May 2007 Archive

Email is your friend. Email is your enemy.

May 29th, 2007

How often do you check your email? Once or twice a day? Obviously it’s not really necessary to check email more regularly than this. Well, speaking from experience, this is a bit of a fantasy world. Hands up everybody who I checks their email at least twenty times a day? Read more »

The head of your main funding body knows it was you who said his last paper was crap

May 22nd, 2007

From the Nature peer review blog

In short: wordprocessors embed author details in metadata, and downloads from websites can be tracked using tools such as Google analytics.

Solutions? Well partial ones at least.

Submit your review in plain text, and make sure no metadata is attached. Download data from public repositories, or from Google cache.

Call for contributions: special edition of Bio::Blogs

May 20th, 2007

Bio::Blogs logo

Bio::Blogs is a monthly round up of what’s being discussed on bioinformatics blogs. In addition, to next month’s edition at NodalPoint, there will also be a special edition here at Bioinformatics Zen. The aim, a community generated article of tips for computational biologists.

I hope that the text of the article will be generated by submissions from the bioinformatics community. That’s means you reading this now. What would be your best piece of advice you would offer someone starting out in bioinformatics? Databases, coding, organisation?

Send your suggestions, with your website if you have one, to the Bioinformatics Zen email address. Everything will be compiled and posted with the next edition of Bio::Blogs, on June 1.

Keep focused, keep an up to date list of ten specific questions

May 20th, 2007

  • Does your immediate work answer questions that begin with “Are”, “Does”, or “Is”?
  • Do you spend a shameful amount of your day checking for email, reading websites, and playing flash games?
  • Do you find it a pain to get out of bed in the morning?
  • Is reading the literature an extremely dull activity, and you rarely read a paper completely?

Ok, so these questions aren’t perfect. Nobody reads scientific papers for fun, and you’re a lucky person if you leap of bed with the expectation of a day solving the world’s scientific problems. But you get my point I’m trying to make. Being a computational scientist is hard work. No one really knows what you do, day-to-day. You have to be your own boss - is the next slice of code you write going to move you any closer to your goal?

Read more »

ggplot: a plotting alternative to R base, and lattice

May 14th, 2007

If you found the tutorial on drawing graphs using R a bit of a kerfuffle, there’s a good introduction on drawing graphs using the ggplot package. An alternative to the R base and lattice packages - so now you’ve got three to choose from.