Chemistry on Tablet Computers

Sunday morning at 8:10 am in Indianapolis saw the opening of the technical symposia for the Chemical Information Division, and one of the two sessions at that time was on “Chemistry on Tablet Computers.” Chemistry on mobile devices has been a constant theme for the last several meetings, appearing both in the COMP and CHED Divisions, as well as in CINF. This meeting highlighted a number of interesting developments in this area.

Tony Williams kicked off the session with a talk on Apps and approaches to mobilizing chemistry from the Royal Society of Chemistry.” He discussed a strategy of using mobile apps to tap into the resources on the cloud for retrieval of data as well as computations. While the RSC Mobile app provides access to all of the journal content, RSC has supported development of a number of third party apps that integrate data from ChemSpider as well as other web resources. In addition to basic name searching and structure drawing and searching, these supported apps include things like Green Solvents, Lab Solvents, and Open Drug Discovery Teams. RSC is also working on a robust API for ChemSpider so developers can create their own apps for chemical information. In this way, RSC is focused on making all of their content to be mobile accessible – journal content, database content, and structure and substructure searching across all of their content. (slideshare)

Layne Morsch, University of Illinois Springfield (UIS), and Hans Keil, PerkinElmer, described collaboration between PerkinElmer, McGraw Hill, Saint Louis University, and UIS. The project involved using tablet computers (iPads provided by PerkinElmer) equipped with ChemDraw for iPad and a “flick-to-share” collaboration service to study the use of these tools in the university chemistry classroom.

For PerkinElmer, this represented a new market opportunity and a chance to see how the ChemDraw app performed with real users in somewhat stressful circumstances. For the faculty members, it represented a chance to examine the benefits and challenges of using new technology in teaching and learning.

Morsch used the iPad to lecture in his classroom, including drawing structures, with the iPad projected to a screen. Using the flick-to-share functionality, problems involving structure drawing could be sent to student iPads, students could enter a structure and send the result back to Morsch. These techniques were used during lectures, but were also used for tests. The first 2 or 3 questions on an exam made use of the flick-to-share functionality, followed by distribution of the rest of the exam on paper. He did not use the flick-to-share questions on the final exam because students could flick answers to each other, in addition to the professor.

Morsch found a 100% level of engagement in classroom exercises, since the structure drawings were sent back to him. In addition, the students learned to use ChemDraw, a benefit for those continuing in chemistry, and because of the capabilities of ChemDraw, were able to draw more accurate reaction mechanisms.

Some drawbacks were that using ChemDraw was slower than drawing freehand, no text tool was available and note taking required switching apps, and the variability between students was much greater as well. However, Morsch and Keil felt that the experiment was very much a success.

Jeff Lang, American Chemical Society, gave a presentation on “Can I get that to go? Reading research articles on a tablet.” He presented a number of statistics showing that while the sales of tablets and other mobile devices are increasing, many people, and many in the student demographic, use tablets largely for games and entertainment. Even though there is a lot of usage from both the website and the mobile app, it still accounts for only 5% of total usage. Reasons for this include the availability of scientific content via mobile devices when researchers are off campus, and the fact that 90% of downloads are still for the PDF format of the article. While the PDF format is readable on mobile devices, especially tablets, there is a difference between what Lang termed a grazing mode, looking to make connections between works as well as scanning at a cursory level for articles of interest, and digestion mode, reading for deeper understanding of relevant articles. Lang described the development of a more interactive version of the PDF, which provides the composed version of the text, but also allows for incorporation of linking capabilities normally associated with HTML. He also described a responsive approach, where the server would identify the device characteristics and connection speed, and automatically deliver the best version of an article.

The Java-based JMol has become one of the standards for molecular visualization on the Internet, but in addition to lack of support on tablets, within the last year, Java has been the target of many security problems. The U.S. Department of Homeland Security recommended disabling Java in web browsers in January, 2013. Bob Hanson, St Olaf College, presented a talk on “JSmol: Full-service molecular visualization on the Web without Java,” describing the migration of the Java-applet based software to a purely JavaScript environment. Hanson used Java2Script, an open source program developed by Zhou Renjian, to begin the conversion. Over the course of several months, Hanson got the JavaScript version, called JSmol, working in basic form, and then was able to get all of the Jmol functionality working, and finally optimized it so it was nearly as fast as the Java applet version. JSmol now works on tablets and smartphones as well as desktop and laptop operating systems. In order to compensate for the speed of the mobile devices, JSmol detects the speed of the device and uses that to decide how to render the molecule. Hanson is now working on a conversion of JSpecView to JavaScript.

Tamsin Mansley, from Dotmatics, presented on “Enabling Chemistry on the Go.” The philosophy behind Dotmatics is that scientists should be able to access their own data, with whatever tools, wherever they are. To implement that philosophy, Dotmatics employs cloud hosting and web-based and app-based access to that cloud. The data workflow comprises an electronic laboratory notebook, and includes importing, querying, analyzing, visualizing, and sharing data. The web-based tools are designed to be tablet friendly, allowing all of the dotmatics capabilities across devices in a familiar interface. Dotmatics also has an app version of their structure drawing utility, called Elemental, which also includes property calculation, and database searching.

Simon Coles, University of Southampton, discussed “Tablets in the lab: enabling the flow of chemical synthesis data into a chemistry repository.” Coles has been involved with chemical data management and cheminformatics for a number of years. These have resulted in a rich environment with ontologies to describe reaction plans, enactments, observations, and outcomes, expressed as RDF triples. Web-based LIMS and ELN environments, for example, labtrove.org, have been created. A recent paper published in Chemistry Central Journal included electronic supporting information submitted directly from an ELN. One of the challenges, though, is that in order to start the digital lifecycle of the experimental data, the experimental procedures from the lab must be created in an ELN environment, usually by transcribing from a paper lab notebook. Coles and coworkers are currently looking at how to introduce tablets into the lab as a way to aid in that process. This can be a challenge, especially in organic synthesis, where introducing a tablet into the lab might be a source of problems, not the least of which could be damage to the tablet. The study currently underway has focused on surveys and observations about how researchers use their paper lab notebooks for capturing data about the experiments, and what those same researchers do to prepare the data for publication. The main findings were that researchers cannot lose the functionality of the paper notebook. They need to be able to “scribble” and to have the flexibility to deviate from the plan. A tablet app does not have to be a full ELN, but a lightweight version that interfaces to the main ELN and only performs operations that are absolutely necessary for recording in the lab. A number of apps have been created to support these requirements, including Notelus and Plan Buddy. These allow for scribbling, note taking, and incorporating of photos.

Steve Muskal of Eidogen-Sertanty finished the session with a talk on “New strategy to engage mobile computing users and developers.” Muskal has described a number of standalone mobile apps in recent meetings, with increasing capabilities for those apps to talk to each other, and to store and access data in the cloud. However, as with all apps, those were limited because they were basically stand-alone, vertical applications and it was cumbersome to move between them. In this talk, Muskal described an app, PP Mobile, which provides an interface to the Accelrys Pipeline Pilot Science Cloud. The app allows any Pipeline Pilot report, in either HTML or PDF, to be deployed to a mobile device. In addition, a dashboard allows interaction between the app and the Pipeline Pilot cloud.  For example, the camera and GPS on a smartphone could be used to take a picture of a barcode on a sample bottle and record time, date, and location in addition to the sample identity. Protocols can be launched from the mobile device to run on the server. The user can come back later to review the results. Through this environment, users now have broad access to a variety of tools and services within Pipeline Pilot. Muskal concludes that this could be a game-changing app for tablet users to interact with their chemistry in the cloud. (slides)

Martin Brändle and David Martinsen, Symposium Organizers

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Slide courtesy of Antony Williams