Posts about best practice

How to save the world and make everyone happy - one powerpoint presentation at a time

July 9th, 2007

Computers and the Internet have made things great for scientists, particularly for us, since our jobs are sitting in front of them analysing data all day. Imagine being a bioinformatician without a computer, multivariate statistics is more of a pain than usual, genome sequence alignments need large pieces of paper. There would however be an upside to this analog dystopia - no more powerpoint presentations. Computers have arguably had a detrimental effect on the presentation of research, they allow the easy creation of big, text heavy slide sets. The emphasis of a talk leans towards the slides, and not the speaker.

Being asked to give a talk is viewed as a dull task: time taken away from research plus the discomfort of public speaking. If you’ve already decided beforehand that it’s going to be a dull, pointless exercise then don’t bother, not only will you be wasting your own time but also the time of everyone watching. It’s true that this is a very critical attitude to express; boring presentations are symptom of our scientific culture rather than the fault of the individual, but how many times have you been sat in conference and thought that you could have been using your time much more usefully? Now imagine, for a second time, a world where we have both computers and great presentations. The chance to give a presentation is greeted with enthusiasm, as an opportunity to teach the world about what you commit most of your time to, and to get valuable feedback on it. But we don’t need to imagine this place, we’re the generation of scientists coming through: the professors and PI of the next 30 years, we can start this revolution now.

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Bio::blogs 11 - special edition

June 1st, 2007

Short and to the point - the tips & tricks supplement to this month’s bio::blogs edition has been compiled. The link to the pdf is at the end of this post. But first I want to thank those who contributed.

Thanks to Dan Swan, Pierre Lindenbaum and Konrad Forstner, who contributed particularly large articles covering every aspect of being a bioinformatian.

Euan Adie (Stew) wrote about revision control, creating applications and blogging. Bertalan Meskó sent in a list of genetic disorder databases. Roland Krause offers tips on managing and searching data sets. Ryan Castillo wrote about his experiences in bioinformatics. Paras Chopra offers advice for undergraduates on how to use their summers. Pedro Beltrao, editor of bio::blogs, discusses the importance of keeping up to date on the literature. Also, Duncan Hull whose observations I was unable to add due to lack of time and space (read: my poor organisational skills)

And finally, special thanks go to Neil Saunders whose entry, on recreating code from bioinformatics papers, was so large I couldn’t fit it in the pdf, but you should definitely go and take a look.

Enjoy.

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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.

Use a hyperlinked document as a bioinformatics lab book

April 13th, 2007

I wrote previously about using the file system to organise your scripts and data. I use this method and it does help my organisation, but it doesn’t replace a lab book. I want a system that explains the relationships between the different set of results, and shows the outline of my work.

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