Chemistry on Mobile Devices: Create, Compute, Collaborate: Meeting Report

Wednesday 7 September 2016, Centre for Molecular Informatics, University of Cambridge, Cambridge CB2 1EW
Organized by RSC CICAG (http://www.rsc.org/Membership/Networking/InterestGroups/CICAG/)
Report from Jonathan Goodman and Chris Swain

Mobile devices are now ubiquitous, there are now estimated to be over two billion SMART phones and tablets in use globally. Each with the computing power to handle most of a chemists needs. The aim of the meeting was to look at the many ways that mobile devices could become the chemist’s essential companion. From searching and consuming content, to performing computational calculations and providing interactive visualizations. From electronic notebooks to devices accessing Cloud based resources. What are the advantages of and the security concerns of an always-connected mobile device, what are the challenges of a touch interface? As befitting a meeting on mobile devices we had presentations given from laptops, iPads and even an iPhone, and all seemed to work perfectly.

Dr Michelle Lynch (Senior Consultant, IHS Markit/CICAG Committee) opened the meeting with an overview of mobile chemistry. Mobile chemistry usage in academia is heterogeneous with many components chosen by the researcher, or local to one institution. Electronic Laboratory notebooks are becoming well established in both academia and industry, and the use of mobile devices to record experiments, in particular photographs was common. Data input is not ideal and the ability to share and collaborate appears to be solved by using features like Dropbox, which has security concerns. Internet of things is likely to have impact on the way things communicate and will require open APIs and standard ways to provide security, mobile devices could be at forefront of these technologies.

The RSC has an ongoing project looking at the way that chemists interact with the products and services provided by the RSC. James Stevens, (Product Manager, Journals and Books, RSC), & Paul-Jervis Heath, (Founding Principal, Modern Human) gave a joint presentation entitled Lab on the bus: Designing for academic modes of reading. This exercise included video recording or observing chemists at work in an effort to better understand the way that chemists search and consume content across multiple devices. Whilst the PDF has become the standard way of distributing content it is clear that it does not provide the ideal format for viewing on different screen sizes. Whilst the RSC website provides an increasing amount of functionality this also serves to take the focus away from the content on devices with restricted screen real estate and has a significant impact on page load times. The RSC are now making efforts to reformat content to be better viewed on different devices.

Professor Nick Greeves, (Department of Chemistry, University of Liverpool), gave an interesting talk on Mobile devices in chemistry education. In particular thinking about the way students consume and retain information. Clearly electronic devices provide vastly superior means for searching, but once found, sometimes the students then prefer to read the content in hard copy format. Lectures can be provided as video recordings and notes/handouts as electronic files. However the ability to annotate on mobile devices was somewhat limited, in particular the ability to accurately draw chemical structures, curly arrows etc. The iPad Pro and pencil seem to provide sufficient performance to overcome these issues, but at a substantial price. Mobile phones also provide a means of impromptu polling/voting during lectures to increase engagement. Airplay could be a useful way of sharing content in small meeting or tutorials, but there is need to control what is displayed rather than the current “free for all”.

In an exciting development Dr Jonas Boström, CEO and Magnus Norrby, CTO (Co-founders EduChem VR) chose this meeting to announce the founding of a new company EduChem VR (http://www.educhem-vr.com) and gave a talk entitled, Virtual reality smartphone apps making chemistry look and feel cool. This project aims to enhance the learning experience for school chemistry lessons by providing virtual reality viewing of molecules using inexpensive Google Cardboard viewers (https://store.google.com/product/google_cardboard) that work with any modern smartphone. They already have apps for viewing small molecules, bonding in the different states of water, and biomolecules from PDB and are very interested hearing about possible collaborations.

They brought a couple of viewers to the meeting and gave a very popular series of demos during the lunch session. The flash poster session was intended to offer the opportunity for developers to give a brief intro to new apps, and we were treated to two very interesting freehand chemical drawing applications. Historically chemical drawing packages have relied on a series of menu item or templates to build chemical structures. Whilst now well established they don’t really emulate freehand drawing of chemical structures using pen on paper. Paul Wallace (Perkin Elmer) and Eufrozina Hoffmann (ChemAxon) gave impromptu demos of freehand chemical drawing apps.

The history behind the Handbook of Medicinal Chemistry and Medicinal Chemistry Toolkit app - tablet delivery by design was described by Dr Andy Davis, (Projects Director, RIA Innovative Medicines, AstraZeneca). The project started as an extension to the very popular Medicinal Chemistry training course organized by the RSC, initially as an e-book with links to external resources. This then evolved into a stand-alone iPad app (https://itunes.apple.com/gb/app/medicinal-chemistry-toolkit/id910073742). The Medicinal Chemistry Toolkit app is a suite of resources to support the day to day work of a medicinal chemist. Based on the experiences of medicinal chemistry experts, these otherwise difficult-to-access tools are now available in a portable format for use in meetings, on the move and in the lab.

It is important to note that the calculations are done locally on the iPad and not via a web service, this is important for confidentiality when dealing with proprietary compounds. Properties are calculated as you sketch in the molecule so you can actually see the contributions of functional groups as you add them. The Cheng-Prusoff equation is probably the most important equation for medicinal chemists involved in the design of inhibitors to understand

As an example for kinase inhibitors the Ki will vary depending on the concentration of the substrate ATP. It is therefore vitally important to understand the likely range in ATP concentration in the target locations, and to be aware that accumulation of the substrate (ATP) will have an impact on inhibition. This can be part of the reason why shifts in activity are observed when moving from a biochemical assay to a cell-based assay. Andy then asked for feedback on possible future directions, people have asked for it to be ported to other platforms, the ability to add extra functionality, user defined filters, other ADME models. All of which are possible but it was not clear how this might be funded or supported in the future. Dr Dan Ormsby, (Principal Application Scientist, Dotmatics Limited) gave a talk originally entitled “Challenges of developing electronic lab notebooks for mobile devices and substructure searching on iPad” but which was updated to include new developments on connecting laboratory instruments and devices into and electronic labnotebook environment. [Elemental](https://itunes.apple.com/app/elemental/id518655328) is chemical drawing package that is available multiple platforms and was designed to provide the same user experience on both desktop and mobile devices. Whilst the chemical intelligence is all written in C for portability, the interface uses javascript to provide a consistent user interface.

Elemental has been downloaded many 100,000’s of times and accounts for 15% of the links to the company website, underlining the role of small mobile apps as advertising aids. As an extension [ElementalDB](https://itunes.apple.com/us/app/elementaldb/id627422287) provides a demonstration of an iPad application that does a substructure search of a 1,500,000 structure database in less than a second. The sdf records have been compressed to reduce size and put into a sqlite database. They then use classing path-based fingerprints for the structure-based searching, and calculate some physicochemical properties.
If you click on the CHEMBL id a link is opened in the browser displaying the ChEMBL report card. There was some discussion about users being able to import their own structure files, the technology is there, Dotmatics will consider making it available.
The DotSDMS product enables integration via attaching legacy devices (and new devices) to a central repository of experimental files. So the machines work automatically recording their data to a central place. It works like Dropbox where a client task bar icon is displayed to show it is monitoring a folder for new files, however you don’t have the security concerns of uploading to the internet. As new files appear they are checked (to see if they actually changed (md5sum style)) and if changes are seen it is uploaded to SDMS. Versions are stored if the same file changes (some instruments always write to the same filename it seems.) The client code is in straight python so works on Linux/Raspberry Pi/ODROID (http://www.hardkernel.com/main/) like hardware so Linux collection machines of an instrument can post updates to SDMS too. For a legacy machine there are a couple of options. One is a Moxa box. This attaches to the rs232 connection and when the user presses the button on the device (to record pH or MW) the output that would have gone to a simple printer goes instead over ethernet to a PC running the SDMS client and listening on a (virtual) COM port (up to 256 per PC). When the device does a beep it mean the COM port message was sent and also means the virtual printout is now uploaded to the SDMS server (each button press gets its own entry). In the SDMS client you can now navigate to the machine ID and see the readout with its timestamp. Information like who pressed the button simply isn't available. It is a simple device that only really knows the button was pressed and what the MW or pH was reported to be. Holding your phone/iPad in your hand at this moment helps as you can immediately see the MW/pH on your device or more likely a pair of readings to calculate a diff to know what the weight was before and after (for example) tipping out/in some reagent. Another option is rs232 to an ODROID/Raspberry Pi like system where it is the COM port (rs232 to USB) and it uploads to SDMS directly.
Daniel Fitzpatrick, (PhD Researcher, Ley Group, University of Cambridge and designer of ChemInventory: https://www.cheminventory.net) gave a very interesting talk entitled “Around the World Synthesis: Controlling Reactions in Cambridge through Tokyo”. Robotic synthesis is an increasingly popular area of research, monitoring these reactions from multiple devices is a very useful extension. Using his phone, he showed us data being gathered from instruments in the laboratory, whilst the lecture proceeded. Setting aside time for demos over the lunch break was a great idea, and Jonas Bostrom provided exciting hands on experience of chemistry virtual reality. In the discussions I had with people I heard about 1 new product idea generated at the meeting, 1 person who had a coding problem solved, 2 collaborations that were initiated, and a discussion about making an existing product open source

Last updated 8 September 2016.