I guess I’ve been around bioinformatics for the best part of 15 years. In that time, I’ve seen almost no improvement in the way biologists handle and use data. If anything I’ve seen a decline, perhaps because the data have become larger and more complex with no improvement in the skills base.
It strikes me when I read questions at Biostars that the problem faced by many students and researchers is deeper than “not knowing what to do.” It’s having no idea how to figure out what they need to know in order to do what they want to do. In essence, this is about how to get people into a problem-solving mindset so as they’re aware, for example that:
- it’s extremely unlikely that you are the first person to encounter this problem
- it’s likely that the solution is documented somewhere
- effective search will lead you to a solution even if you don’t fully understand it at first
- the tool(s) that you know are not necessarily the right ones for the job (and Excel is never the right tool for the job)
- implementing the solution may require that you (shudder) learn new skills
- time spent on those skills now is almost certainly time saved later because…
- …with a very little self-education in programming, tasks that took hours or days can be automated and take seconds or minutes
It’s good (and bad) to know that these issues are not confined to Australian researchers: here is It’s time to reboot bioinformatics education by Todd Harris. It is excellent and you should go and read it as soon as possible.
…is the new community blog from PLoS ONE. They write:
This blog is for authors who have published with us and for users who haven’t and it contains something for everyone.
You’ll need a WordPress.com account to contribute; it’s a quick, unobtrusive sign-up and why not start a blog there too, if you haven’t already done so.
and spread the word, outside of just twitter and friendfeed ;-)
*Cough*. Quiet, isn’t it? I’ll tell you what’s been happening soon.
In the meantime, BioSysBio 2009 is underway. Lots of interesting coverage:
So, you’d like to submit a URL to Open Laboratory 2008, you want to know if it’s already in Bora’s list and your machine runs Ruby? I thought so!
Save the following code as “bora.rb”, make it executable and run:
You really want to read the rest?
Couple of new blogs in my Google Reader that you may want to investigate:
- Bioinformatics on Rails
Few posts, updated infrequently – going to follow for a while and see where it goes.
- Bench Press
“We’re four science and tech geeks who decided that the world needs yet another science blog.” A good recent post on electronic lab notebooks.
The new best of FriendFeed feature is proving to be a hit. It also provides material for people who are too busy to write real blog posts. Here’s my top 10, according to FriendFeed, from the past 7 days:
ResolveRef, a RESTful way to resolve PubMed queries by journal, year, volume and page is Andrew’s port of OpenRef to App Engine. Simple, but very effective and a nice illustration of how to get to grips with the App Engine environment.
Keep those “App Engine apps for researchers” rolling in, folks.
This blog seems to become more about social networks/open science and less about bioinformatics every week. Perhaps that’s no bad thing. Here’s a few highlights from the activity stream this week.