Sixth Bioinformatics Open Source Conference

Shipud writes "The sixth Bioinformatics Open Source Conference will take place this June in Detroit, MI. Open source licensed software has proven to be the most popular and useful for bioinformatics research. This includes the EMBOSS suite for sequence analysis, the Biopython; Bioperl, and Biojava collaborativelty constructed toolboxes; the ubiquitous RasMol and PyMol molecular visualization tools, and more, much more. Here is one opinion as to why open source and collaborative development have been such a raging success even at big pharma, despite the apparent IP hurdles."

Comments

as opposed to the closed source

[Anonymous Coward]

Bio-VB

Re:as opposed to the closed source

[WGR]

Ny daughter is taking bioinformatics in University ( Carleton University). In a software development course for biologists, here required language was VB6 becuase that is all the instructor (a biologist) was familiar with.

Imagine trying to get BLAST working with VB!!

Error: acronym overloaded

[phaze3000]

Will people please stop using the acronym 'IP' for that most annoying of phrases, 'Intellectual Property'?

• IP already has a meaning to 'nerds' - Internet Protocol
• 'Intellectual property' is confusing term - arguably deliberately so. You can read an excellent article on the subject by everyones favourite GPL creator.

Re:Error: acronym overloaded

[smartdreamer]

I agree it can bother at occasions. But within context, it is fairly easy to determine which one it is. So... not much trouble here.

There is much better things to worry about out there. ;)

Re:Error: acronym overloaded

[Anonymous Coward]

Blaming GW Bush for the Iraq war is like blaming Ronald McDonald for the poor quality of food.

Are you saying that Bush is a fictional character created by an evil corporation, bent on global domination? Or do you mean Ronald McDonald actually exists? Did he order the attacks on White Castle (which everyone agrees had to be done) and engage in a protracted war over non-existent secret sauce with Burger King? Where are the WMDs (Whoppers of Meaty Deliciousness)?

Ah, now I see it: Bush is Ronald McDonald, Rove is the Hamburglar, Cheney is Grimace, Condoleeza is Birdie, and all the other criminals are the Fry Guys.

Re:Error: acronym overloaded

[heinousjay]

Does that make Saddam the Burger King or Wendy?

Re:Error: acronym overloaded

[Shipud]

This is the submitter... and I agree with phaze that I should have least put quotes around "IP". Yes, intellectual property is a deliberately confusing term which goes contrary to everything open source stands for. My redeeming point, if any, is that I wanted to show how even the staunchest suppporters of the "IP" term are using open source tools.

Re:Error: acronym overloaded

[Anonymous Coward]

"Intellectual Property" is a perfectly valid term and Stallman's arguments against it are uniformly inane.

C'mon, you don't have to go groveling at some guy's feet just because he plays the "RMS says you can't say that!" card. Your helpful link is a bigger contribution than he's ever made to free anything.

Bioinformatics.org

[gotgenes]

Many of these open-source projects are hosted at bioinformatics.org. The site also contains great information in the FAQ such as definitions of bioinformatics, colleges and universities that offer programs, both undergraduate and graduate level, in bioinformatics, and discussion of skills required or suggested for the area of study.

hello? bioruby?

[OmniVector]

i like how the submitter listed all those off, and failed to mention bioruby. thanks

See also Linux for Biotechnology cdroms

[Anonymous Coward]

www.randomfactory.com/ distribute collections of Biotech packages prebuilt for Linux.

Re:hello? bioPascal?

[Anonymous Coward]

C'mon laugh! It's funny!

Re: Try bioknoppix too

[ianbean]

The knoppix LiveCD - now fortified with extra bioinformatics! It's a BLAST.

http://bioknoppix.hpcf.upr.edu/

R and Bioconductor

[mattstat]

Two other wonderful, and interrelated, open source packages are R, the open source statistical software project, and Biocondutor , basically a set of R functions.

Give me Liberty from acronyms or give me lawyers

[WillAffleckUW]

I think the reason that the press (and i include bloggers in this realm) use IP to refer to Intellectual Property (as if the human genome is for sale) is that the press kowtows to lawyers such as those who fill the legislative branches.

Meanwhile, in the real world, IP still stands for Internet Protocol and we're still waiting for IPv6 ...

How's the career?

[Linuxathome]

Please overlook my seemingly sarcastic title, but in all seriousness, can any of you please let me know if you're solely in the field of "bioinformatics" and if you are, how happy are you? To many of us, gratification is measured in so many different ways---albeit monetarily or academically such as by the amount of publications, tenure, or student satisfaction---so please clarify how you view your current position's gratification. My impression with this whole "bioinformatics" craze is that there is little in the way of career paths for pure _bioinformaticians_. Rather, researchers tend to learn a few bioinformatics tools here and there when they need to, but at the end of the day, they're still just biologists, chemists, clinical scientist, etc. Am I wrong?

Re:How's the career?

[Anonymous Coward]

I love my job and feel happy too. I have a degree in computer science and another in biochem. There are days i spend analysing data, running experiments in our wet lab, and days when I work on databases or small programs. The fact is, i never get bored and my name ends up on alot of our publications. There are bioinformatics people who only work with computers and develop algorithms and programs. It all depends on your background -bioinformatics is basically a combination of computer science and biological sciences.

Bioinformatics IS a field now. Alot of schools across Canada and U.S are offering undergrad and grad bioinformatics degrees. No, it is possible to be cosidered ONLY a bioinformatician and nothing else...

Re:How's the career?

[J.Y.Kelly]

I think that a more realistic view of bioinformatics is slowly emerging. A few years back everyone was saying that purely theory based bioinformatics was going to replace much of the current bench work - and this has largely failed to materialise.

What has happened is that bioinformatics has become more pervasive in the general research community, and this has presented opportunities for pure bioinformaticians. I think that there are two potential roles for bioinformaticians:

1. Development/Research - These are the people who develop new analysis techniques and write the tools which eventually become available to everyone. They are usually grant funded and work like any other research group.
   
   
2. (What I do - and am very happy with thankyou!) Practical Bioinformatics - Bioinformatians who work alongside wet bench groups to help manage and analyse their data. They use and adapt the techniques developed and make them accesible to bench science.

Unfortunately it seems that a lot of the new batch of bioinformatics graduates (mostly MScs) don't fall easily into either of these camps. They often transfer straight from a biology BSc to a bioinformatics MSc, and emerge at the end with computing skills too basic to take up a development post, and have no experience to be able to undertake a practical or advisory role. Not surprisingly they then have problems finding the job they expected to be waiting for them.

Re:How's the career?

[DrJohno]

My job is purely bioinformatics, and I love it. It's exciting research, and it pays well. Our group has been trying to hire more people, but there are not many candidates out there with the right qualifications. It's best to have a Ph.D. in one of the life sciences (mine is in Biochemistry) and a lot of practical experience with programming, data analysis, and application development.

I think bioinformatics is now an accepted research specialty, like X-ray crystallography or proteomics. You need to collaborate with people generating real data to make strong contributions, but those labs are often looking for a bioinformatics expert anyway, so there are many opportunities to collaborate.