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."

Re:as opposed to the closed source

[WGR]

Ny daughter is taking bioinformatics in University ( Carleton University [carleton.ca]). 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 [newsforge.com] 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

[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.

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 ...

Bioinformatics.org

[gotgenes]

Many of these open-source projects are hosted at bioinformatics.org [bioinformatics.org]. The site also contains great information in the FAQ [bioinformatics.org] 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 [bioruby.org]. thanks

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 [r-project.org], the open source statistical software project, and Biocondutor [bioconductor.org], basically a set of R functions.

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

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

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 - T

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 col