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Thursday, January 25, 2007

Open Science going Mainstream?

It is encouraging to see more and more articles in the mainstream press on Open Science and the changes in scientific publication. For example USA Today has "Is this the end of scholarly journal?" Here are the examples cited:
Two new scientific publications, both available only online, may signal what's ahead. The PLoS ONE (plosone.org), a journal begun by the Public Library of Science (PLoS) last month, aims to put as many new scientific articles as possible on the Internet to be read by anyone, free of charge. The Journal of Visualized Experiments, or JoVE (myjove.com), is a kind of YouTube for researchers. It operates on the theory that a short video showing how an experiment is done is better than thousands of words that attempt to describe it.


Since its launch Dec. 20, PLoS ONE has published well over 100 papers and expects to publish 15 to 20 more per week. Readers access the articles for free. PLoS ONE pays its way by charging authors $1,250 to publish an article. While that might seem a barrier to publication, Surridge says most research is financed by grants or large institutions, meaning individual scientists rarely have to pay themselves. But just in case, PLoS ONE is waiving the fee for any authors who request it.
I had not really considered PLoS ONE to be a vehicle for our work because of the hefty author charges but I might consider it now if they really are serious about waiving the fee simply by request. From my conversations with people at the NC science blogging conference, such fees are not that much of a barrier for molecular biologists who are used to paying page charges. But things are different in chemistry.

I also have reported on JoVE and I think that it is a great idea, especially since there are no fees for authors or readers. But don't discount YouTube for science - I think it is perfectly suited to communicate experimental details.

Thanks to Deepak for the link.

Wednesday, January 24, 2007

Google co-op Workshop

Update: the recording is here.

I am running a workshop on the use Google co-op to create customized search engines for teaching on Monday Jan 29, 2007 at 11:00 in 4020 MacAlister at Drexel. The session is filling quickly - please RSVP if you would like to attend.

The event will be recorded and posted on the CoAS E-Learning Podcast.

Monday, January 22, 2007

Back from Science Blogging Conference

The North Carolina Science Blogging Conference turned out to be a much needed opportunity for physically meeting a lot of the people that have only interacted online. Most notably, I finally got to meet Bill Hooker, author of Open Reading Frame and a strong supporter of the open science movement. We discussed concrete ways of collaborating and I look forward to continuing the discussion online.

Based on the discussion during my Open Source/Open Notebook Science session, there appeared to be significant interest in ways of doing science more openly and of understanding the consequences of doing so. The typical issues came up: intellectual property, recognition, archiving and getting scooped. I had planned on updating a wiki page with ideas generated from the session in a way that Dave Warlick had done at PodcasterCon last year. However, I found that there was not enough time to do that and engage in the discussion. Next time I'll try asking someone to take notes, like Dave did.

My presentation was recorded and is available here.

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Wednesday, January 17, 2007

Science Blogging Conference in 3 Days

There are still a few more seats available for the Science Blogging Conference in Chapel Hill, NC this Saturday Jan 20, 2007.

Here is a rough agenda for my breakout session on Open Notebook/Open Source Science:

This session will cover the dissemination of primary scientific information via blogs, wikis and other non-traditional vehicles.

Types of information.

* raw experimental data (Open Notebook Science)
* analyzed data
* hypotheses
* “failed” experiments
* generalized protocols
* traditional article format


* Intellectual Property
* Referencing and claims to priority
* Academic Validation
* Peer Review – mandatory and elective


* Increasing productivity in terms of universally usable knowledge units
* Making explicit the nature and quantity of work in collaborations
* Using semantically rich formats and automation at zero publication cost – is this the way to the technological singularity?

Monday, January 08, 2007

2007 Winter term starts

I had the first session of my Organic Chemistry II class this morning. I took some time over the break to take this course to what I see as the next level. Although students are still able to take in the content via archived screencast lectures in multiple formats (mp3 podcast, m4v vodcast, streaming Real or downloadable AVIs), this content is password protected due to copyright issues.

Instead of simply re-recording the lectures using unencumbered reference material, I decided to make full use of multimedia resources that would not be as intuitively available from a screencast. In the place of lectures is a detailed summary of the content to be covered with links to high quality resources. This is still a work in progress and I will add, remove and clarify as I come to appreciate what works and what doesn't during our workshops.

This ties in nicely with the assortment of sources that I pulled together in a Google co-op search for high level organic chemistry. Although I was not planning to include it, Wikipedia has turned out to be so useful that I have added it to my Google co-op collection. There is probably not enough in there to make a university level organic chemistry course entirely out of it but it does fill in some useful gaps between textbooks. If it stops being useful for any reason, Google co-op gives me the flexibility to block out certain pages or just remove it entirely. We'll see how it goes.

The main free online textbook I have been using so far is Reusch but there are several others to choose from. The Poon organic pre-lectures on iTunes also look like they could have a place when we get to the latter part of the course.

I will still be recording some brief screencasts to fill a need that is still largely open for this material: the screencast explanations of problem solutions. For example, under the practice problems section for alkynes, I have included a pic of a problem. Clicking on the image will open up my explanation of the solution in YouTube. This is an extension of something I started to do at the end of last term and I think that this is a place where screencasts shine. These will complement the links to interactive tutorials that I have also listed in the problem sections.

The first workshop is Wednesday - it should be interesting.

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