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.

Spectral Game talk at ACS Fall 09

Yesterday (August 17, 2009) I gave my talk on the Spectral Game at the Using Technology to Enhance Learning in Organic Chemistry symposium at the American Chemical Society meeting. I was not able to attend the entire symposium but luckily I did catch David Soulby's talk on using Google groups to distribute NMRs for labs that require many students to submit samples. I am a fan of using free and hosted services to simplify workflows of all types.

Also in attendance at the symposium were Liz Dorland and Bob Hanson. It was good to catch up with them. Bob shared a story of how he has been assigning his students tasks in his organic chemistry class which lead to updating Wikipedia. There is so much potential for using the educational infrastructure to create better scientific content for everyone.

My talk on the Spectral Game highlighted the role of openness in teaching and research to create new educational tools, especially for learning NMR. Tony Williams said a few words at the end about ChemSpider, RSC and some upcoming opportunities to publish synthesis articles on ChemSpider.

Spectral Game ACS Fall 09

View more presentations from Jean-Claude Bradley.

Streamlining automated solubility measurements with NMR JCAMP-DX files

Two months ago I reported on a protocol for measuring solubility using NMR JCAMP-DX files and a web service set up by Andrew Lang called from within a Google Spreadsheet. Things were going well until David at ORU was a little too productive and crashed the server from too many requests.

Andy had to change the way the script worked and used this as an opportunity to make the service more broadly usable. It turns out that the compressed JCAMP-DX files produced by different NMR instruments are not created with exactly the same standards. A way to address that issue is to convert the files to an uncompressed XY format. Unfortunately, there was a glitch in JSpecView which created XY formatted spectra displaying in Hz instead of the standard ppm.

Now all of these issues have been resolved and the process is simpler than ever. Robert Lancashire fixed the glitch in the April 26, 2009 release of JSpecView. And Andy not only made his integration web service work for the new release but also created another service to display JCAMP-DX spectra directly from the the DX file (see here for an example). In the past students had to create an associated HTML file to display JCAMP-DX files and this was just another point in the process to introduce errors and slow things down.

The new process for the semi-automated measurement of solubility (SAMS) using NMR is as follows:

1) Make a saturated solution in a given solvent (sonicate for at least 30 mins - more on this in a separate post)
2) Transfer about 0.1 mL to an NMR tube with some compatible deuterated solvent (for locking)
3) Take the NMR spectrum and export the JCAMP-DX file (on our machines these are in a compressed format)
4) Open the initial JCAMP-DX files in JSpecView and save as JCAMP-DX XY format
5) Upload the converted file to the ONSC server in the spectra folder
6) Fill out the requested information in the SAMS spreadsheet and you have the solubility calculation (first open the SAMStemplate and save as a copy with a new name)

We can now easily finish processing the backlog of measurements that the ONSchallenge participants have been obtaining and record them in the SolubilitySum spreadsheet for querying.

Automatic Back-Up of ONS files: Google Spreadsheets, JCAMP-DX, Flickr

As many of you know, we have been heavily dependent upon publicly editable Google Spreadsheets for storing results and calculations relating to our Open Notebook Science projects. We have recently integrated automated processing of NMR files in JCAMP-DX format to calculate solubility data by using web services called directly from within the Spreadsheets.

That represents a lot of distributed technology that is susceptible to network or server problems. Andy Lang, who wrote the web services that currently calculate the solubility, has enabled the recall of previously calculated values via a quick database look-up. While this substantially reduces server load by avoiding lengthy calculations, it does mean that the final numbers do not exist in the Spreadsheets themselves.

In addition to these concerns, every time I give a talk to a group of librarians the issues of archiving and curation of new forms of scholarship are raised. These are valid concerns and I've been trying to work with several groups to deal with the problem in as automatic a way as possible.

We had initially considered a spidering service that would automatically follow every file linked to the ONS wikis and download the documents on a daily basis. This has turned out to be problematic because many of the links don't terminate directly on files, but rather user interfaces. For example, a typical link to a Google Spreadsheet does not lead to a simple HTML page that can be copied but rather to an interface to add data and set up calculations.

It turns out we can take a semi-automated solution that gets us to where we want to be but requires a bit more manual work. Google Spreadsheets can be exported as Excel spreadsheets, which store the results of web service calculations as simple values and include the link to the web service as a cell comment. All calculations within the Spreadsheet are also retained in this way. The trick is to "publish" the spreadsheet using the advanced option of exporting as an Excel file. This then becomes a simple URL.


Now, the only manual step left in the process is to copy these URLs to another BackUp Google Spreadsheet. Andy has created a little executable that steps through a list of these URLs and creates a backup on any Windows computer under a C:\ONS directory. It is simply then a question of setting up a Windows Scheduler service to run once a day and call the executable. All the files are named with the date as a first part of the name for easy sorting.



Besides Google Spreadsheets backed-up as Excel files, spectral JCAMP-DX files and Flickr images can be processed in the same way. In both these cases the user must specify the JDX or DX or JPG file directly. In Flickr you have to go through a few clicks to the download page for a given image but once you have that it works fine.

Andy has versioned this as V0.1 for good reason. It does do exactly what we want but there are a few caveats:

1) Any errors in specifying a file will abort the rest of the back-up. In future versions there would be tolerance for errors, with appropriate reporting of problems, perhaps by email.

2) Files don't necessarily have the correct extensions. For example, backed up Wikispaces pages have to be renamed with an HTML extension to be viewed in a browser. Note that Wikispaces has its own sophisticated back-up system that will put the entire wiki with all files directly uploaded onto the wiki into a single ZIP file - in either HTML or WIKITEXT format. Of course this will not include files residing outside - like Google Spreadsheets. Still I think there is no harm in including the wiki pages in the the list of files to be backed-up by Andy's system.

Going forward there are two types of collaborations that could help a lot:

1) Librarians who would be willing to archive UsefulChem and ONSChallenge files. Right now these are just a few Megs a day but this will increase as we continue to add to the list. To be reasonable about space I could see a protocol of keeping only one back-up per week or month for dates more than 30 days in the past. This is about what the Internet Archive does I think. It would certainly be unambigous to know for certain what was known at what time with multiple libraries maintaining archives.

2) Someone who knows how Google creates URLs for downloadable XLS exports would be mightly helpful. Similar for Flickr and JPG exports. Even just writing a script to spider all HTML pages linked to the wikis and blogs would save a lot of manual labor. The nice thing is that the results of the spidering code would just have to be dumped into the Back-Up Google Spreadsheet - which already backs itself up conveniently.

Web based Spectra Game

Yesterday I used the NMR game in Second Life during our 2-hour Friday workshop in CHEM242. (We used a new location on Drexel island SLURL) The students who attended had looked at little or no material prior to the workshop. By the end I ended up explaining chemical shifts, complex coupling patterns and diastereotopic hydrogens differentiated by the presence of a chiral center. The only concept we didn't cover is integration, although we used peak size to take a guess about groups with lots of hydrogens (like trimethyl).

I think it was a very efficient way to teach NMR and the students can now go off and continue to practice till our next workshop Monday. Second Life has some advantages - such as the ability to mediate group study sessions where students from remote location can come together to play and discuss spectral assignments using either voice or chat. It is also nice to see the molecules in 3D, especially for bridged cyclic systems.

However, there is a bit of a learning curve to get into Second Life and not all computers have a suitable video card. So it is nice to now have the ability to play the game on a web browser. Andy set up the game play so that the score reflects the number of correct answers obtained in a row. There are also only 3 molecules to choose from instead of 5 in Second Life.

We're using JSpecView to render the spectra so expanding peaks simply requires dragging the mouse across the area of interest. It is also possible to integrate and view the metadata by right clicking.

Currently we mainly have H NMR spectra but we'll be adding lots more C NMR, IR, UV, MS, etc. It all depends on how many Open Data contributions we can find. If anyone has spectra to donate please upload them to ChemSpider and don't forget to check the box for Open Data.

This has been a wonderful example of rapid collaboration by Andrew Lang, Rajarshi Guha, Antony Williams, Robert Lancashire and myself.

Give the web Spectra Game a spin and see if you can beat the high score....

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)

JSpecView Article on Chemistry Central

Robert Lancashire has just published an article in Chemistry Central Journal:

The JSpecView Project: an Open Source Java viewer and converter for JCAMP-DX, and XML spectral data files

Our lab has found this software to be key for communicating organic chemistry results within an Open Notebook Science environment. All NMR raw data and metadata are automatically recorded and users from anywhere can mine the spectra by expanding and integrating at will from a browser interface. This is an enormous improvement over the traditional method of storing and publishing spectra as images that cannot be expanded.

The article describes other useful applications, such as the integration of JSpecView with Jmol, to show the assignment of specific peaks.

The other reason I really like this article is that Robert has used some UsefulChem blog posts as primary references. This is an important way for the scientific blogosphere to get incorporated and accepted by the mainstream.

Abstract

The JSpecView Open Source project began with the intention of providing both a teaching and research tool for the display of JCAMP-DX spectra. The development of the Java source code commenced under license in 2001 and was released as Open Source in March 2006. The scope was then broadened to take advantage of the XML initiative in Chemistry and routines to read and write AnIML and CMLspect documents were added. JSpecView has the ability to display the full range of JCAMP-DX formats and protocols and to display multiple spectra simultaneously. As an aid for the interpretation of spectra it was found useful to offer routines such that if any part of the spectral display is clicked, that region can be highlighted and the (x,y) coordinates returned. This is conveniently handled using calls from JavaScript and the feedback results can be used to initiate links to other applets like Jmol, to generate a peak table, or even to load audio clips providing helpful hints. Whilst the current user base is still small, there are a number of sites that already feature the applet. A tutorial video showing how to examine NMR spectra using JSpecView has appeared on YouTube and was formatted for replay on iPods and it has been incorporated into a chemistry search engine.

JSpecView Java Fix

Two months ago, I reported a serious problem with the new Java update and JSpecView.

Although we could band-aid the situation by uninstalling the latest Java update, most people didn't know that and would have reached dead links when trying to open our NMR files via a browser.

Robert Lancashire has now provided a fix and UsefulChem spectra are now back up. ChemSpider spectra also depend on JSpecView and are now available as well.


(taken from EXP132)

Batch Decompression of JCAMP files

I have developed a Java package to decompress NMR data taken from our Varian instrument and stored in JCAMP format. This software was adapted from Robert Lancashire's jspecview program, specifically the JDXCompressor.java and Coordinate.java classes. It reads a set of compressed JCAMP NMR files according to a configuration file with the following format:

<?xml version="1.0" encoding="utf-8" ?>
<Configuration
InputFiles="Exp0541261050.jdx,
            Exp0541261056.jdx,
            Exp0541261058.jdx,
            Exp0541261102.jdx,
            Exp0541261125.jdx,
            Exp0541261219.jdx,
            Exp0541261248.jdx,
            Exp0541261251.jdx,
            Exp0541261546.jdx,
            Exp0541261739.jdx,
            Exp0541261822.jdx"
OutputFile="output.jdx"
Title="##TITLE=Exp054"
JCAMPVersion="##JCAMP-DX=5.01"
DataType="##DATA TYPE=LINK"
/>

The program's output is a BLOCK JCAMP file, in this case output.jdx, containing the decompressed data from the input files. Right now only a few of the header fields are retained, those needed for reaction kinetics analysis using Excel VBA software (work in progress!).

In order to use, place all compressed jdx files in the same folder where all these files are located. Modify the configuration.xml file using Notepad to list the compressed files then double click on the run.bat file. The BLOCK file with the name output.jdx will be created. Note that this program just copies the titles in the original jdx files so make sure to put something meaningful in the TITLE parameter of the compressed files to keep track of them when using the Excel tool to calculate kinetics or JSpecView to visualize.