Covering the bioinformatics niche and much more

A Plea to Mankind, News Outlets and Even Scientists

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Species name notation is not rocket science, does not require one to be a brain surgeon and in some ways help communication at large. Now that science, thanks to the internet, in getting more tangled into our lives (even companies and political parties have DNA), it is important to have some standard, especially in written text in order to make information exchange easier.

I know is easy to understand that when someone is writing homo sapiens, he or she is referring to a human of the species Home sapiens, or when someone writes E.Coli, it’s clear that Escherichia coli is the target. Most newspapers (with blogs and online presence) have writing standards and manuals; maybe including a rule that species names have to be written following the Binomial Nomenclature:

From Wikipedia:

* Species names are usually typeset in italics; for example, _Homo sapiens_. Generally the binomial should be printed in a font different from that used in the 
normal text; for example, "Several more _Homo sapiens_ were discovered." 
* The genus name is always written with an initial capital letter.
* In current usage, the species name is never written with an initial capital.

For example, the entire tiger species is Panthera tigris. Simple, eh? So, on your next seminar, C. elegans might be correctly set to C. elegans


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I love Bioconductor, I really do. It’s a great framework, nice set of tools that do anything that you want (not that I would want to do phylogeny with it, topic for another post). But as anything scientific it has its drawbacks, and I can point three of them:

1 – Installing packages – we’re having problems running one package, what requires us to modify R’s compilation parameters from time to time, uninstall and reinstall things. And the most annoying thing is when you have a fresh R binary and framework, you do a basic install first and when you want another package installed if it has dependencies that are already in the system, they are downloaded and installed again.

2 – Website – Looking from the design and navigation point of view, it’s good. Looking at the functional side is bad. Sometimes you’re looking for the package page right away and Googles’s first hit is the package’s page, but for an older version of R and Bioconductor. Maybe if the URL for the current release were different than the legacy ones, would be easier for the user and for indexers to get the actual relevant item. Of course, some people might be looking for legacy stuff, and if you put links for the other version in the package’s page, everything would be easier.

3 – Documentation – That’s not Bioconductor team’s fault, but some of the packages have very poor documentation.

Apart from that, I’m quite happy to have an open source powerful toolset for my data analysis. Well done.

What’s More Important: The Publication or the Product? The Publication.

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This was asked by Neil, and I think I can answer it. Clearly, the publication is way more important than the actual product, sadly so.

The paper (or letter, comment, correspondence, whatever it is) that he points out is a complete joke, the website is a complete joke, as the most complete page on it is the CV of each member in the project. It seems that in this case there’s no peer review involved, but I bet the “authors” will dutifully used the reference in their CV.

I can say from experience that even with peer review, the actual product is irrelevant, at least in some of the cases. Sometimes software that I published were completely dissected by the reviewers and it was clear that they installed the application and tested. In other cases, usually the rejected ones, the software wasn’t even described in the review. It didn’t mean that we included a good documentation for the end-user, it didn’t mean that we worked on portability or an efficient code.

Also from experience, I can tell many stories of published software (by others) that is broken, doesn’t compile, has no documentation and fails to deliver what is supposed to be delivered.

Sometime to publish software, the authors’ names are the only thing that matters.

It’s S$@t Like This, Scientists

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$1,000 reward offered for stolen cancer research laptop:

Medical researchers in Oklahoma are offering a no-questions-asked $1,000 reward for the return of a stolen laptop that contains years of research on prostate cancer.

Sook Shin lost the 13-inch white MacBook last Sunday after thieves smashed the window of the car she shares with husband, Ralf Jankecht, and made off with the laptop. Data on the machine was not backed up.

So, you never backup your data or have an extra copy, and, at the same time, value “years” of research just one thousand dollars. Pathetic.

I’ve Failed

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I tried to write 365 posts, or one per day in 2010. I’ve failed, just published 100 of them. This will be my goal for 2011.

In the meantime, Happy New Year to everyone that stops by. See you on the other side of the calendar.


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How many times did you hear that city/government/company/university has to have an Open Source Software policy or it will end up paying Microsoft more money? At the same time, how much Microsoft profit has gone down?

Just askin’.

Brazil, the Country of the Future. Always.

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A perfect comment on Hackernews, in response to this article:

No, it’s not. Most of my extended family is in Brazil so my wife and I decided to work remote from Brazil for a couple months this fall. It’s hard to really understand how crippling the culture of bureaucracy and corruption is until you experience it.

Internet. $200/mo USD for a theoretical 1MB connection. That’s assuming the power stays on. Lots of people use the internet (mostly at cafes) but it’s only for games and social networking — nobody thinks of it as legitimate way to make money.

Crime. In many parts of Sao Paulo and Rio people don’t even stop at stoplights because the risk of getting shot and carjacked is too real.

Education. Completely broken. Cheating is so rampant most teachers don’t even try to prevent it from happening. That’s at the private schools where my cousins have attended— public schools are apparently far worse.

Entrepreneurs. Most people literally don’t even have a mental category for this. At best they make vague negative associations about you being a “capitalist.” The dream job is either working for the government or getting an engineering position at some multi-national corporation.

All of this is unfortunate because the Brazilian people are really delightful and quite creative. My wife is a designer and she says some of the best design is coming out of Brazil right now. Unfortunately corruption and regulation has completely driven out the spirit of innovation and that is unlikely to change anytime soon.

Nailed it.