On Tuesday, November 3rd, the scientific community suffered a great loss with the passing of Warren DeLano. Most people know him as the creator of PyMOL, a popular and extremely powerful molecular visualization tool, but most – including myself, until recently – may not know all of the other unique qualities that made Warren a [...]
Archive for the ‘Open science’ Category
In memoriam: Warren DeLano
Posted in Life, Open science, Science & technology, tagged molecular graphics, pymol, warren delano on November 7, 2009 | Leave a Comment »
The evolution of scientific impact
Posted in Academia, Open science, tagged article-level metrics, filtering, impact factor, peer review, PLoS, plos one, publishing on August 6, 2009 | 16 Comments »
In science, much significance is placed on peer-reviewed publication, and for good reason. Peer review, in principle, guarantees a minimum level of confidence in the validity of the research, allowing future work to build upon it. Typically, a paper (the current accepted unit of scientific knowledge) is vetted by independent colleagues who have the expertise [...]
Can’t attend ISMB 2009? The next best thing.
Posted in Academia, Open science, Science & technology on June 26, 2009 | 1 Comment »
One of the biggest scientific conferences each year is Intelligent Systems for Molecular Biology (ISMB), put on by the International Society for Computational Biology (ISCB). I had the pleasure of attending the conference in Toronto last year, meeting many familiar names in person and collaborating with a number of them to microblog the sessions. That [...]
What type of open notebook science are you? (Plus, more logos)
Posted in Academia, Design, Open science, Science & technology, tagged creative commons, Design, lab notebooks, licenses, logos, ons, open notebook science on February 25, 2009 | 7 Comments »
A scientist’s notebook is like an artist’s sketchbook mixed with captain’s logs. It can be extremely personal and yet it is the definitive record for both day to day scientific research and for higher-level brainstorming. It can be haphazardly disorganized or meticulously organized. But until electronic media came around, we were stuck with pasting pieces [...]
I got a senior scientist blogging!
Posted in Miscellaneous, Open science, tagged blogging, nature, science blogging, science blogging challenge, scifoo on February 2, 2009 | 10 Comments »
It’s already all over the intertubes by now, but I figured I should post it myself as well just to preserve it in my own blog archives:
My advisor, Russ Altman, and I won the “Get a senior scientist blogging” challenge sponsored by Nature!
Nature Network announced it today and there’s supposedly a press release as well. [...]
Little trouble on the Big Island: thoughts on organizing a workshop and tourist notes
Posted in Academia, Miscellaneous, Open science, Science & technology, Travel, tagged conferences, hawaii, Open science, psb09, psb09-openscience on February 1, 2009 | 2 Comments »
As some of you know, I helped organize a workshop on Open Science at this year’s Pacific Symposium on Bicomputing. I was grateful to have as my co-chair a certain Cameron Neylon, who has spent far longer pondering the issues we were going to discuss and has organized some similar meetings in the past. Cameron [...]
Taking conference reporting to a new level
Posted in Open science, Science & technology, tagged conferences, friendfeed, ismb 2008, microblogging, PLoS, science communication, twitter, web 2.0 on January 31, 2009 | 3 Comments »
Who would have thought a year ago that we’d see an article in a major scientific journal about and inspired by microblogging? But indeed, PLoS Computational Biology published yesterday our report on the ISMB 2008 conference:
Saunders N, Beltrão P, Jensen L, Jurczak D, Krause R, et al. (2009) Microblogging the ISMB: A New Approach [...]
On the flip side of openness
Posted in Open science, tagged clay shirky, revolution, tools on January 12, 2009 | 3 Comments »
In Clay Shirky’s Here Comes Everybody, he says, “Revolution doesn’t happen when society adopts new technologies – it happens when society adopts new behaviors.” His point is that while new technology is necessary for revolution, it is far from sufficient. The real shift occurs once the technology permeates society enough so that new behaviors come [...]
When you don’t get what you pay for
Posted in Open science, tagged open access, publishing, rants on December 31, 2008 | 2 Comments »
This is by now an old problem but one that is not yet obsolete. You work at a place that does not have access to journals containing articles of potential interest to your research – that’s problem #1. But, maybe your institution or company has some kind of budget for paying for those articles. Huzzah! [...]
The Science Blog meme: why do we blog?
Posted in Academia, Open science, Science & technology, tagged martinmeme, science blog meme on November 17, 2008 | 2 Comments »
There’s a set of questions going around concerning the “science blog” meme, which started over at Nature Network and has since been picked up by dozens of science bloggers. It’s probably good to do a bit of reflection every now and then, and now seems like a good time because 1) it’s been just almost [...]
