Actually this is not the first biohackathon.
This is a follow up to the fist which was held
in Arizona.
Before they turned shit. Brings a tear to my eye. And by that I don't just mean the tip of my penis lubricating itself with pre-cum either.
Although it is.
"Why did they cancel my favorite Sci-Fi show? I downloaded ALL the episodes!"
and already slashdoted..... impresive... think they can bio hack the bandwith/server they have? :)
happy troll tuesday!
Niggers have computers?
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.
------
Today's Top Deals
They will be serving cake?
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.
The Scoop is dying fast. Hear is the soop. Computer buffs chase a common language Open-source software is ideal for managing human genome information, but research units are not working together Science and Education Correspondent ONE whiteboard, 20 hackers and the mysteries of the human genome are the base ingredients for the world's first ever biohackathon, now under way in Cape Town. It brings together the world's top bioinformatics programmers one woman and a group of young men (their average age is 26) who make the powerful software that allows scientists to manage the massive amounts of data that accompany research into the human genome. Unlike traditional licensed software, open-source software is usually free. But more importantly, it comes complete with its programming code, enabling the user to customise the programmes or remove bugs. It can be developed much faster than licensed software and is particularly well suited to the fast pace of developments in the life sciences, including research into the human genome. Around the world, different research groups have given rise to their own programming communities, operating in different "open source" programming languages such as Java, Perl and Python. The big problem facing the bioinformatics community is that because they have worked out their own solutions for their own projects, their programmes do not necessarily "talk" to each other, says Tania Broveak Hide, MD of local firm Electric Genetics. And that is why she has gone into partnership with US publisher O'Reilly & Associates, and brought the open-source bioinformatics community together for the first time to "crack code". They call themselves hackers, but there is nothing underhand or illegal in what they do. They just have a few things in common with hackers their youth, a passion for computers, and since most of them are students, they tend to punch out their programmes long after midnight. The group first met in Tucson, Arizona, two weeks ago, and are now in Cape Town for the second part of their ambitious project. They sit classroom fashion in front of their laptops, with their tasks laid out on the whiteboard. There is no leader and tasks are identified and allocated by consensus. You might expect egos to collide in such an anarchic set up, but it is quite the opposite, director of the Open Bioinformatics Foundation in the US, Chris Dagdigian says. "It's quite simple. Whoever writes the code wins the argument." Some hackers are working on the "libraries" of programmes that enable people to build their own applications, hoping to make the different pieces compatible, even though they are written in different programming languages. The hackers also hope to make data exchange more efficient and improve the visualisation tools used to look at genome sequences. "At the moment, genome data is posted at centres all over the world, rather like houses that are managed by different estate agents. We want to create a system that will enable you to make a single query and search for data from all over the world." Since the mapping of the human genome two years ago, scientists have a pretty good idea of the sequence of genetic material, or DNA, it contains says Broveak Hide. Scientists know that the sequence of DNA spells out the exact instructions for the creation and destruction of each and every cell in our bodies. In other words, the human genome is the road map for our genes the units that determine what we look like and, when they go wrong, which diseases we will succumb to. Although scientist have identified genes associated with more than 30 disorders, their understanding is limited, says Ewan Birney of the European Bioinformatics Institute. Trying to understand which bits of the human genome do what is a bit like trying to translate Russian with an incomplete phrase book. Since understanding the mechanisms of disease offers hope of prevention and cure, the human genome is the subject of intense research worldwide, particularly by the big pharmaceutical companies. "The amount of data on the human genome in the public domain has grown exponentially in the past few years. Managing that data is probably the single biggest challenge facing computational biology today, "says Dagdigian, "As the body of knowledge expands, scientists can increasingly do experiments on computers instead of in laboratories, giving them tremendous efficiency gains," says Birney. "Competitive advantage comes from what you do with these programming tools, not the complex algorithms within the tools themselves," explains Dagdigian. As a result open source programmers traditionally share information, he says, a philosophy that marries well with the way science has worked for centuries. "If you publish your research in peer review journals, you have to tell the scientific community the steps you took to get your results. That concept of sharing materials and methods fits with the open source bioinformatics approach," says Dagdigian. With its hope of delivering new and freely available software to the scientific community by the end of this week, the biohackathon might sound like a socialist's dream. But do not be misled, says Birney. Just as an athlete's stamina, not her shoes, will help her win a marathon, this software is merely the enabling tool for scientists and pharmaceutical companies in their high-risk, high-return race to find drugs and vaccines. It is up to them what they do with it. Feb 26 2002 12:00:00:000AM Tamar Kahn Business Day 1st Edition
I find your British humor 'amusing', especially all the jokes about asses.
"Why did they cancel my favorite Sci-Fi show? I downloaded ALL the episodes!"
After all, mp3s are evil and deprive Lars Ulrich of his regular supply of crack cocaine.
"Why did they cancel my favorite Sci-Fi show? I downloaded ALL the episodes!"
Lets just say "hack" or "hacker" a ton of times watch the people swarm there!
Saying Java is nice because it works on all OS's is like saying that anal sex is nice because it works on all genders.
Aires, the other trolls are starting to tire of your self-delusional and selfish demeanor. You are not the one to lead the revolution. There is not even a revolution. In the coming days you should stray from your "blind and barbarous" charges into the frontlines of battle. Balance your self-aggrandizing trolls with humility or brotherhood. You blazed a trail through the e-wilderness but now you have blitzed your penis into a brick wall. Start looking for that balance with the universe and its inhabitants which you lack, lest you blindly and bluntly charge your erect manhood into ESR's sweaty, pulsing, and filthy anus. And you don't want to do that, do you?
Taurus
You provide foundation and structure to trolldom. If there be an Empire, then let its roots be your works. Yours is the first earthly manifestation of our combined and unified beauty, but now you have a choice. You can either lazily roam the fertile pastures and suck the sweet honey of victory, or you can help build Babel to the heavens. Beware, the former might lead to you sucking the semen from Taco's cock, while the latter, although lifting you from your sacred footings and unnerving yourself, may prove to be the wisest choice.
Gemini
You have many talents. Your trolls can be beautifully written, exhibiting your natural communication talents. Your mind is quick and flighty. Have you ever realized the variety of your pieces? One night you might write a homosexual expose on Linux faggotry, while the next day it is a craftily written legitimate troll. Your dual nature puzzles most and maybe even yourself. Some might not even see it outright. De Broglie contends that all matter is a wave on some level. Are you a wave, wayward Gemini? Another example is that you are a troll but you revel in using open source programs. You hide yourself well. You are a whore in most ways. And as a whore you will never be fulfilled. You may have had your fun about a week ago, but now it is not your time. It will be a while before you pull yourself back together again. But stick around, the dregs take entertainment in your plights and facetious ways.
Cancer
Remember that time you once tried to troll? Remember when everyone laughed at your pitiful attempts? Remember how you withdrew immediately and started to masturbate wildly to Hentai? Remember how once you came the neurotransmitters immediately pulsed through your being and took you to a pleasant place? The lesson here is that you are a pussy-mama and have no trolling talents. Masturbation is not a talent, fool, and you will never have your love be accepted in trolldom, or the world for that matter.
Leo
You know those days when no one seems to be trolling? Well Leo, you are our light in those dark days. You carry the torch, albeit in a conceited and self-centered way, but nonetheless you keep the Path alive. The shadow has yet to hold us sway. Don't get to full off yourself, because while you can keep a warm castle for us, you can't build us an Empire. Know your limitations sir, and also take care not to trample over the visionaries that can take you to the Next Level.
Virgo
You trolling style reeks of prudishness. To spice your life, I recommend throwing in some good bathroom humor or homosexuality into your writings. Your endless crapflooding, although detailed and nonsensical, lacks something special. You are a machine, a practical worker for the cause. You can best manifest your greatness when you are working for someone else. You should find a good Gemini (yeah I know that's an oxymoron), Libra, or Aquarius to give you inspiration and work. You need some mental stimulation right now. Actually, you could use any stimulation now, and for that, find a Libra.
Libra
Much like your cardinal counterpart Aires, you are a pioneer. But unlike Aires, your talent begins in the mind, inciting thousands of blood-thirsty trolls to rally to the cause. You lead is bond, and your bond is beauty. But did I mention you're a fake, arrogant bastard. Your superficial way can't last. Also, did you ever wonder why you rarely troll? Well, I'll tell you. You're an indecisive bastard. You start a story but then can't make up your mind over some unimportant detail. Becoming frustrated, you start jerking off to the homosexual undertones contained in your trolls. This is a mistake. Harness and channel your energy of creativity and destruction, and in the balancing of the two you might find success.
Scorpio
You are the true master of the art of covert trolling. Under the innocent guise of a harmless introvert lies a cold calculating killer brooding for the taste of blood and seminal fluids. You manipulate, scheme, lie, and sleep your way to the top. You could be a star in the sky, but you usually end up bound up in your own web of deceit. Sometimes you unconsciously look forward and plot this conclusion. In the depths of your sick twisted hell lies the key to transformation. The phoenix is birthed in the abyss, only to catch ablaze and fly soaring to the heavens. This probably won't happen to you though.
Sagittarius
You have the ability to show us "The True Path", but you would rather drink yourself to oblivion with a bunch of forest nymphs. Honestly, who here wouldn't do that? I have a desire to party with the forest nymphs tonight. Sag, let us hang out, drink much stout and wine, and fornicate with some nymphs. Fuck trolling, my carnal nature calls.
Capricorn
Always trying, always failing, always overcoming. Are you part of the allied forces, or do you contribute to the vile structure that threatens us all? Nobody recognizes your struggles because you manage to write in an earthy and uninspired monotone. What does this mean? Well, I don't know exactly what it means but I do know that you're a homosexual.
Aquarius
We all have problems, but you, Aquarius, have problems that affect us all. You fancy yourself a leader. Why? We never asked for you to bare the water to our thirsty lips. We never asked you to refine the Troll Empire into your own sick sadistic world. Once outcasted among "proper" trolls, some sick spirit from within told you, "If you build it, they will cum." Fuck those talentless bastards. The structure is now built, and the talents are ready to be poured. It is your duty to pour your metaphorical homosexual semen all over trolldom, and the world. Do not falter, for the revolution looms, and the sun will rise yet.
Pisces
Oh, what an old soul you must be. In some ways you are the flowing talent that Aquarius bares. This is doubtful though, as your inner water is probably stagnant and swarming with mosquitoes. You embody the best of the of the Zodiac. Don't get to full of yourself, because you also embody the worst. That is the key to your constant failures. You should get very angry right now and create a storm with the raging sewage inside of you. Pound trolldom from the heavens with your bile, and then cry. You may feel that no one understands you, and hell, you're probably right. That doesn't matter now, because the world needs your "talents" right now.
Just sounds like a complex term for 'wanking'
now that we had cyborgs that ate and slept as well we could concentrate actively on just being so that in the end everyone would turn into a beer.
Have I got the right name for this event!
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...
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.
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!)
-Billco, Fnarg.com
Whoa! Could this possibly be the most unpopular Slashdot thread ever? Let's see if it stays under 3 digits.
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.
... 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.
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.
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?
Or the smell.
Dirty hippies.
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 :)
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
You crack me up every time!
Have you ever seen a program called "Mister Been"? That rubber faced jester ALWAYS brings tears to my eyes.
"Why did they cancel my favorite Sci-Fi show? I downloaded ALL the episodes!"
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.
I stole this Sig
is a site that houses open source Bioinformatics applications. You might want to try there.
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
-- Each tock of the Planck clock is a new world and here we are still life. --
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?
Perhaps it would give some insight into how the CONSCIOUSNESS-TRANSFER mechanism works.
I am a sentient ATM.
No way! I bet it's a BLAST!
*groan*
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???).
I Am My Own Worst Enemy
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
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
Never go to sea with two chronometers; take one or three.
...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]
Big Daddy, Johnny, Burp, Aunt Zelda, Scott, Slurp, Big Momma