Wednesday, October 24, 2007

How this blog works

I've been blogging for about 6 months now, and it has definitely been more interesting and productive than I initially thought it would be. One thing I've found I don't like about blogging is that most blogs just throw stuff out there. I understand this is part of the blogginess of blogging, but it makes it really hard to get oriented. When you go to someone's blog for the first time, it often feels like random stuff is just being tossed onto the web. Only after following the blog for a while will you really figure out if the author has an overarching point.

So this post is just to help new folks orient themselves to my blog.

J's blog is primarily focused on developing and abiding by an Open Science system. Since Open Science is a relatively new idea, things are changing as I go along, and no one really has any standards yet, because Open Science people (and in particular Open Notebook Science People) are still trying to figure out best practices for science in the open.

That said here is my current schema:
  1. Open Ideas: I try to blog all of the experimental ideas that I'm considering pursuing. The hope is that I can find other folks interested in the same things as myself, and if I don't pursue the ideas, perhaps they'll be of use to someone else. I maintain an index of these Open Ideas on this blog.
  2. Open Projects: The Open Ideas I decide to pursue become a chapter in J's Lab Notebook. Following the basic idea of Open Notebook Science, all of raw data for the projects I pursue is publically available in real time (updated nitely). The hope is that folks who might find my work useful don't have to wait two years until I publish it. I know following someone's experiments in raw form can be difficult, but similar to reading someones computer code, I think we need some rules or general guidelines to make such tasks easier. I do not expect folks to read and follow the notebook as I go along. Rather I expect folks to stumble upon the notebook through internet searches and such. Whereupon, folks can email if they're interested in more information or clarification of anything. I maintain an index of these Open Projects on this blog.
  3. Open Publishing: After I finish projects, I typically publish them in scientific journals. In the future, I hope to publish the failed or smaller experiments to this blog or to an archive. Because the current set of open access journals doesn't yet cover the entire range of experimental and computational biology subjects, I do not publish exclusively in Open Access journals (though I think Jonathan Eisen has some interesting ideas on this topic, I think it's a little early to limit yourself to only open access journals unless you're already well known [which Eisen is] ). I maintain an index of these completed projects on this blog.
So if you're new to my blog, and you'd like to learn more. You might start by skimming the short descriptions available in the indexes: J's Open Ideas index, J's Open Projects index, J's Open Publishing index.

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