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Monday, June 25, 2007

Spring 07 Post-Mortem

With the term now over, it is time to reflect on my CHEM241 Organic Chemistry I class.

Following up on the last post-mortem, I continued to use a content page and Google co-op when appropriate during workshops with students. Again, like last term, this did not cause the majority of students to change work habits but it certainly did help some.

Also, with the recent Blogger podcasting problems, I ended up just creating a few large zip files with all the mp3s and all the m4vs. That turns out to be a much simpler way to distribute the archived lectures. Students don't even need iTunes, just Quicktime. The lesson is: for archival materials with no new updates, stick to old school delivery. (Although it is still really handy to have links to individual files in different formats (Flash, m4v, pdf, mp3) on the blog or wiki)

But, of course, the big change this term was using Second Life from the start of the term, instead of Unreal Tournament. About half a dozen students out of 100 participated. I continued to make use of the blue obelisk quiz objects on Drexel Island in the form of races and giving out books and molecular model kits to the winner.

I found that Second Life vastly surpassed Unreal Tournament on several levels. Students did come for the races but they also looked around and interacted with the environment, each other and visitors. In addition to accessing Second Life off campus, some students brought their laptops to the workshops. Wireless access was fine in most cases.

Chat was fine in most cases to interact but next time I would like to use whiteboards so that we can draw molecules as well. I would also like to encourage them to do their extra credit assignments on Second Life. That should prove to be an engaging and collaborative experience for everybody.

Saturday, June 23, 2007

Chemistry in Second Life Article

Sarah Everts from Chemical and Engineering News has just published an article about chemistry activities in Second Life. Drexel Island got a mention:

My avatar was then deposited at a place in Second Life called Orientation Island. As I walked my avatar into a geodesic information dome, I happened to notice the "Fly" button. Intrigued, I wasted no time pressing it—and I shot up into the air, hitting the ceiling of the information dome like a clumsy goth-bird. It was around this time that Horace Moody, the avatar of a real-life chemist at Drexel University named Jean-Claude Bradley, came to the rescue and offered to teleport me to Drexel Island. Horace has been experimenting with Second Life as a way to teach undergraduate organic chemistry, a topic he says can definitely benefit from 3-D visualization. Several of his students have met on Drexel Island to challenge each other's organic know-how by touching an obelisk, which then flashes a sequence of quiz questions on Newman projections and Lewis dot structures.

I think that there are some terrific opportunities in Second Life for people with an interest in chemistry at all levels to explore and contribute. (see here for a recent example on molecular docking)

It is certainly a good way to meet curious and smart people.

Thursday, June 21, 2007

Nature Precedings Rocks

Following up on my initial comments, my first two posts in Nature Precedings have appeared.

Most people have been posting Powerpoint presentations so I started there with a recent presentation at the American Chemical Society about Open Notebook Science.

Open Notebook Science Using Blogs and Wikis (doi:10.1038/npre.2007.39.1)

Next, I posted an update on the CombiUgi project by basically combining two blog posts (one and two).

It took a lot longer to do this than I expected, experimenting with the format and trying to make it fairly self-contained. I ended up using Powerpoint, which I like for its modular nature and flexibility with image-rich materials. For example, it is easy to spin off as a SlideShare document (which I just noticed supports hyperlinks while embedded - nice!).

There are a few reasons I think Precedings will be one of the key breakthrough apps for Open Science.

1) Nature Publishing Group brings a serious amount of credibility to the table. That is going to make it much easier to convince people in mainstream scientific circles to contribute and read.

2) Flexibility of format: although files must currently be submitted as Powerpoint, Word or PDF file types, the organization of the information within these files is fairly open. The "article" format is not currently required. Although there is no peer review requirement, there is definitely editorial control (which I experienced as I was asked to rewrite my first abstract). They want to make sure that submissions are genuine scientific communications.

3) Referenceability: each accepted submission gets a DOI and clear citation instructions.

4) A convenient system for acknowledging collaborators as co-authors, including affiliation info.

5) Web 2.0 bells and whistles: tags, comments, RSS feeds, etc.

6) The price is right - free read/write.

7) Creative Commons License - Non-Commercial Use with Attribution.

What they do not yet accept are large data files but it looks like that is coming down the road.

Wednesday, June 20, 2007

Molecule Docking in Second Life

A while back, I posted about how we have been experimenting with representing our research work on UsefulChem in Second Life. With the help of Andrew Lang (Hiro Sheridan on SL), we put up one of the molecules that we had been trying to make as an anti-malarial compound.

Hiro has now taken this to the next level and has the molecule actually moving into the binding pocket of the targeted enzyme (enoyl reductase) upon clicking on it. There are 4 hydrogen-bonding interactions between the molecules and the atoms involved are tagged in green.

I'm grateful that Hiro took the time to show the self-docking animation because it is really hard to manually connect these two 3D puzzle pieces in Second Life (give it a try! - slurl).

In order to get to this point required a considerable amount of collaboration and I would like to thank everyone involved: Goeff Hutchison, Keith Davies, Sean Gardner, Tsu-Soo Tan and Eloise Pasteur.

Monday, June 18, 2007

First Full Drexel Second Life Workshop

Last Friday (June 15, 2007), I ran the first Second Life workshop at Drexel after the general announcement to the entire university.

About 25 people from all areas showed up and a few listed their interests on our DrexelIsland wiki. I'm using that page to enable people to sign up for future workshops as well. The next one will be on Friday June 22, 2007 at noon.

It was basically a Q & A session and this is probably a useful way to see how one moves around in Second Life and what types of activities are possible for teaching and informing.

That morning, Eloise helped me create some more free user-friendly basic tools, like a board that links to the web simply by placing the URL in the description. See the school store for the full list.

Since the workshop, most of the activity has been from our Colleges of Medicine and Nursing.

Monday, June 04, 2007

Drexel Island Wiki

I have created a wiki to help people get onto Drexel Island on Second Life:

It has basic instructions for people with no Second Life experience, a map of the island and a presentation showcasing what we have done so far.

There are also pages for individuals (like faculty) and groups (like CoAS, Libraries, DEL, iSchool, etc). This can be handy for looking up avatar names of people you know. Also you can include a slurl (Second Life URL) that will link directly to your part of the island.

If you are involved with Drexel Island, feel free to contribute a summary of what you have done or include your plans.

Saturday, June 02, 2007

City of Pods

This has been a productive week with setting up Drexel Island on Second Life. We have settled on a pod tree structure to house departments and faculty in the College of Arts and Sciences. Eloise helped with the pods and Beth and I selected most of the content. The chemistry pod has a list of recent student awards, some images of our equipment and a 3D Bunsen burner and molecule.

The faculty pods are arranged like leaves hovering above the departmental base pods. There are plenty of spaces that we'll populate as we get more faculty involved. For my pod, I have my picture, a link to my organic chemistry class wiki, my research wiki and an example of a quiz obelisk. Other pods have desks. I think that this would be a nice arrangement for virtual open houses where prospective students could visit a few professors from each department in their pods.

The library is now also set up with this pod city framework, organized by guides to literature and databases. There are teleports connecting the chemistry department pod (slurl) to the chemistry resource pod (slurl) in the library section. I think that this type of navigation is important to leverage our resources and make the island as useful as possible to students and faculty.

I ran a Second Life workshop on Friday for CoAS and assisted more faculty from English and Math to set up their avatars. Already we have had participation from Enrollment Management, Drexel E-Learning and the iSchool in the main building. It looks like Nursing is next...

Here is a presentation that I used this week with some representative screenshots:

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