Visualizing Chemistry in Second Life ACS Talk Recording

The American Chemical Society has processed the recording of the talk that Andrew Lang and I gave at the Spring 2010 ACS meeting in San Francisco on March 23, 2010:
Visualizing Chemistry in Second Life

Back from ACS San Francisco Meeting 2010

Last week I co-hosted a symposium with Noel O'Boyle and Andrew Lang on "Visual Analysis of Chemical Data" at the American Chemical Society meeting in San Francisco (March 22-23, 2010). The ACS recorded almost every talk in our symposium and I'll provide the link here when available (they tell me mid April).

Liz Dorland kicked off the symposium with a great keynote presentation covering effective visualization in a number of fields and the special challenges faced in chemistry. There were several talks about QSAR and I particularly enjoyed Edmund Chapness who incorporated the visualization of confidence in predictions with an intuitive colored molecule map. Geoff Hutchison gave an informative overview of Avogadro.

Perhaps the biggest revelation was the "iTunes for Cheminformatics" project by NIH researcher Ajit Jadhav (leading the team which includes Rajarshi Guha). The alpha version will be available for testing on April 5, 2010 and many of us are eagerly anticipating being able to give it a spin. From what I understand the system will automatically be able to identify scaffolds (fragments) in a collection of molecules and make it easy to search for and filter assay results.

Carmen Drahl covered in minute by minute detail announcements about new drug candidates on Twitter. Following the FriendFeed feed for the conference flagged a very interesting post about a Cold Fusion Symposium that was being held. In spite of the notorious lack of wireless availability at ACS conferences, attendees seem to be making due with accessing their social networks via their cell phone devices.

Andrew Lang and I spoke about Visualizing Chemistry in Second Life - our slides are here - hopefully I'll be able to post the recordings as well soon.

Visualizing Chemistry in Second Life ACS SP2010

View more presentations from Jean-Claude Bradley.

Science Online 2010 Thoughts

This year's Science Online conference at the Research Triangle Park, NC was a satisfying experience.

I had the pleasure of meeting face to face for the first time people I have gotten to know quite well over the blogosphere: Steve Koch, Hope Leman, Walter Jessen, Pawel Szczęsny and Andy Farke. This is probably the best conference for me to catch up with friends and collaborators - Bill Hooker, Tony Williams, Cameron Neylon, Deepak Singh, Carmen Drahl, Dorothea Salo, Christina Pikas and several others.

My session on Second Life Saturday didn't work out so well. We had major connectivity problems both at the conference side (bandwidth maxing out and even the router getting unplugged at one point!) and on Second Life. We spent quite a bit of time before the session trying to get things under control but SL voice failed for everyone there after working briefly. I also got kicked out repeatedly and had trouble teleporting. I did manage to follow Max Chatnoir to her always impressive Genome island but only saw her type a few lines of chat.

That was very disappointing and I'm not sure I'll attempt another live demo like this again. After so many years in operation the Second Life servers really should be reasonable stable, given the annual fee we pay for our islands. I think a better use of the technology might be a parallel but separate track only on Second Life, where some of the presenter can display their posters for several days and visitors can leave comments or arrange to meet at certain times. This is what Andy Lang and I did for ACS island a while back and it worked fairly well.

The session on Open Notebook Science I co-chaired with Cameron Neylon and Steve Koch on Sunday went a lot better. I provided a context by demonstrating the utility of ONS in resolving the NaH oxidation controversy followed by the example of the aqueous solubility of EGCG, where the lack of access to raw data in the literature and company catalog leads to an necessarily confusing situation. At the end I mentioned the case where simply reading the lab notebook of Alexander Graham Bell exposed a scandal detailed in Seth Shulman's new book "The Telephone Gambit".

Within that framework I provided an overview of the ONSChallenge and the Wikispaces/Google Spreadsheet/Blogger system we use in my lab. Cameron then spoke a bit about the LaBLog system he uses and the broader scope of incorporating automation in the creation of the notebook records. Finally Steve reflected on his experience with OpenWetWare in both a teaching lab and his research group. He displayed some positive comments he received about ONS in a recent grant application. The discussion afterward moved into the challenge of archiving large amounts of data. I mentioned that we are still looking for a library partner for our ONSarchive project.

On Saturday night during dinner there was an "Ignite" style session where speakers are given about 5 mins to go through their slides, which change automatically every 20 seconds. I presented with Tony on Games in Chemistry. It turned out to be an eclectic collection of talks and are worth a watch when they are posted.

I enjoyed Jonathan Eisen's session on Open Access and Peter Binfield's on PLoS ONE article level metrics. I learned that the DOI must be used for the blog citation metric to work properly and that all the statistics can be downloaded as an Excel file. The scientific world operate much more smoothly if the mainstream adopted a fraction of the philosophies espoused in these sessions.

My favorite session was Andy Farke's demo on the Open Dinosaur Project to crowdsource the measurement of bones. It was exciting to see that his data management system using Google Spreadsheets is similar to our ONS Solubility Challenge. It is possible that he could use the code that Andy Lang wrote to activate bots to flag discrepancies and perhaps semi-automatically publish a book with a summary of the results in a similar way that we do. Instead of pictures of molecules his entries would have images of dinosaurs. We'll follow up to see what is feasible.

#scio10

Cheminfo Retrieval First Class FA09

I gave my first lecture yesterday (Sept 24, 2009) for my Chemical Information Retrieval course at Drexel. One of my main objectives for the course is to provide the most current information about how to best find and review chemical information.

To this end, I set up a wiki (http://getcheminfo.wikispaces.com) which should become considerably enriched over the course of the term. I invited students to help contribute useful links to the resource page - and even before I finished giving the first lecture they added several really good ones. I also invite any chemists or librarians to add links to resources we may have missed. Just request to join the wiki to contribute.

The wiki will also be used for students to write a report on a chemical topic making use of cheminfo resources. Right after the lecture I made sure the students joined the wiki and created two pages: one for their report and one for a "research log". The idea is that students will report significant steps in conceptualizing their projects and how they are searching databases. I can then comment directly on their log pages for quick guidance. I suppose anyone with helpful suggestions that I missed could also comment - again just request an account on the wiki.

This class has traditionally required a written report. This term I'm adding a twist: the minimum number of words can be reduced somewhat if students elect to incorporate a multimedia or other creative component. To provide examples of what that might look like I visited Drexel Island on Second Life and demonstrated 3D molecules, interactive NMR spectra and a chemistry museum (from Sandy Adam). There is a lot of chemistry possible on Second Life (see Lang & Bradley) At the end of the tour on the island we visited a wildlife area recently built by Robert Brulle for a project related to environmental science (more on this in a later post). I got a hug from a panda and got sprayed when I tried to pet a skunk - just to give a taste of what kind of fun things can be constructed in a virtual world. Other projects could involve screencasts, Jmol, games, Facebook, etc. As long as it requires students to access chemical information, I am pretty open to ideas. Students will work through their ideas on their log page and the final product will also be available on the wiki. These projects could provide interesting examples for others interested in the topic of chemical information.

At the end of my lecture I provided a brief overview of the NaH oxidation controversy. There really could not be a better example of the importance of staying on top of new communication channels to follow and participate in chemical research. This year the most important of these new tools are probably blogs, wikis and FriendFeed. Next year it might be something else - Google Wave?

My talk at ACS FA09 on Social Networking Tools and Teaching Chemistry

Yesterday (August 19, 2009) I gave my last talk at the American Chemical Society meeting in Washington. I presented on Using social networking tools a la carte for organic chemistry education: Wikis, blogs, Second Life, and more for the Symposium on Using Social Networking Tools to Teach Chemistry, organized by Laura and Henry Pence:

12:05 PM Wikis in chemical education: The best of two worlds
Laura E. Pence
12:25 PM ChemPaths: Learning to meander — an online portal to ChemEd DL resources for intrinsically linked learning
Justin M. Shorb, John W. Moore
12:45 PM ChemEd DL WikiHyperGlossary
Robert E. Belford, J. W. Moore, Daniel Berleant, Michael Bauer, Jon L Holmes, Kyle E. Yancey
1:05 PM Social media: Immersion and its discontents
Elizabeth M. Dorland
1:35 PM Using social networking tools a la carte for organic chemistry education: Wikis, blogs, Second Life, and more
Jean-Claude Bradley, Andrew Lang
1:55 PM SNS, IM, and textng vs. traditional e-mail and voice messaging as a means of facilitating instructor-student contact: Trends and habits of student usage, and techniques to avoid electronic overload (or withdrawal)
Robert B. Gregory
2:15 PM Faculty development, collaborative inquiry, and Web 2.0
Joanne L. Stewart
2:35 PM Are netbooks the next big thing in the chemistry classroom?
Harry E. Pence
2:55 PM Managing laboratory research data using cloud computing as an organizational tool
Harry E. Pence, Jacqueline Bennett

It was a really entertaining symposium. Laura Pence talked about using Wikispaces (the same platform I use) for student projects and emphasized how helpful it is to compare wiki page versions to evaluate each student's contributions. Justin Shorb presented on his work to wikify a chemistry textbook. Despite a broken arm, Bob Belford did a great job in presenting his Wikihyperglossary project. It marks up chemistry terms on web pages, similar to the approach taken by ChemMantis.

Liz Dorland provided a wonderful overview of how Second Life can be used from an educational standpoint, very much complimentary to the content I had on my slides. There is just so much content and so many projects now on that virtual world that it is difficult to appreciate without actually going in and taking a tour but sometimes a good talk can motivate people to give it a closer look.

Robert Gregory's talk was very funny and somewhat shocking: he gave out his cell phone and asked his students to contact him 24/7 - including 2:00 AM when he was sleeping. Joanne Stewart gave an overview of how inorganic teachers kept in contact using various social networking tools and valuable it was for both collaboration and support.

Harry Pence gave two very humorous talks at the end. The most interesting point for me was his collaboration with Jacqueline Bennett, who used Google Spreadsheets to collect experimental results from her students. An example of that work recently appeared in Green Chemistry, 2009, 11, 166 - 168. This is especially relevant for our research - because we also use Google Spreadsheets to aggregate results - but her reaction involves finding the right solvent for mixing an aldehyde and amine and obtaining a pure imine as a precipitate, exactly the same approach for our preparation of Ugi products. Perhaps there is a future collaboration there.

All of the presentations were recorded and I will post a link when available.

Here is the summary of my talk and the recording:

Jean-Claude Bradley describes the use of social networking tools to teach undergraduate organic chemistry. Public free wikis can be used effectively to manage class information as well as serve as a versatile platforms to process student assignments and provide rapid feedback. Examples of using Second Life to deliver quizzes, play games and offer students an environment to create projects involving 3D molecules, spectra and posters are detailed. The continuously evolving role of blogs, podcasting, screencasting and newer faster interactive platforms such as FriendFeed will be outlined. New technologies create the need for new skills to be taught to students - some relating to networking and some involving knowlege of the language to navigate the chemical webspace (such as SMILES and InChI).

Using social networking tools a la carte for organic chemistry education: Wikis, blogs, Second Life, and more

View more presentations from Jean-Claude Bradley.

ONS talks at the British Library, ACRL and a Slideshare feature

Update: the Columbia panel on Open Science video is now available.

This past week I gave two talks and participated in one panel discussion - with no jetlag or airport burn-out. Gotta love technology for allowing for that to happen.

My first talk was on Feb 11, 2009 at a session on Digital Lives at the British Library. This was a hybrid conference with a presence in the physical world as well as Second Life. I could see and hear the speakers in London from within Second Life and I'm assuming they saw my presentation just as clearly. Joanna Scott from Nature coordinated the SL session.

I then participated in a panel in Second Life on "Stepping into Science" on Feb 13, 2009. There was as good discussion about using Second Life for educational applications. The other panelists included:

• - Troy McConaghy (Scientist and Educator who has been involved with Second Life for over three years)
• - Dr. George Djorgovski (Caltech and Meta Institute for Computational Astrophysics (MICA))
• - Joanna Scott (Writer for Nature and manages Second Nature on Second Life)
• - Adrienne J. Gauthier, M.Ed. (Instructional Technology Specialist, Steward Observatory)
• - Tony Crider (Elon University)

Then on Feb 17, 2009 I presented for the Association of College and Research Libraries using Acrobat Connect Pro. Hope Kandel from LearningTimes did a great job in coordinating the technology and people several weeks before the event. The attendees used chat to ask questions during my talk then John Howard moderated by summarizing some of the questions verbally at the end. It went well I think.

And I just heard that my ACRL presentation on Open Notebook Science is currently showcased on Slideshare under the Education category.

Now I'm on my way to a physical conference at Columbia with Bora: Open Science: Good For Research, Good For Researchers?

Carmen Drahl visits my lab at Drexel

On Wednesday Jan 21, 2009 I had the pleasure of spending the day with Carmen Drahl from Chemical and Engineering News. She showed up bright and early an hour before my class (CHEM242) started at 9:00. And this was helpful because we had to get her computer set up on the Drexel wireless system.

That morning I was running a Second Life "race", where students compete to complete a series of questions about basic material they should recall from last term's organic chemistry course (CHEM241). Nobody completed the quiz within the duration of the class so there was no actual winner. Regardless of the motivation, the exercise of actually attempting these quizzes certainly can't hurt for the upcoming test this week. Carmen is to my right in this picture and the others next to the quiz obelisks are students:


Carmen spent the rest of the day trying to get an idea of what my students and I do on a typical day. She looked at the equipment we use to measure solubility and we discussed the Open Notebook Science Challenge in detail. This was a good opportunity to demonstrate the value of the interactive ways we have of querying the solubility data, mainly thanks to Rajarshi Guha and Andrew Lang. Finally I showed her how I use FriendFeed to collaborate and rapidly share scientific information with colleagues. This should make for an interesting read when it comes out in a few weeks.

Interactive Visualization of ONS Solubility Data

Rajarshi Guha and Andy Lang have been very busy during the past few weeks developing visualization interfaces for the Open Notebook Science Challenge solubility data.

Information in a database is only as useful as the tools to explore it. We are striving to create interfaces that enable synthetic organic chemists to find actionable information in as intuitive a manner as possible.

To search for specific solubility measurements for a given solute in a given solvent (or to search for all solvents for a given solute), we have been using Rajarshi's handy web browser interface providing drop-down menus of available selections. The query results directly link back to the relevant pages from the laboratory notebook for further analysis. (For details of the coding see Rajarshi's blog)

We now have to ability to look for patterns in the dataset. Solubility measurements can now be plotted on a surface using Andy's service. First select a solvent, 2 molecular descriptors, a solubility cutoff value and the maximum point size from drop-down menus:

Then explore the chemical space.

In this example the solvent is methanol and molecular weight is plotted on the x axis and ALOGP is plotted on the y axis. Up to a maximum defined above, the size of the points relates to the value of the solubility, averaged from all available valid measurements. Measurements that have been judged invalid as marked as DONOTUSE in the SolubilitySum spreadsheet. That way researchers can investigate for themselves the reason for rejection of the data point. As an example, insufficient mixing time has been a cause of invalidation.

As synthetic organic chemists, we are mainly interested in how our reagents and products will behave in a given solvent. The compounds in this chemical space are starting materials for Ugi reactions and are color-coded by functionality. Red points are aldehydes and blue points represent carboxylic acids. We selected 2M as the cutoff point for point shape because it is a convenient concentration to use to mix reagents participating in the Ugi reaction, especially when considering automation. (see JoVE article) With this selection, disks are below 2M and diamonds are above.

Some interesting insights can be gleaned quickly from this plot. There are three low solubility disks among a group of diamonds near the top of the plot. The diamonds in this region represent mainly highly soluble aromatic aldehydes. By positioning the mouse over each point we can discover the details of each compound and its solubility. As shown, 2 of the disks are aromatic nitroaldehydes.

We may infer from this that methanol may not be a good solvent choice for nitroaldehydes in general. At the very least we can formulate the hypothesis and follow it up with additional measurements or re-investigate outliers. Such a pattern is difficult to observe when measurements are stuck in tables - or worse - only in lab notebook pages.

One of the limitations of a 2D plot like this is overlap of points. We can control this to some extent by making the points smaller but that doesn't eliminate the problem in all cases. One trick that we can use is introduction of a third molecular descriptor to separate points in 3D space.

Andy has done this recently in Second Life - here is a picture we took yesterday with our friend Viv on Drexel island (SLURL). The balls we are sitting on are the solubility points. The larger the ball the greater the solubility. Clicking on the balls opens a browser window to the measurements in the laboratory notebook.

Our eventual goal is to provide robust quantitative models to predict non-aqueous solubility. To see where we stand on that front see Rajarshi's recent report.

In the meantime I think we can continue to provide intuitive tools to get non-theoretical organic chemists to play with the visualization of solubility. Almost all organic reactions are performed in non-aqueous solvents so solvent selection is a very important part of the process of doing chemistry. This is especially important if one wants to engineer non-chromatographic product isolation.

SciFoo Preview Area

Timo Hannay asked me to help with establishing a Second Life presence for the upcoming SciFoo meeting August 8-10, 2008. I think that a poster area in the style of SciFoo Lives On would work well.

To kick things off, 23andMe will be presenting tomorrow June 24, 2008 at 10:00 PDT / 13:00 EDT/ 17:00 GMT on Second Nature island. Berci Mesko had already made arrangements for them to speak - and since they will be at SciFoo this is a convenient way to get things started.

Other SciFoo presenters coming soon...

The presentation area is next door to the SciFoo Lives On section: SLURL

Jon Udell Interviews me for ITConversations

Update: the transcript is now available.

My interview is now available on the ITConversations podcast. Jon Udell did a great job of covering lots of territory:

• Open Notebook Science and UsefulChem
  and a mention of our Mettler-Toledo trial
• our collaboration with Rajarshi Guha and Phil Rosenthal
  
• screencasting (a term coined by Udell by the way)
  
• teaching chemistry (in collaboration with Andy Lang) with Second Life
• Nature Island and ACS Island
  
• intellectual property and Open Science
• the role of competition in science
• the role of wikis and blogs in ONS
• Drexel Island on Second Life (a mention of Beth Ritter-Guth)
  
• the avatar effect
• poster presentations in Second Life
• Jon teaches me how to do a screencast inside Second Life
  

Amino World Exhibit on Second Life Today

The unveiling of Resident Chemist Andra Renard’s Amino World Exhibit is taking place today on ACS Island!

Andra (Kenyon College biology professor Joan Slonczewski in real-life) and her assistant, Daniel, will be voice-enabled and accepting questions via text. The unveiling will be at 12 Noon PDT (SL time)/ 15:00 EDT on Wednesday, June 11, at http://slurl.com/secondlife/ACS/124/124/21

Read more about it on the ACS blog.

Chemical Heritage Foundation Talk on Second Life

Earlier this week, I attended the LISE08 conference at the Chemical Heritage Foundation in Philadelphia. The theme this year was New Media and Technology in Science Education and I talked about using Second Life in the chemistry classroom.

David Shaffer gave a very entertaining and thoughtful presentation on epistemic games. These are games simulating complex systems like urban planning.

Tom Tritton reviewed the conference for CHF.

NMR viewer in Second Life

Andrew Lang just finished coding this nifty little JCAMP-DX viewer in Second Life. The video shows that you can expand any area of the spectrum by typing zoom followed by the desired range in the chat box.

You can also type "back" and "reset" commands. It essentially functions like Robert Lancashire's JSpecView if it were running in Second Life (although integration is not yet implemented).

There are still a few kinks to iron out but it should work with any spectrum that can be represented in JCAMP-DX format: IR, CNMR, HNMR, UV-vis, MS, etc.

This should extend considerably the set of tools available to chemistry teachers who use Second Life to interact with students.

Give it a try on Second Nature island: SLURL. (You'll need the most recent version of Second Life to run this and click the link from within IE, not Firefox)

Back from Spring08 ACS

The American Chemical Society meeting in New Orleans proved to be as hectic as usual. I didn't get to spend as much time with everyone I was hoping to touch base with but I did get some useful things done:

1) I presented on the use of Cheminformatics in Open Notebook Science and Teaching Chemistry with Second Life. Since the ACS oral sessions are so short (15-20 mins before questions) this is a good opportunity to get our work recorded in a concise format. Speakers like to complain that they need a full hour to do justice to their elaborate projects but the shorter format seems to match the attention span of most attendees.

2) The Sci-Mix session on Monday was very hectic. I presented two posters related to my talks and helped out with the opening of the poster session on ACS island. We had 20 posters in Second Life and it was great to finally meet a few of the presenters and the organizer Kate Sellar (Finola Graves) in person. Kate was running Second Life on a large screen right at the poster entrance and giving out t-shirts. Andy Lang (Hiro Sheridan) was also helping out remotely from within Second Life. By all accounts it was well received. The posters will remain up on ACS island for the next few months and it will be possible to contact presenters via bells next to their posters.

3) I also finally met several people that I have known only virtually for some time: Rajarshi Guha, David Wild, Rich Apodaca, Noel O'Boyle and Warren DeLano. Rajarshi, Rich, Noel, Warren, Geoff Hutchison and I went out for the Blue Obelisk dinner on Tuesday night.

4) I had a good brainstorming session with Rajarshi about representing experimental workflows in XML. He suggested using Taverna to create "null" workflows - since our lab experiments are physical rather than executing code. Noel suggested using Knime. The idea is to represent experimental steps leading to a result in a standard machine readable (and thus minable) format. We're going to start very simply by limiting the workflow space to Ugi reactions.

ACS Island Party Tonight

As I mentioned previously, the American Chemical Society is gearing up for a poster session in Second Life on April 7, 2008 immediately following the New Orleans ACS meeting Sci-Mix session at 20:00 EDT. There are currently 16 presenters from diverse chemical fields.

In anticipation of this event there will be a little party on ACS island tonight (April 2) at 18:00 EDT. Everyone is welcome to attend.

Just type "ACS" in the Second Life map search function to find the island.

Campus Technology Article about Molecules in Second Life

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

Science Bloggers SFLO Session

Berci led yesterday's (Oct 15, 2007) SciFoo Lives On session on Science Bloggers.

Sandra Porter, Bora Zivkovic and I (UsefulChem) discussed why and how we blog about science.
Bora really had a lot of problems with his video card and I was impressed that he persisted to deliver a great presentation and participate. I've been there so I know how frustrating that can be. Unfortunately a lot of people assume that is the typical Second Life experience and give up.

Berci live blogged the event here and did a tremendous job in representing the flow of the session. The transcript and other links are here.

3D Periodic Table in Second Life

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).

Open Notebook Science Case Studies SFLO Session

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.

Second Life Science Center

Troy McConaghy has set up a wiki to keep track of science initiatives in Second Life.

One really nice feature on there is a Google calendar for upcoming events. SciFoo Lives On sessions are listed there.