Five resources for beginning bioinformaticians
Back from a weeks holiday in Hungary just in time for my, hopefully, last ever year as a student. Last month I had a flurry of work completing a report and poster for the end of my second year, but now I'm aiming to work hard and try and get at least two papers out in my final year: in time to write up my thesis.
But now, to coincide with the beginning of the academic year, and the time that new PhD and Masters students start, I thought I would share some the resources that I found useful through out the course of my own Masters degree, then first two years of PhD.
Presenting - PresentationZen.com
I can't rave enough about how much this website changed thinking about my giving presentations. Producing results is great, but then that presenting them to your peers, and at conference deserves attention and practice. One problem I see is that that sometimes presentations can be rather boring and long-winded, perhaps not recognising that scientists are human beings and can only process finite amounts of information. Garr Reynolds goes some way to deconstruct this, giving great examples of slide types and presentation styles.Writing - Strunk & White (available online)
Like presenting, writing is another requirement for communicating work. Writing is often even more of a burden than presenting, and something that I liked doing least. After all isn't it more fun to write program code and produce results, than it is to write up the results? However I've found that the better you get at writing, the less tiresome it becomes. Things like the comma, colon, and semicolon, rather than being a set of esoteric rules, can make text smoother to write for the author, and easier to read for audience. This book simply and elegantly gives examples of good written English.Programming - O'Reilly Books
If you come from a computer science background you probably already know this, but the O'Reilly books are great for all things computer related. Whether you're learning Perl, Java, or Python, or Ruby; O'Reilly have a comprehensive catalogue with more than a few books on each subject, in particular look out for the well-written HeadFirst books. The Java book had no small role in me passing my exam during my Masters. Having written that, and to prove that I'm not getting commission, Apress and Pragmatic Bookshelf also have a set of good books, so it's usually worth comparing the reviews of each book on Amazon.Managing your research - wordpress.com/wikispaces.com
This was the most difficult lesson for me in the last two years. Managing what my research is and how I approach it. The way I started to get on top of the problem is to write everything down on a wiki, which has since changed to a blog. Writing things down regularly helps clarify my thoughts. Like speaking things out loud, it forces you to make the semi-formed ideas in your head more concrete. This then often translates into the identification of the weak points, and results that can become a foundation for further work. Once written up, you can send it to your supervisor for feedback.Wordpress allows you to run a blog, and wikispaces a wiki, both for free. For me it's personal preference and I gave both a try. If you're worried about privacy, both also allow password protection.
Statistics - Statistics: An introduction with R
Most of my research is spent quantitatively analysing transcriptomic and proteomic data so you could say that I think statistics is pretty important. However I acknowledge that this might not be the case for everyone, but if you do need to a learn a smattering of statistics and how to carry it out in R, I really recommend this book.I know it's a bit rubbish when someone writes a list of resources, and some of the things on the list aren't free, especially when students aren't the best paid people in the world. However all the things here that cost money are books, so first have a look in the library. Most universities, if they have a computing science department will have a few O'Reilly books on programming. Second if you're in a bioinformatics department, send out an email to ask if anyone has a copy, or knows of a copy. You'd be surprised, there's usually a lot more people on these lists than just the people in the offices near you. Finally if you can't get hold of the book any other way, just steal it from a shop. I'm joking of course, stealing is very wrong, is responsible for global warming, kills fairies etc., and I don't endorse it all. But seriously if you can't get hold of a book, there are usually various funds, such as your grant, that allow you to buy things you need. After all so a few books won't break the bank, especially if they're second hand from Amazon.
Certainly this list isn't comprehensive, any comments or suggestions are welcome.
Creative Commons The photo used in this post is taken from Brimley on flickr and used under a creative commons licence.