Drexel CoAS E-Learning

Open Medicine Editorial

2008-02-18T08:47:00.001-05:00

The Journal "Open Medicine" has published a very thoughtful editorial on "Open science, open access and open source software at Open Medicine" by Sally Murray, Stephen Choi, John Hoey, Claire Kendall, James Maskalyk and Anita Palepu.

Not only are they writing about it but they want to get their hands dirty as well:

Open Medicine is an open access journal because we believe that free and timely access to research results allows scientific knowledge to be used by all those who need it, not just those who can afford expensive journal subscriptions or user fees for individual articles. But is access to the final polished version of research enough? Could we do more to encourage the collaborative reuse and reanalysis of existing data, or the verification of analyses? Could we move from open access to open science?

Virtual Poster Session on ACS Island

2008-02-13T16:04:00.001-05:00

The American Chemical Society will be offering a virtual poster session in Second Life from selected posters at the Sci-Mix session taking place April 6, 2008 at the next national meeting in New Orleans.

I'm helping out with that effort and I'm pleased to say that we have our first submission from Jodye Selco, Mary Bruno and Sue Chan: "Safe and economical chemistry inquiry for the K-12 classroom".

ACS island has the same shape as its logo of a phoenix, thanks to the skilled hand of Eloise Pasteur who carved out the Drexel island's dragon shape. The posters will be placed on the right wing, next to a "chemistry museum" area, also under development.

ACS island is currently open to everyone - feel free to stop by and explore as we develop the area (Andrew Lang, Hiro Sheridan in SL is also on the project). Gus Rosania has been a very active "resident scientist" - you can see his activities on drug transport near the middle.

Kate Sellar (Finola Graves in SL), who spearheaded this initiative at ACS, has just started a blog where she will chronicle activities on the island.

The easiest way to find the island is to type ACS in the Map search box in Second Life.

Chemical Heritage Foundation Podcast

2008-02-04T12:13:00.000-05:00

Drexel Island and my teaching of chemistry on Second Life is covered in a recent Chemical Heritage Foundation podcast "Distillations". Cyrus Farivar interviews me and my student Charles Sineri.

Campus Technology Articles about Teaching in Virtual Worlds

2008-01-09T06:16:00.000-05:00

Linda Briggs wrote a nice article in Campus Technology about using Second Life to teach and highlighted the chemistry application that I used last term:

Creating Life-Size Molecules in Second Life

A Conversation with Drexel University's Jean-Claude Bradley

1/9/2008

By Linda L Briggs

CT: Conversely, what are some things that work really well in Second Life?

JCB: One thing new that I've done this term is have students do a project in Second Life.

CT: Yes, you recently wrote in your blog that one of your students created a life-size model of a molecule as part of that. That sounded really cool.

JCB: Right. To be able to stand next to a molecule that is as tall as you are, and to have your teacher be able to walk around it with you and comment,... that's pretty useful.

[....]

CT: Do you have advice for instructors who want to integrate Second Life into their course?

JCB: You should have a really good reason to do it. The best advice is to find another teacher who is actually using it, and try to experience what the student is experiencing. You'll get some ideas and advice from that. I was just talking to another teacher an hour ago who might be doing some things in Second Life. She's also an organic chemistry teacher. I told her, just send your students to Drexel Island; have them interact with my students, click around on the quizzes, and if you think it might make sense, you can spawn off from that.

A lot of people have bad experiences in Second Life because they don't have a good reason for going there. It's like having people go to the Internet without a Web address. You want to be guided. That's the best possible scenario.

It's just another tool. I wouldn't teach exclusively on Second Life. We have WebCT Blackboard; I have my wiki; I have my blogs; and those things all have their strengths. You've got to leverage them all.

Drexel Island also got a mention in Matt Villano's article in Campus Technology: 13 Tips for Virtual World Teaching

Fall 2007 Post Mortem - the Closed Book Problem

2007-12-27T13:03:00.001-05:00

Another quarter done at Drexel and it is time for a brief post-mortem analysis of my teaching this term.

I taught CHEM 241, introductory organic chemistry.

In order to standardize testing conditions with other instructors of the course, my tests were run under closed book rules. Many years ago I opted for an open book policy after comparing performance under open and closed conditions. There was no significant difference, which I would expect for subject matter that has more to do with understanding rather than memorization. Open book tests are much easier to monitor and I was able to run a walk-in testing policy lasting several days using only video surveillance.

Moving to closed book conditions required a proctor. This would not be a big problem for a small class. But my class had 175 students and our computer rooms only have about 25 machines and are usually in demand. Based on previous student behavior with a walk-in policy in effect, not more than half the class typically showed up before the last day. So I booked a room with more time (at least 6 hours) on the last day and shorter sessions on previous days.

This worked fine for the 90 minute tests but we ran into a crunch on the last day of the final exam with a 3 hour duration. Luckily, I had an extremely competent and flexible proctor who handled the situation by finding additional rooms and extending the time. In fact the proctor was there for a total of 13 hours on the last day.

In terms of security, I made use of the "proctor password" tool in Blackboard/WebCT and changed it at least once per day. Although there is some IP filtering possible with BB/WebCT, the restriction is not specific enough to isolate specific classrooms.

Next term, we can solve a lot of these problems by allocating specific students to designated classrooms and using a printed class list where the students will show ID to the proctor and check off their name immediately before taking the test.

Unfortunately, this removes the convenience of multi-day walk-in testing, which many students appreciated.

There are probably many instructors out there with large online classes and I would like to get some feedback on how they handle testing under closed book conditions.

From what I gather most online programs rely on the honor system.

The other major news this term is that one of my students executed his extra credit assignment building molecules in Second Life.

Virtual Biomed Workshop on Second Life

2007-12-18T13:24:00.000-05:00

On Friday November 30, 2007 I was part of a panel for a Virtual Biomed Workshop at Drexel. I gave a little tour of Drexel Island. My account froze for a few minutes. Luckily Sean Brown took the reins and showcased the Biomed Floor that he built in the main building. The projection screen was huge and the video recorder did a great job of capturing the tour.

Watch my presentation here.

Chemistry Assignments in Second Life

2007-12-17T11:20:00.000-05:00

This term, the students in my organic chemistry class were presented with an opportunity to do an extra credit assignment using Second Life to represent concepts they learned in the course.

When I was an undergraduate, finding molecules in articles was mainly done using the Chemical Abstracts books. A convenient way to find a specific molecule would be to look up the molecular formula and find the corresponding IUPAC name. Theoretically, one could figure out the IUPAC name from scratch but this can be very tricky for complex molecules and prone to error. With the correct name, I could look for analogues of a molecule of interest in alphabetical catalogues by understanding how the chemical name works.

But when computer databases started to be used in chemistry, using the name of a compound became far less important. Searching for molecules now comes down to drawing them on computer screens and using computer generated text representations like SMILES and InChI. Knowing how to use these tools on free software and services is key to being fluent and flexible on the chemical web. And I think that is the most important benefit that students get from doing these assignments.

As an example, take a look at the project created by my student Charles Sineri (Chaz Balbozar in SL). In the image below he is standing between two molecules of camphor that are mirror images of each other, demonstrating the concept of chirality that we covered in class. This is a particularly difficult example to demonstrate on paper.

Using molecular models that are bigger than my body is not something that I have ever done in real life and it provides an interesting perspective to what the molecule really looks like. Another advantage is that you can fly the molecule like an airplane by wearing it. Here is Chaz flying up to a buckyball on his camphor ship:

In order to get his project done Chaz had to learn about and use SMILES, InChIs, ChemSpider and ChemSketch. These are free tools that he will use again in future chemistry applications.

The main challenge in getting this implemented in Second Life is providing tools that are easy to use. We used Andy Lang's (Hiro Sheridan in SL) molecule rezzer to do this because it now has the capability of understanding InChIs and SMILES. Hiro was kind enough to make some further modifications to make it even easier to use. It was gratifying to see that it understood chiral SMILES code.

Visit Chaz's project on Second Nature island - see SLURL.

Nature's Role in e-Science Talks

2007-12-09T17:50:00.000-05:00

Berci Mesko will be moderating a session on Nature's Role in e-Science on SciFoo Lives On (in Second Life) tomorrow Monday December 10, 2007 at 12:00 ET/17:00 GMT.

There will be 4 talks:

Matt Brown: Nature Network
Ian Mulvany: Connotea
Hillary Spencer: Nature Precedings
Helen King: Dissect Medicine

Run for Malaria in Philly

2007-12-06T05:19:00.000-05:00

For anyone in the Philadelphia area who cares about malaria:

Drexel University Crossings Stair Run

Beta Beta Beta and the Office of Residential Living will sponsor a stair run Saturday, December 8, 2007, from 9 a.m. to noon in University Crossings (101 N. 32nd Street).

Registration is $3 per person, $5 if two people sign up together. Sign-up in the lobby of University Crossings.

All the proceeds generated from the event will purchase mosquito netting to be placed over beds for an African village. Each net costs $10, and can potentially save three people, as children in the villages typically share beds.

More information about this initiative is available at http://malarianomore.org/.

Cameron's Drexel Talk on ONS

2007-11-04T16:26:00.000-05:00

Cameron Neylon gave a very thoughtful talk at Drexel on Friday about using blogs to capture the science going on in his group then deciding to open his laboratory notebooks to the world.

He was refreshingly honest about his progress and motivations. For example, at one point he noted that a gel image was missing on one of the posts. Instead of glossing over it, he pointed out how this just makes transparent how difficult it is to properly maintain a laboratory notebook. As long as you don't have to show it to anyone, it is tempting to claim that your lab notebook is better maintained than it really is.

And this is a positive thing - science is messy and even through the human failings of ideal record keeping, science gets done. Now if we finally admit to that and are willing to work transparently, we have an opportunity and an incentive to set a higher standard.

That is one of the tangible benefits of Open Notebook Science.

Cameron's talk was recorded and is available here.

Cameron Neylon ONS Talk at Drexel

2007-10-05T08:43:00.000-04:00

I am very pleased to announce a talk by Cameron Neylon at Drexel next month:

A Beginner’s Guide to Open Science
(not for beginners but by beginners)

2:00 Friday November 2, 2007
Disque 109, Drexel University
32nd and Chestnut streets, Philadelphia, PA

Cameron Neylon, STFC Rutherford Appleton Laboratory and School of Chemistry, University of Southampton

The modern biochemistry or molecular biology laboratory generates large quantities of data that are generally stored across multiple computers attached to multiple instruments. Much of this data is never published and the majority languishes on old computers and is ultimately lost. At a local level this is a frustration for investigators who will often struggle to obtain specific pieces of data produced in their own laboratory. On a larger scale this is becoming a much more serious issue with the obligation of researchers to funding bodies to both preserve research data and make it available to other users increasingly becoming a formal a condition of publicly funded grants. Systems are required that can capture and preserve data along with sufficient information and metadata to make it possible for others to use this data.

In parallel with this a movement is growing within the research community that advocates greater openness in providing both the raw data from published studies as well as making available the large quantities of data that are never published. The logical extreme of this approach is Open Notebook Science [1], pioneered at Drexel University [2], where the researcher’s laboratory notebook is made available on the internet as it is recorded. Achieving the aims of Open Notebook Science also requires systems which can capture data and provide it in a useful format. In addition these systems must make the data visible to relevant online searches.

We are developing and using an electronic laboratory notebook based on a Blog format to capture experimental data in a biochemistry laboratory [3,4]. Within the system each sample is recorded in a single post. Analysis and manipulations of the sample are recorded in separate posts with links back to the input sample and forward to any products. All the information is made immediately available on the Web as it is recorded. The Blog engine has been specially built in house and has a number of features designed to enable and encourage the effective capture of data and metadata in the environment of a biochemistry laboratory. I will describe the Blog system and our evolving approach to capturing metadata as well as the process of integrating this with other web services to provide an open environment for recording work in the laboratory, laboratory materials, and validated procedures. The challenges and problems encountered in reconciling the twin aims of capturing data and making it available and readable will also be discussed along with the similarities and differences emerging between different approaches to Open Notebook Science [2,5,6].

[1] http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html
[2] http://usefulchem.wikispaces.com/
[3] http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/10
[4] http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/13
[5] http://www.jeremiahfaith.com/open_notebook_science/
[6] http://www.michaelbarton.me.uk/

Periodic Table in Second Life

2007-10-02T10:31:00.000-04:00

Further adding to the set of chemistry tools in Second Life, Hiro Sheridan has created a 3D periodic table with rotating atoms. Although not directly proportional, the relative sizes of the spheres are in the correct order. Clicking on them provides basic information about the corresponding element.

The 3D periodic table is available on the Chemistry Corner on Drexel Island (SLURL).

The Value of Dark Data

2007-10-02T04:14:00.001-04:00

Tom Goetz wrote a thoughtful article "It's Time to Free the Dark Data of Failed Scientific Experiments" in Wired this week.

So what happens to all the research that doesn't yield a dramatic outcome —or, worse, the opposite of what researchers had hoped? It ends up stuffed in some lab drawer. The result is a vast body of squandered knowledge that represents a waste of resources and a drag on scientific progress. This information — call it dark data — must be set free.

...

There are some islands of innovation. Since 2002, the Journal of Negative Results in Biomedicine has offered a peer-reviewed home to results that go negative or against the grain. Earlier this year, the journal Nature started Nature Precedings, a Web-based forum for prepublication research and unpublished manuscripts in biomedicine, chemistry, and the earth sciences. At Drexel University, chemist Jean-Claude Bradley practices "open notebook" science — chronicling his lab's work and sharing data via blog and wiki. And PLoS is planning an open repository for research and data that is other wise abandoned.

The main focus of the article is on results that don't make it to an article because they are not interesting enough. "Failed Experiments" in this sense are those that do not uncover a hoped for correlation or, in synthetic organic chemistry, those where the desired product is not obtained.

However, there are many more shades of Dark Data. One large category often downplayed consists of experiments aborted because of mistakes and accidents. For example in EXP096, the product was spilled and lost. But all of the spectra and data collected up to that point are still perfectly usable for someone wanting to repeat this or a similar experiment. That is the reason researchers don't tear out pages from their lab notebooks when accidents happen. The same logic applies to Open Notebook Science, where the audience extends to the whole world.

Thanks to Attila for posting an early report.

Open Notebook Science Case Studies SFLO Session

2007-09-23T16:45:00.000-04:00

Just a reminder that the ONS case studies session on SciFoo Lives On is tomorrow Sept 24, 2007 at 9:00 PT/12:00 ET/16:00 GMT.

The idea here is to get our hands dirty and look at the guts of our operations. What is working/what is not -what technologies are we using and where you can get them.

Cameron Neylon and I will be presenting but we hope there will be lots of discussion.

ChemBioFoo Area First Poster

2007-09-08T19:30:00.000-04:00

Ding dong - one of my bells emailed me today.

Someone was at the gate of the BioChemFoo area on Nature Island in Second Life and wanted assistance with setting up a poster.

When I logged on I found Lali Ewry (a researcher) and Bronwen Pizzicato (from Nature Precedings) still waiting there. Since there were no posters yet in the ChemBioFoo area I took them over to the adjacent SciFoo Lives On section to show them examples of what posters can look like in Second Life.

Lali had some slides available so I gave her one of Hiro's boards and showed her how to upload, re-size and move the poster. (By the way Hiro's boards have the nice feature that, as a presenter, you can go backwards in your presentation and the boards reset to the starting slides after a few minutes of inactivity)

We took her board to the ChemBioFoo area and Lali positioned it at poster #1. She also put a bell so others could summon her to discuss her work on "Transcription of Inflammatory Genes in Crohn's Disease". There are wonderful images in that presentation about the mechanics of the disease and Lali is still adding more. She had some animations that have to be converted to still images before posting.

Lali's real name is Laura Ferrero-Miliani and she is at Herlev Hospital, Medical-Gastroenterology Lab 54O3 in Denmark.

This is a perfect example of what I had in mind for ChemBioFoo. In keeping with the SciFoo un-conference, the SciFoo Lives On area has some great posters to promote and discuss Open Science and new Science Communication Technologies. However, I think there needs to be a place to host domain-specific scientific discussion as perpetual poster sessions in Second Life.

This is actually very much in keeping with the format of the Nature journal itself. The articles are typically high level and are collected from various scientific fields. I am starting with Chemistry and Biology because I feel that these areas have a strong potential for improving human lives directly (in terms of affecting disease processes for example). Also these areas are most closely related to my domain specific research of organic synthesis and drug design. (And we only have 36 booths in this area for now). Of course I would be happy to assist anyone in creating a poster area with another scientific focus.

I often tell people that they should only enter Second Life if they have a good reason for doing so. By putting posters that are similar in format and content to those that the typical researcher is likely to find at the physical conferences that they attend is probably a pretty good way to attract traditional scientists to media platforms like Second Life. If they see a poster that is interesting they can ring the bell, talk with the presenter then decide how that experience compares with a physical meeting.

So I am asking for anyone interested in contributing to let me know (or Lali - she is trained now to help the next presenters after all).

My presentation is coming up - I have a few more slides to put together. Tony Williams from ChemSpider also sent me a presentation that I'll put up shortly.

PodCamp Philly at Drexel

2007-09-02T12:45:00.000-04:00

For anyone in the Philadelphia area, PodCamp Philly starts this weekend Sept 7-9, 2007. Topics include anything related to podcasting and social software.

I'll be doing a session on Drexel Island and Second Life.

The event is free but you must register.

Ring for SciFoo Service

2007-09-02T09:23:00.000-04:00

If you wander around the SciFoo Lives On area, you will notice that some of the poster booths have bells.

If the text above them is green, it indicates that the presenter is somewhere in Second Life. The visitor can then just click on the bell to summon the presenter with a quick message.

If the text is red, the presenter is not in world. However, a message can still be sent and it will show up the next time they log in.

Now this can be problematic for users who created a Second Life account exclusively for the purpose of presenting or attending a SciFoo Lives On session since they are unlikely to login again and retrieve IM messages. There is a trick around that: in SL hit control-P and turn on the setting to forward IM to email.

This effectively transforms the SciFoo Lives On area into a perpetual session with the cumulative content of all prior sessions, which now include "Tools for Open Science" and "Medicine and Web 2.0". We are now getting ready for the "Definitions in Open Science" session on Tuesday Sept 4, 2007 at 16:00 GMT and there are still slots available to present.

The bells can be purchased for 150L (about 60 cents) on PixelTrix Island (SLURL) - thanks to Ron Comer for help in locating these!

The location and list of all upcoming SciFoo Lives On sessions can be found on the SFLO wiki.

SciFoo Lives On Upgrade and Wiki

2007-08-30T15:16:00.000-04:00

There have been a few additions to the SciFoo Lives On area on Nature Island in Second Life.

The area has been divided into 36 numbered plots and most posters from the first two sessions have been moved to fill the first 10 spots. Posters for future sessions will be added sequentially as they are created. (Thanks to Eloise and Beth for help with this!)

This makes the area much more appealing and permits regular poster sessions where people can meet at any time to present and discuss. I have been a huge fan of the effectiveness of poster sessions in Second Life after my first experience. We will still do talks at the scheduled sessions but afterwards groups can break out to posters from any previous SciFoo Lives On session.

I have also created a wiki to keep track of dates and topics of past and future sessions. Presenters are welcome to record their names (Second Life and Real Life), affiliations and presentation titles next to their poster number.

First SciFoo Lives On Session on Tools for Open Science

2007-08-20T15:54:00.000-04:00

We had our first SciFoo Lives On session today on Nature Island (Second Nature) in Second Life. We had about a dozen people participate.

The topic was "Tools for Open Science". I wanted to explore more fully the actual technology that people are starting to use towards doing more open science. I started off by showing screenshots of UsefulChem wiki and blogs from my poster. The other posters there (and still there) included MyExperiment, Nature Precedings, Bill Hooker's Thoughts, Knowble and Connotea.

Overall it went very well I think. Initially I was disappointed that most people did not have voice working but it turned out to be a good thing because I was able to capture the entire chat transcript (see below).

Based on Berci's suggestion, we'll do "Medicine and Web 2.0" next week on Monday Aug 27, 2007 ET noon. So bring your posters and join us!

Here is the transcript:
[9:00] You: I think many of you were at scifoo
[9:00] You: one of the problems is ther was not enough time to cover everything
[9:01] You: this is a continuation on that
[9:01] You: on Tools for Open Science
[9:01] You: this really should be a discussion
[9:01] You: so we'll just take a few minutes each to explain
[9:01] You: I'll start on the Open Notebook Science poster
[9:02] You: then we'll go to the right and around the corner
[9:02] You: please stop me if you have a comment or question
[9:02] You: I was hoping to do this by voice but not enough people have it
[9:03] Max Chatnoir: good to have the chat record.
[9:03] Berci Dryke: sure
[9:03] You: what I would like for my 5 mins is to show screenshots of our Open Notebook Science
[9:03] You: so we have one component that is a blog
[9:04] You: the idea is to record everything from ongoing research in my lab
[9:04] You: I'm skipping over stuff because I don't want to take 1 hour :)
[9:04] You: we started tracking molecules in my lab using a blog like this
[9:05] You: but now we are moving this to Chemspider
[9:05] Stew Alito: Um.... can Phoenix move to the side a bit? It's the wings... can't see!
[9:05] Berci Dryke: lol
[9:05] You: we started tracking experimnents using a blog
[9:05] You: but there were too many edits
[9:05] Troy McLuhan: To adjust your camera position, hold down ALT and then click-drag with your mouse
[9:05] You: so we moved to a wiki
[9:06] You: the wiki has all the lab notebook pages and organization pages
[9:06] You: the wiki tracks nicely the contribution of everybody over time
[9:06] You: and we can prove who-knew-what-when
[9:06] You: with each version
[9:07] You: we use Wikispaces because it is free and offers thridparty time stamps
[9:07] Max Chatnoir: These are suggestions for the synthesis?
[9:07] You: which one max?
[9:07] You: there were comments from others yes
[9:08] You: but it turns out our collaborators prefer to use our mailing list to share
[9:08] You: so the wiki is mainly my students in the lab
[9:08] You: I will leave the rest here - tha's it for me
[9:08] You: any comments/questions?
[9:08] Berci Dryke: What about competition?
[9:09] You: you mean fear of being scooped berci?
[9:09] Berci Dryke: yes
[9:09] You: I think that this is safer than many other things scientists do
[9:09] You: like proposals
[9:09] You: because all this is indexed quickly in google
[9:10] You: it would be very embarrasing to get caught stealing text
[9:10] Max Chatnoir: So this is a sort of ongoing multicontributor proposal presentation?
[9:10] Max Chatnoir: But very publicly documented!
[9:10] Stew Alito: Have you ever been scooped, to your knowledge?
[9:10] You: max this simply our standard lab notebook on a public wiki
[9:10] You: no I don't know of anyone having "stolen" anything
[9:11] Max Chatnoir: So the contributors are mostly your own students?
[9:11] You: max - yes the wiki is mainly my students
[9:11] Berci Dryke: your wiki can be edited by anyone (or just those who have access to it?)
[9:11] You: on the mailing list we have great collaborators like
[9:11] Max Chatnoir: Do you get external contributions as well?
[9:11] You: Rajarshi Guha that does docking for us
[9:11] You: max - you have to register
[9:12] Troy McLuhan: Which mailing list service/software do you use?
[9:12] You: simply because otherwise my students forget to login!
[9:12] Max Chatnoir: But the registration is open?
[9:12] You: we use Google groups
[9:12] suhky Rezillo: now I am here
[9:12] You: we are ALL google - blog, wiki, lists
[9:12] Berci Dryke: why is better than creating an own wiki (I mean used in an internal network)
[9:12] Max Chatnoir: Like WebCT?
[9:12] You: Google has been a huge gift to open science
[9:12] You: what is like webct maX?
[9:13] Max Chatnoir: Internal network.
[9:13] Stew Alito: Do you share references with Zotero or Connotea etc.?
[9:13] Max Chatnoir: I was adding to Berci's question.
[9:13] You: I have used Connotea with my class students
[9:13] You: but not systematically
[9:13] Rakerman Yellowjacket: I wonder about the amount of information - do you think there's any difference between someone getting a protocol from your notebook, or a "refined" version from myExperiment or Nature Protocols?
[9:14] You: good point raker
[9:14] Corwin Carillon is Offline
[9:14] You: Nature protocols is great for established protocols
[9:14] You: but it takes time to get the info in there
[9:14] You: UsefulChem is real time so by necessity messy
[9:14] You: BUT - the question is can scientist use the info
[9:15] You: and based on the types of searches we observe - I say yes
[9:15] You: we can always collect and publish these as full papers later
[9:15] Rakerman Yellowjacket: I am wondering - if everyone published their lab notebooks online, what would google search results look like - how would be be able to find the most relevant results? Would online notebooks s scale?
[9:15] You: well we have to add metadata
[9:15] Adastar Galsworthy: how do people feel about citing online resources?
[9:15] Max Chatnoir: So this is one way to get "tried this, didn't work" into a publicly accessib le space.
[9:16] You: for example in chemistry we tag with inchis
[9:16] Adastar Galsworthy: particularly informal resources
[9:16] You: each field will have to add metadata
[9:16] You: do we have our myexperiment guy here?
[9:17] You: ok, someone want to say a few words about Precedings?
[9:17] You: we can move to that poster
[9:17] Max Chatnoir: Can people not in your class register for the wiki?
[9:17] You: max - yes they can
[9:18] You: suhky?
[9:18] suhky Rezillo: yes?
[9:18] Max Chatnoir: So, Berci, that would be why it is in a public forum rather than an internet network like WebCT or Blackboard.
[9:18] You: would you like to say a few words about precedings
[9:18] Berci Dryke: understood, Max :)
[9:19] Joanna Wombat: Hilary's just coming now
[9:19] You: I've use precedings myself
[9:19] Joanna Wombat: I think she can say something about precedings
[9:19] suhky Rezillo: one moment Hilary will talk about Nature Precedings as she co-developed the site...
[9:19] You: and I think it is a fantastic addition to tools for open science
[9:19] You: oh good
[9:19] Max Chatnoir: Indeed!
[9:19] Hilary Serevi: hi everyone
[9:19] Troy McLuhan: Would it make sense to publish the transcript of this discussion on Nature Preceedings?
[9:19] Joanna Wombat: Hi Hilary
[9:19] You: hilary you have the floor
[9:19] suhky Rezillo: Everyone, let me well you to Hilary Serevi
[9:20] Berci Dryke: nice to meet you!
[9:20] Hilary Serevi: thanks--I haven't spent too much time in second life
[9:20] Hilary Serevi: but hopefully I can answer some questions about Precedings
[9:21] You: hilary what was your role in precedings
[9:21] You have offered friendship to Krystine Qinan
[9:21] Hilary Serevi: I'm the Product Development Manager
[9:21] Krystine Qinan is Online
[9:21] You: did you make this poster?
[9:22] suhky Rezillo: Yes she did, with Timo Hannay
[9:22] Hilary Serevi: yes
[9:22] You: anyone else here use precedigns?
[9:22] Troy McLuhan: Can you summarize what it is?
[9:22] You: basically you can publish in any format
[9:22] You: the submissions are editorially reviewed
[9:22] You: but not peer reviewed
[9:23] Hilary Serevi: that's correct, Horace
[9:23] You: but it does not have to be an article format
[9:23] You: I have published blog posts there
[9:23] You: well the poster will stay there after this session
[9:23] Berci Dryke: can I have a personal question about it?
[9:23] yucca Gemini is Online
[9:23] You: yes berci
[9:23] Berci Dryke: I'm a medical student and have a presentation about web 2.0 and medicine (Medicine 2.0). Why would it be good for me to publish it on Precedings? And could I publish it?
[9:24] You: they do have a lot of presentations
[9:24] You: I published my ppt as well that we were loking at
[9:24] You: let's move on
[9:24] You: Bill could not make it
[9:24] You: so I'll say a few things
[9:25] Stew Alito is Offline
[9:25] You: Bill Hooker has been reporting on Open Science for a long time
[9:25] Hilary Serevi: since we've moved on, perhaps I can answer your question later, berci
[9:25] You: and he asked me to ask you about what you thought about the def o open science
[9:25] Berci Dryke: ok, Hilary
[9:25] You: sorry hilary
[9:26] You: please answer
[9:26] You: does anyone have thoughts about the definitions?
[9:27] You: the term open science has been used so much we don't know what it means somtimes
[9:27] Samara Barzane is Online
[9:27] Rakerman Yellowjacket: it's more like "publically shared pre-publication science"
[9:28] Adastar Galsworthy: i have a thought about the reasons for the need for open science
[9:28] Troy McLuhan: PLoS is open though, and is for publication
[9:28] Adastar Galsworthy: I think it was in the middle of the 18th century that the last man to have read everythin lived,
[9:28] Emile Pintens: Rakerman, I do not know if that it has to be pre-published. I think the ultimate goal would be for pre-published, and published works to be open.
[9:29] You: so you don't consider precedings to be "published"
[9:29] You: according to patent law that is certainly a publication
[9:29] Hilary Serevi: so precedings doesn't "publish" documents--they'i think that the term "open access" tends to be applied to peer-reviewed publication
[9:29] You: it is not peer-reviewed
[9:29] Troy McLuhan: Sorry, that's what I mean
[9:30] Hilary Serevi: i think the definition of a "publication" is changing with the development of the internet
[9:30] You: so when people say pre-publication they mean pre-peer-reviewed
[9:30] Emile Pintens: Isn't Precedings screened? It isn't peer-reviewed, but it is reviewed
[9:30] Rakerman Yellowjacket: pre-peer-reviewed is maybe a better term
[9:30] Troy McLuhan: I guess what I really mean is, does the tenure review committee consider it "published"?
[9:30] You: definition confusion was big at scifoo i think
[9:30] Hilary Serevi: It's screened, but the screening process is mainly to prevent the posting of obviously commercial documents (e.g. spam)
[9:31] Hilary Serevi: or pseudoscience
[9:31] Hilary Serevi: although pseudoscience is also another term that is difficult to devine
[9:31] Hilary Serevi: define--sorry
[9:31] You: but without defining "peers", it is hard to define peer review
[9:31] Emile Pintens: Ok thank you for the clarification. Is there a time lag between an item being submitted and the time it makes it on the site?
[9:31] Adastar Galsworthy: in peer reviewed journals there is plenty of pseudo-science. that was my experience as an editor for a few smaller physics journals for a while
[9:32] Hilary Serevi: yes--the mean time between submission and posting is less than a day
[9:32] DrDoug Pennell is Offline
[9:32] You: yes precedings made me change my abstract to they did read it!
[9:32] Adastar Galsworthy: I'd like to jump the discussion back a few rungs
[9:32] Max Chatnoir: That's a really fast turnaround.
[9:33] suhky Rezillo: Horace - what or how much do you submit to precedings?
[9:33] Adastar Galsworthy: less about the specifics of what the mechanics of open science are, and discuss the issue of accreditation
[9:33] You: suhky - I only submitted 3 times
[9:33] Troy McLuhan: Preceedings is quite new I think
[9:33] Hilary Serevi: it's because we don't send the submissions out to scientists currently working in the field
[9:33] Emile Pintens: Change the abstract? Thats the first time I've heard of that happening in Preceedings
[9:33] You: Emile - well they had some good points
[9:34] Emile Pintens: Ah gotcha
[9:34] Troy McLuhan: Adastar - What do you mean by accreditation?
[9:34] You: told me to be more explicit
[9:34] Max Chatnoir: The fact that there is some editorial review should carry some weight with things like tenure committees.
[9:34] You: absolutely max
[9:34] Adastar Galsworthy: the point someone raised earlier about the leve of acceptance by tenure committees and so forth.
[9:34] You: we have to explain it to the tenure committees
[9:35] Hilary Serevi: Adastar--is your question about whether accredation is a prerequisite for participation in open science?
[9:35] Emile Pintens: The question is how long with the tenure committees take in accepting Web 2.0 tools like the ones we are talking about
[9:35] Emile Pintens: How long will*
[9:36] You: it is certainly an issue (accreditation) and that is why it is important that we continue to talk
[9:36] You: we will need each other to support what we are doing
[9:36] Max Chatnoir: I would think that this kind of publication would at least have the status that a presentation at a meeting would have.
[9:36] You: to explain, to validate
[9:37] You: max that is true presentations count and are not peer reviewed
[9:37] Adastar Galsworthy: I'm working for Nature, and there is certainly belief within this comapny that such metrics will emerge.
[9:37] Max Chatnoir: Also, you're putting your work out in a very public venue, so there is a very wide potential peer pool for comments.
[9:37] Troy McLuhan: I don't think it's a matter of accepting tools. Scientists are always bringing new tools into use. It's a matter of determining "what counts". For example, the recent proof of the Poincare Conjecture was never published in a Peer Reviewed journal as far as I know, but certainly "counts"
[9:37] You: adastar - we are looking for Nature to take some lead in that
[9:38] Emile Pintens: Adastar, metrics from where?
[9:38] Hilary Serevi: there's an interesting paper by the PLoS medicine editors about how impact factor will change in response to web 2.0 tools
[9:38] Berci Dryke: Hilary: could you please give a link to that?
[9:38] Hilary Serevi: troy's reference is to Perelman's use of ArXiv rather than a math journal to distribute his work
[9:38] You: hilary - yes Heather Piwooar
[9:38] You: piwowar
[9:38] Hilary Serevi: doi: 10.1371/journal.pmed.0030291
[9:39] Berci Dryke: thank you
[9:39] Hilary Serevi: the chronicle of higher education also had an article about that
[9:39] Hilary Serevi: i don't have the link available
[9:39] Rakerman Yellowjacket: I think scientists need to push back against impact factor and move to a concept of "science portfolio" - what work have you done - there are going to be all different types of contributions
[9:39] Adastar Galsworthy: at the moment we are building social tools, but they are mostly in their first generation
[9:40] You: racker very good point - metrics are limited compared to portfolios
[9:40] Adastar Galsworthy: the obvious things to start looking for are the spoead of influence of ideas through social networks
[9:40] Adastar Galsworthy: but there is a bit of a way to go before anything solid is around to this robustly
[9:40] You: but we can still play with metrics - let just not give everything else up
[9:41] Adastar Galsworthy: however, I want to stress that I feel the reason that we need to do this is so that we can support open science, which I happen to think is vital in the presence of too much information to sift through
[9:41] Adastar Galsworthy: open science goes hand in hand with social networking, and this provides a platform for collaborative filtering
[9:42] You: Ada - do you wnat to talk about Connotea/Emile about Knowble
[9:42] suhky Rezillo: Doesn't Connotea acknowledge users' contribution to the site?
[9:42] Rakerman Yellowjacket: ISI algorithms shouldn't be the end-all of evaluating a scientist for tenure and promotion - we already have a system to evaluate grants - tenure committees should recognize the full work of the scientist - SOME of which must pass both the review of peers and hopefully be tested through being reproduced
[9:42] Emile Pintens: I can talk about Knowble anytime
[9:42] Emile Pintens: Am I next?
[9:42] You: sure
[9:43] Emile Pintens: Knowble is a knowledge community for researchers to connect, communicate, and collaborate.
[9:43] You: hold on
[9:43] Emile Pintens: ok
[9:44] You: sorry emile not for you - go on
[9:44] You: brb
[9:44] Emile Pintens: O ok, sorry.
[9:45] Emile Pintens: I came up with the idea while I was an undergrad at UNC, and we received funding from the School of Medicine as a part of UNC's CTSA proposal.
[9:45] Emile Pintens: Right now we are in Beta, but the idea is to provide a common community where researchers, professors, and scientists may connect based upon common research areas or methodologies.
[9:45] Max Chatnoir: Brilliant, Emile.
[9:45] You: I've tried Knoble recently
[9:45] Troy McLuhan: Wow this is a great idea
[9:45] Berci Dryke: is it similar to Tiromed.com?
[9:46] You: to specify our need for a docking expert
[9:46] Hilary Serevi: Over here!
[9:46] Emile Pintens: We are taking an approach similar to Facebook where we must accept your institution before a person may be able to register.
[9:46] Emile Pintens: I have not seen Tiromed.com
[9:46] Emile Pintens: Hilary, you have a question?
[9:46] Max Chatnoir: I just discovered that, Emile!
[9:46] Berci Dryke: that is a medical community site with the same goals
[9:46] Hilary Serevi: sorry - no
[9:47] suhky Rezillo is Offline
[9:48] You have offered friendship to Troy McLuhan
[9:48] Troy McLuhan is Online
[9:48] Emile Pintens: Ah ok. While the School of Medicine provided the initial funding, we are moving to allow researchers from really any discipline to join. Our tools are not at the level of any discipline, but we are working on it. An example, we are linked to PubMed, which some professors at UNC feel it does not include all of their works.
[9:48] Rakerman Yellowjacket: how does knowble compare to pronetos and other scholar community sites?
[9:48] You have offered friendship to Rakerman Yellowjacket
[9:48] Rakerman Yellowjacket is Online
[9:48] You have offered friendship to Xantha Oe
[9:49] You have offered friendship to Joanna Wombat
[9:49] You have offered friendship to Hilary Serevi
[9:49] Emile Pintens: From what we know about Pronetos, they are focused on Publishing. We are focused on connecting people.
[9:49] Hilary Serevi is Online
[9:49] Emile Pintens: But since Pronetos isn't online yet, I do not know for sure, but we wish them luck!
[9:50] Troy McLuhan: I gather that Knowble is mainly for scientists and academics, as opposed to the general public with an interest in science?
[9:51] Joanna Wombat is Online
[9:51] Xantha Oe is Online
[9:51] Emile Pintens: Right now yes. We are trying to ensure a fairly tight user base. In time, I would not count us out in opening up to the general public.
[9:52] Emile Pintens: We are in beta, so user feedback is being gathered and we will be making further changes in the coming weeks.
[9:52] Emile Pintens: Are there any further questions?
[9:52] You: Ada do you want to say something about Connotea
[9:52] Adastar Galsworthy: sure
[9:52] Troy McLuhan: What is the underlying development tools for Knowble? A CMS? A web language?
[9:53] Emile Pintens: Troy, we use LAMP
[9:53] Adastar Galsworthy: first, sorry about the mess
[9:53] Visitor Counter 1.8: Welcome Xantha Oe. You have been counted.
[9:53] Adastar Galsworthy: I just threw these together 1/2 an hour ago.
[9:53] Visitor Counter 1.8: Welcome Berci Dryke. You have been counted.
[9:53] Adastar Galsworthy: am giving a talk on friday and will post the full presentation here in a nice format next week,.
[9:54] You: thanks ada
[9:54] Adastar Galsworthy: as many of you know there are a bunch of tools for bookmarking on hte internet
[9:54] Adastar Galsworthy: the great grand daddy is delicious.
[9:54] Adastar Galsworthy: Nature, and me spcifically, work on a tool for scientists called connotea
[9:55] Adastar Galsworthy: there are about three other specific tools out there for scientists.
[9:55] Adastar Galsworthy: I'd say take em for a test drive and pick the one you like best (as long as it's conotea ;)
[9:56] Adastar Galsworthy: as I was alluding to earlier, one of the things we are trying to do with connotea is make it into a rccomendation engine for scientsits
[9:56] Adastar Galsworthy: to help filter the huge number ot papers out there
[9:56] Adastar Galsworthy: but it is early days yet
[9:56] Adastar Galsworthy: There is an api and some people have bulit some cool apps using conontea as an engine
[9:56] You: what is an example ada
[9:57] Adastar Galsworthy: most of the exentions are greasmonkey extensions.
[9:57] Hilary Serevi: can you use greasemonkey to connect to the api?
[9:57] Adastar Galsworthy: one called Stack it, creates digg like buttons next to doi's on any poge and lets you see if the paper has been bookmarked
[9:58] Adastar Galsworthy: another called the entity describor (which was just provisionally released last week, so give it another week or so)
[9:58] Adastar Galsworthy: connects tags in conntea to a structured ontology, such as the MeSH ontology
[9:59] Adastar Galsworthy: There is another that uses conntoea as a backbone for connecting XML stlysheets for scehmas representing systems biology7
[9:59] Adastar Galsworthy: you can see them at http://www.connotea.org/wiki/ConnoteaTools [9:59] You: Ada - do you think you would be able to take Nature Predecings posts in connotea
[9:59] Adastar Galsworthy: yes, we are working on that
[10:00] Adastar Galsworthy: rather than waiting for everything to be perfect our philosophy is torelease and improve
[10:00] You: that would really help push the more open side
[10:00] You: thanks adastar!
[10:00] Adastar Galsworthy: no probs.
[10:00] You: before we go -
[10:00] You: any suggestions for the theme of the next session?
[10:00] Berci Dryke: medicine and web 2.0 :)
[10:01] You: nice berci
[10:01] Max Chatnoir: Horace, it it always in this time block?
[10:01] Hilary Serevi: i'm very intested in the ethical issues associated with putting medical
(theraputic/clinical) infomation on the web
[10:01] You: max I think same time next week
[10:01] Adastar Galsworthy: I gotta go now, thank's guy's
[10:01] Berci Dryke: Hilary: this is a crucial question...
[10:01] Adastar Galsworthy is Offline
[10:01] Hilary Serevi: thanks for organizing horace
[10:01] You: I'll post the transcript also on usefulchem.blogpspot.com
[10:01] You: sure my pleasure
[10:02] Berci Dryke: thank you, Horace!
[10:02] Max Chatnoir: Sigh.... I'll have a class then, but will look for the TS!
[10:02] You: thank you all!
[10:02] Berci Dryke: I'll also post about it with many images
[10:02] Max Chatnoir: Excellent, Berci.
[10:02] You: yes please send me you images it you want
[10:02] You: we'll leave these posters up
[10:02] Max Chatnoir: Got a RL faculty meeting. Thanks, Horace!
[10:02] Emile Pintens: I have already made a post in the Knowble blog! http://www.knowble.net/blog/
[10:03] Berci Dryke: next week, same time?
[10:03] You: so Berci lets do that then
[10:03] You: yes same time
[10:03] Emile Pintens: Same time next week sounds good
[10:03] You: thanks to joanna too for the space!
[10:03] Hilary Serevi: nice meeting everyone
[10:03] Hilary Serevi: thanks again!
[10:03] Joanna Wombat: thanks!
[10:03] You: bye everyone
[10:04] Berci Dryke: Bye!
[10:04] Emile Pintens: thanks Jean-Claude this was great! Talk to you soon
[10:04] Max Chatnoir is Offline
[10:04] Joanna Wombat is Offline
[10:05] Troy McLuhan: If you're interested in science-related events in SL, feel free to join the Science Center group
[10:05] Emile Pintens: Troy how do we do that?
[10:05] Rakerman Yellowjacket: thanks Jean-Claude

SciFoo Lives On Second Life

2007-08-07T15:25:00.000-04:00

After complaining that there was not enough time to cover everything at the Science Foo Camp, and after getting some very positive feedback from our chemical reaction mechanism representation in Second Life, it occurred to me that it would make sense to attempt to continue the conversation in a virtual medium.

I have previously presented a poster in Second Life and I was thoroughly impressed with how well it worked. People would walk around, look at my poster, ask me for more information and share their experience. And just like in real life, when there was a lull in the traffic, I would chat with my poster neighbor. One big difference was that I didn't have a draining and expensive trip to deal with.

Yes, I know that there is no replacement for face to face interactions during lunch and breaks. But it is surprising just how much one can get out of the experience, given the minimal effort it takes.

So I have set up an area on one of Nature's islands called SciFoo Lives On. I have put up my poster on Open Notebook Science. Clicking on the images flips to the next one in the presentation. Clicking on a side panel opens a browser to a screencast recording of my presentation. I have also included a headshot of myself - clicking on that takes you to my UsefulChem research wiki.

But Second Life allows not only images but also 3D objects. As examples, I included a molecule and an obelisk that generates an organic chemistry quiz upon clicking. Later on I'll copy the reaction mechanism that is currently on display on Drexel Island.

I invite any other SciFoo participants to put up a poster. If you have a Powerpoint presentation it is fairly easy to put it up. Just let me know if you need help. Powerpoint style panels are available for free at the Drexel Island store but you will need to be invited to Nature's island by either by a member like me or the owner Joanna Wombat (Joanna Scott in real life) to build there.

Although we can create a nice place to visit and view posters anytime, it would be very interesting to see how un-conference sessions would work. Keep in mind that Second Life now has voice in addition to chat.

I propose to moderate a session on "Tools for Open Science" at noon EDT (9:00 PDT, 16:00 GMT) on August 20, 2007 for the convenience of our European and US West coast participants. In the spirit of SciFoo, this will be a discussion, not be a presentation, although we should feel free to use pages from our posters to facilitate communication.

I will also set up a thread on the Second Life section of Nature Networks for people to propose sessions.

SciFoo Lives On slurl.

SciFoo07 Ends

2007-08-05T19:12:00.001-04:00

The past few days have been quite stimulating.

The SciFoo conference started right after I got off the plane in San Francisco on Friday evening around 18:00 and lasted till midnight. With the jetlag from the east coast I was exhausted but the energy of the meeting definitely kept my interest.

Friday night was the only part of the conference deliberately set up with the traditional format of speakers. The most impressive talk was on the big picture of planetary energy input and consumption. It was refreshing because the speakers seemed genuinely concerned with reporting on the actual state of things, instead of building up evidence to support their pet eco-solution. Lets just say things look grim for maintaining current energy consumption with existing renewable and non-renewable energy sources. (However, since we haven't been good at predicting scientific discoveries in the past my guess is this model will become irrelevant in 100 years). If the slides are released I'll link to them in an update.

On Friday night people suggested sessions for Saturday and Sunday and I tried to attend as many of them related to Open Science and scientific publication. The idea of this "un-conference" was to create brainstorming and discussion sessions. A few sessions really were like that but most ended up with significant presentation portions, some taking up the whole slot.

There was just enough time during the hour long sessions for people to state their opinions but not enough to innovate and make progress. That will have to wait for discussions and collaborations following the meeting. Anyone following the discussions in the blogosphere on Open Science and scientific publication will be familiar with the debates: peer review, academic credit, fear of getting scooped, etc.

The discussion was much like the blogosphere, except that the more introverted individuals probably did not contribute as much as they would have liked. I'll find out what they were thinking when they get to update their blogs and post comments.

Sometimes it felt like the Googleplex was the tower of Babel. It is apparent that there are enormous differences in the way science is done in various fields. Terms like raw data, peer review, experiment, reproducibility, citation, publication, workflow, etc. can have very different meanings.

This was probably the source of some heated discussions at times. As an organic chemist, if I find a report of a synthesis on the web with full characterization of the product, I can inspect the raw data from the spectra fairly quickly and determine if it makes any sense. I can then use that information to make that product or similar compounds with confidence. In that case, the presence or absence of peer review does nothing to affect my ability to use the information. For a cosmologist, analyzing raw data is so time consuming that the analogous situation does not apply. The only way to remove these misunderstandings is to continue to have conversations. This may be one of the most important functions of science blogs.

I met several scientists who expressed their intent to move at least part of their research to a more open format, beyond the framework of the traditional journal article. I also discussed collaboration on our drug-discovery efforts with a few people. As these materialize, I will be sure to blog about them.

Drexel Island in the Bulletin

2007-08-02T12:47:00.000-04:00

Adam Paul wrote an article on Drexel Island on August 2, 2007 in the Philadelphia Evening Bulletin : Drexel Students Get a "Second Life".

USA Today Second Life Article

2007-08-02T08:11:00.000-04:00

Beth Sussman's August 2, 2007 article on Second Life in Education has appeared.

Drexel Island got a mention:

Jean-Claude Bradley, chemistry professor and e-learning coordinator for the College of Arts and Sciences at Drexel University, says he uses it as an optional study tool but wouldn't be comfortable teaching a class exclusively in Second Life.

Bradley says only about 10 of his 200 organic chemistry students used Second Life more than once last spring. But those who did found it an effective way to study.

"This is a new way to interact with me and each other," he says. "I can show them molecules in three dimensions. We can walk around the molecule and discuss it."

"Kids who used Second Life put more time into the class," says chemistry major Tim Bohinski.

Bradley is trying to get more departments to use the "land" the university bought in Second Life; Drexel Island is shaped like a dragon, the school's mascot.

Universities and other academic institutions pay a reduced rate to buy land to build structures and develop the environment. The first-time cost for a 16-acre private university island is $980, and monthly land fees are $150.

Drexel also pays for developers to build up the island, Bradley says. Students can sign up for free basic membership and use Second Life at no cost, just as anyone can.

Beth's work was also featured:

On a Tuesday night, Beth Ritter-Guth joins her eight literature students for class. Next to a grave.
Well, not a real grave. She teaches her contemporary literature course online, in Second Life.

The class met on Willow Springs-Mama Day Island, designed around the novel that the class was reading, Mama Day by Gloria Naylor. The students visited the grave of a character, then wrote obituaries.

"I build environments where students can really explore the literature," says Ritter-Guth, of DeSales University in Center Valley, Pa., and Lehigh Carbon Community College in Schnecksville, Pa. "It's the novel in 3-D."

Teaching Chemistry Mechansims in Second Life

2007-08-01T19:36:00.000-04:00

I have previously commented on how organic chemistry can be incorporated into Second Life.

Andrew Lang has created a script to generate 3D structures of molecules and shown how to represent the docking of a molecule in the receptor site of a protein (this is important for demonstrating how drugs can interfere with infectious agents like the parasite that causes malaria).

I have also described how these molecules can be indexed by common search engines, like Google, so that people can discover locations in Second Life where chemistry is displayed.

Now, with the help of Andrew and my students Jessica and Khalid, we can demonstrate a chemical reaction. Andrew came up with an elegant solution for controlling animation in Second Life. Simply by saying "back" or "next" in regular chat next to the molecules, the reaction will proceed to the next step. (see video below)

Jessica minimized the conformation of each intermediate in ChemSketch so that its 3D structure is probably fairly close to what it actually looks like. This should provide an additional perspective to use in the teaching of organic chemistry reaction mechanisms. Walking around a giant molecule with a student is certainly a contrast to looking at a 2D representation in a textbook, especially with the control of animation.

This is actually just the first step in the Ugi reaction that Jessica and Khalid are performing in my lab for the synthesis of anti-malarial compounds. This example starts with the reaction of benzaldehyde with 5-methylfurfurylamine to form an imine. (Note: we generally form the imine without adding an acid catalyst and so the mechanism under basic conditions is displayed).

For the full Ugi reaction keep climbing the staircase on Drexel Island that starts with imine formation here: slurl.

(These reactions are also going to be indexed on the SL molecule wiki)

Drexel Triangle Second Life Article

2007-07-29T09:44:00.001-04:00

The Drexel Triangle published an article about Drexel Island on July 27, 2007.

I think it is great that the library is installing Second Life on its desktop computers:

Drexel opens Second Life campus
By: Nancy Lan

The next time you log in to Second Life, the 3-D virtual world run by its residents, you might run in to a Drexel professor teaching a course.

The University bought land on Second Life, May 9. The property has been named Drexel Island and cost about $900 to purchase plus an additional $150 per month for maintenance, according to Jean-Claude Bradley, E-Learning Coordinator for the College of Arts and Sciences.

Bradley said Second Life can help faculty members take their classroom materials to a new level.

"It's a more engaging kind of environment than, say, a message board or instant messaging … it's a lot more intuitive, I think, than blind chat," Bradley said.

...

Second Life will also be available soon on all desktop computers in the library. Siftar said that this implementation will provide "Heightened fun … all on your own computers collocated in virtual space, flying with one another, going and teleporting to different sites. That's a very teambuilding experience."