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Friday, September 4, 2009

Best Software Licence Ever!

I was looking for some example code of a Mahalanobis distance calculator and came across what I happen to believe is the most entertaining license I have ever seen. I had to share:

The program is free to use for non-commercial academic purposes, but for course works, you must understand what is going inside to use. The program can be used, modified, or re-distributed for any purposes if you or one of your group understand codes (the one must come to court if court cases occur.) Please contact the authors if you are interested in using the program without meeting the above conditions.

The Source.

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Thursday, August 13, 2009

Ridiculous Bioinformatics

I think I've finally figured out why bioinformatics is so ridiculous. It took me a while to figure this one out, and I'm still not sure if I believe it, but let me explain to you and see what you think.

The major problem is that bioinformatics isn't a single field, rather, it's the combination of (on a good day) biology and computer science. Each field on it's own is a complete subject that can take years to master. You have to respect the biologist who can rattle off the biochemicals pathway chart and then extrapolate that to the annotations of a genome to find interesting features of a new organism. Likewise, theres some serious respect due to the programmer who can optimize code down at the assembly level to give you incredible speed while still using half the amount of memory you initially expected to use. It's pretty rare to find someone capable of both, although I know a few who can pull it off.

Of course, each field on it's own has some "fudge factors" working against you in your quest for simplicity.

Biologists don't actually know the mechanisms and chemistry of all the enzymes they deal with - they are usually putting forward their best guesses, which lead them to new discoveries. Biology can effectively be summed us as "reverse engineering the living part of the universe", and we're far from having all the details worked out.

Computer Science, on the other hand, has an astounding amount of complexity layered over every task, with a plethora of languages and system, each with their own "gotchas" (are your arrays zero based or 1 based? how does your operating system handle wild cards at the command line? what does your text editor do to gene names like "Sep9") leading to absolute confusion for the novice programmer.

In a similar manner, we can also think about probabilities of encountering these pitfalls. If you have two independent events, and each of which has a distinct probability attached, you can multiply the probabilities to determine the likelihood of both events occurring simultaneously.

So, after all that, I'd like to propose "Fejes' law of interdisciplinary research"

The likelihood of achieving flawless work in an interdisciplinary research project is the product of the likelihood of achieving flawless work in each independent area.

That is to say, that if your biology experiments (on average) are free of mistakes 85% of the time, and your programming is free of bugs 90% of the time. (eg, you get the right answers), your likely hood of getting the right answer in a bioinformatics project is:
Fp = Flawless work in Programming
Fb = Flawless work in Biology
Fbp = Flawless work in Bioinformatics

Thus, according to Fejes' law:
Fb x Fp = Fbp

and the example given:
0.90 x 0.85 = 0.765

Thus, even an outstanding programmer and bioinformatician will struggle to get an extremely high rate of flawless results.

Fortunately, there's one saving grace to all of this: The magnitude of the errors is not taken into account. If the bug in the code is tiny, and has no impact on the conclusion, then that's hardly earth shattering, or if the biology measurements have just a small margin of error, it's not going to change the interpretation.

So there you have it, bioinformticians. if i haven't just scared you off of ever publishing anything again, you now know what you need to do...

Unit tests, anyone?

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Thursday, January 8, 2009

Elisa for Obesity Proteins.

Ok, I can't resist. I occasionally get emails from random biotech companies promoting products that are invariably useless to me. This one amused me enough that I thought I should share it.

The title of the email is "ELISA Strip for Profiling 8 Obesity Proteins." While I'm sure there are people who have a good use for that, I have no clue why I'd want it. I'm not sure I'd want to go to a doctor who needs to use it to tell if their patients are overweight either.

What ever happened to looking at yourself in the mirror or standing on the bathroom scale and saying, "Oh man, I need to lose some weight!?" Now you're supposed to kit yourself out and do an Elisa to tell if you've got to diet?

Oh well, if you do find you have a use for it, Signosis will be more than happy to sell you one.

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Wednesday, October 15, 2008

Not first on the subject...

One of the challenges of writing a blog is to try and provide new content. I've always thought that there was no point in covering information that someone else has already covered - but it's hard to be the first to break every story. So, I figured I'd do something else, which is useful: provide a few links to things that someone else found first.

Today's breaking news was something I found at, on the new relase of information on Pacific Biosystems' new SMRT technology. The open access article is here. Thanks to ECO for updating with that link! (I was trying to get it all morning, to no avail.)

For humour, I wanted to discuss the IgNobel award winning paper: You Bastard: A Narrative Exploration of the Experience of Indignation within Organizations. However, another blogger on my reading list beat me to it.

I was also going to comment on lawsuit launched by the makers of Endnote against Zotero, but the same blogger also beat me to that. (Though, there's certainly a lot to be said about that case in terms of open standards, and people with antiquated business models fighting technology advances by any means possible...) Since I'm still considering using Zotero for my own research, it's probably something I'll save for another day, when there's more information available about the progress of the case.

Otherwise, there's still the new Apple MacBook, milled out of a single piece of aluminum, and the new Dell Mini 9, which I've been debating buying. Since it now comes with Ubuntu pre-installed, maybe I can forgive Dell for not refunding me for the XP licence that they made me buy at xmas last year with my current laptop.

Oh well. Now you know what I've been looking at while I procrastinate on my thesis proposal, and the mound of code changes I need to make ASAP... and now, back to work!

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Saturday, July 26, 2008

How many biologists does it take to fix a radio?

I love google analytics. You can get all sorts of information about traffic to your web page, including the google searches people use to get there. Admittedly, I really enjoy seeing when people link to my web page, but the google searches are a close second.

This morning, though, I looked through the search tearms, and discovered that someone had found my page by googling for "How many biologists does it take to fix a radio?" And that had me hooked. I've been toying with the idea all morning, and figured I had to try to blog an answer to that. (I've already touched on the subject once, with less humour, but it's worth revisiting.)

Now, bear in mind that I'm actually a biochemist and possibly a bioinformatician - and by some stretch of imagination, a microbiologist - so I enjoy poking fun at biologists, but it's all in good humour. Biology is infinitely more complicated than radios, but it makes for a fun analogy.


This is how I see it going.

  • A nobel prize winner makes a keynote speech, expounding on the subject that biologists have completely ignored the topic of radios. They deserve to be studied and are a long neglected topic that is key to understanding the universe. The Nobel prize winner further suggests his own type of broken radio that he's been tinkering with in his/her garage for several months as the model organism.

  • After the speech, several prominent biologists go to the bar, drink a lot, and then decide that the general consensus is that they should look at fixing broken radios.

  • Several opinion papers and notes appear on the subject, and a couple grad student written reviews pop up in the literature.

  • A legion of taxonomists appear, naming broken radios according to some principle that makes perfect sense to them. (eg. Monoantenna smithii, Nullamperage robertsoniaii). High school students are forced to learn the correct spellings of several prominent strains.

  • A Nature paper appears, describing the glossy casing of the Radio, the interaction of the broken radio with an electrical socket and the failed attempt to sequence the genome. Researchers around the world have been scooped by this first publication, and all subsequent attempts to publish descriptions of broken radios are not sufficiently novel to warrant publication in a big name journal.

  • Biologists begin to specialize in radio parts. Journal articles appear on components such as "purple red purple gold (PrpG), which is shown to differ dramatically from a similar appearing component, "blue green purple gold" (BgpG), and both are promptly given new names by ex-drosophila researchers: "Brothers for the Preservation of Tequila Based Drinks 12" and "Trombone."

  • Someone tries to patent a capacitor, just in case it's ever useful. Spawns three biotech companies, two of which spend $120 million dollars in less than 3 years and fold.

  • Someone does a knock out on a working radio and promptly discovers and names the component "Signal Silencing Subcomponent 1" or "Sss1". 25 more are discovered in a high-throughput screen.

  • X-ray studies are done on Sss22, resulting in a widely acclaimed paper which will later result in a Nobel prize nomination. No one has the faintest idea how Sss22 works or what it does.

  • Science fiction writers publish several fantastic novels that one day we might be able to fix radios by replacing individual parts.

  • The religious right declares biologists are playing god, and that fixing radios is beyond the capacity of humans. The moral dilemmas are too complex. Ethicists get involved. The US president tries to cut funding for biologists doing research on broken radios.

  • A researcher invents a method of doing in-situ component complementation, which allows a single element to be bypassed and replaced with a new one. All new components are attached with green flags attached to them to make studying them easier.

  • Someone else invents a method of replacing a frayed power cord, producing a working phenotype from a broken radio. The resulting media storm declares the discovery of the cure for broken radios.

  • The technique for fixing power cords begins the long process of getting FDA approval. 10 years later (and with a $1bn investment showing that technique also works on lamps and doesn't cause side effects in electric toothbrushes) the fix is allowed to go to market.

  • Marketing is conducted, telling people (with working and broken radios alike) that maybe they should try the cure, just in case they might have a frayed power cord some day too. They should talk to their doctor about if it's right for them.

  • Advertisements appear on tv showing silent smiling people holding on to power cords.

  • Long term studies after the fact show that the new part wasn't as good as it could have been. Sucking on it may cause liver damage.

  • Religious right takes recall as sign that science has failed again. Holistic fixes for frayed power cords appear, as well as organic electricity and antenna adjustment therapies, which work for some people. Products appear on the shopping channel.

  • Technology moves on, the radio becomes obsolete. Several biotech companies acquire each other in blockbuster mergers and begin working on new target components for computer sound cards.

Have a good weekend, everyone. (=

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