Open Science Survey

An Open Access and Science Publishing survey is currently being distributed. Take a few minutes to contribute your viewpoint.

Can Open Source Science be too Open?

Pedro Beltrao brings up some good points on his post about re-thinking the scientific process. He proposes the use of black box modules as a way to make the scientific process partially more open:

Wouldn't it be great if we could find a way to make most of the scientific process public but at the same time guaranty some level of competition? What I think we could do would be to define steps in the process that we could say are independent, which can work as modules. Here I mean module in the sense of a black box with inputs and outputs that we wire together without caring too much on how the internals of the boxes work.

Although I don't agree that it is necessary to hide real-time information to be a productive scientist, I am glad to see that people are having this conversation. And the beauty of current web technologies is that each scientist can set up their own black boxes as they see fit.

We already see that with existing attempts - for example Nature Protocols discloses much more than a typical experimental section in an article, including troubleshooting tables. But we don't get to see the messy series of failed experiments that enabled those troubleshooting tables to be constructed.

Track Wikispaces Visitors

Before my CONFCHEM presentation was to start, I wanted to set up a counter on the Wikispaces page where my document was located. Wikispaces help replied that they do not support arbitrary HTML, which made it problematic to insert the javascript needed for the counter.

I was pleased to notice yesterday that, when editing a Wikispaces page in text mode, an option to embed media pops up on the right. This new feature does in fact allow introducing the script required for the counters like Sitemeter. The versatility of the Sitemeter tracker is such that I can use the same counter for my UsefulChem blog and wiki and tell where visitors landed from the Entry Page view. And the Referrals View shows how they found the site, including keywords used in Google, for example.

The code from Sitemeter that you need to put into the Embed Media text box will look something like this:



If you are using the Sitemeter code in your Blogger account, you will find it at the very end of your Template file.

The HTML for the counter is stored in a Wikispaces database and shows up like this in the Text view:

[[media type="custom" key="646"]]

Note that you can't simply copy this one line to all your Wikispaces pages. You'll need to use the Embed Media box on every page you wish to track.

All of this works with the free versions of Wikispaces and Sitemeter.

Poem about Science and the Web

I just came across Stevan Harnad's poem "Publish or Perish" on Christina's LIS Rant.

Open Source Science advocates, savor this stanza:

For showbiz being what it is today,
work's not enough, you've got to make it pay.
What ratings, sweeps and polls count for our actors,
no less than our elected benefactors,
for Science the commensurate equation
is not just publication but citation.
The more your work is accessed, read and used,
the higher then is reckoned its just dues.
Sounds crass, but there may be some consolation,
where there's still some residual motivation
to make a difference, not just make a fee:
the World Wide Web at last can make Science free.

UsefulChem in C&E News

Chemical & Engineering News is running a story on Open Source Science, with an emphasis on chemistry related projects. UsefulChem got a nice mention.

They also put a pic of me with my students James and Khalid. James is on the left next to the rotovap. Anyone familiar with our malaria research will wonder why there is a blue solution on the rotovap. The photographer wanted us to do something interesting and colorful so James made up a solution of methylene blue for effect. Trying to look serious talking about the blue solution gave everybody the giggles.

Nature Protocols

Nature Protocols is a definite step forward toward open source science. The protocols are peer-reviewed and open for comments. I really like the troubleshooting tables.

Nature Protocols is an interactive online resource for laboratory protocols for bench researchers. Protocols are presented in a 'recipe' style providing step-by-step descriptions of procedures that users can take to the lab bench and immediately apply in their own research. Protocols on the site are fully searchable and organized into logical categories to be easily accessible to researchers.

From The Sceptical Chymist

Dissertation on Translating Open Courseware

For those of you following the open courseware scene, Meng-Fen Grace Lin has just completed her thesis at the University of Houston:

Sharing Knowledge and Building Communities, a Narrative of the Formation, Development and Sustainability of OOPS

OOPS is the Opensource Opencourseware Prototype System involved in translating content from MIT's OpenCourseware.

This thesis offers an unusually candid look into the politics and personalities involved in an open source volunteer-based organization.

The cost of Open Access

Here is a nice little review from the Economist of the current state of Open Access to scientific publications. The financial burden on the author is detailed:

There are, however, a few thorns among the roses. Traditional publishers are often skeptical about the business models of their open-access rivals, and they sometimes have cause to be. The Public Library of Science (PLoS), an American organization regarded by many as the flagship of the open-access movement, lost almost $1m last year. As a result, it is about to increase its charge from $1,500 per article to as much as $2,500, depending on which of its journals an author publishes in.

Since anyone can make their research available for free by self-archiving, presumably the added value is the "blessing of peer-review". But if reviewers are not paid, where does that money go? Anyone out there know?

Thanks to Beth for the link.

LCTI/LCCC workshop

I just returned from doing a workshop at Lehigh Carbon County College (LCCC) and Lehigh Career and Technology Institute (LCTI) in the great Schnecksville, PA. There were about 50 attendees, mostly a mix of college and high school teachers.

In the morning, Beth and I gave some general talks introducing RSS and some applications of blogs, wikis, podcasting, vodcasting and games in education. The attendees were very active in asking questions and I didn't get to finish my slides. That's actually a good sign that there was some real interest and knowledge transfer.

In the afternoon the attendees split up and rotated between our workshops. Beth ran the one on blogging, Marc Bonanni did wikis and mine was on games. That was a lot of people to train in 2.5 hours and we were all exhausted afterwards.

My objective was to have them learn to navigate one of the EduFrag mazes, create at least one bitmap door with Paint then import it into a room using the UnrealEditor (free version, no weapons). There were too many people for me to assist individually in that amount of time so after I trained the more tech savvy attendees I asked them to help the others. It was not possible to do it "lecture style" because people were rotating on their time. I think most attendees who were interested in creating games at least acquired an understanding of how the EduFrag system works to create their own content for their classes without much additional help. I also asked them to create true and false doors based on what they learned in the workshop. If I collect enough, I'll pool the best of these together in one common maze to teach educational web technologies.

Beth discussed a problem in her talk that I ran into directly during my workshop: the blocking of blogs in PA high schools. I was unable to access the EduFrag blog to show the attendees how to download other maps. Luckily, for now, access to Wikispaces was unobstructed and the computers in the workshop room were pre-loaded with the educational version of Unreal Tournament with Beth's grammar and one of my chemistry mazes.

Beth ran her workshop in LCCC, which is a college, and thus was not subject to the blog blocking.

Overall the response was very positive and I look forward to following up on the implementation of some of these technologies.

Here are the workshop blog and wiki.

Here are the recordings of Beth's and my talk.