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laboratory informatics


the scaffold, and a list of substituents can also be obtained. Structure activity relationships can be developed by classifying the scaffold and substituents from within the SAR app. Te next stage is to use SAR to colour code the compounds for bioactivity. Tis can also be used as a dataset for modelling and prediction for new molecules. Te resulting table informs the user on potential molecules of interest. Once a decision has been made on a


compound, the SPRESI mobile app can be used to obtain synthetic information including a reaction mechanism for a potential analogue. Tis is accomplished using a search of the core structure which also produces similar potential structures that may be of interest, and the app will also open links to literature where these molecules appear. Te reaction mechanism can then be imported into Yield101 where the reagents can be customised, quantities added, and the expected yield calculated. Te resulting information can then be exported as a PDF, meaning it can be printed, emailed or just kept on the mobile device to be used directly in the lab. Te reaction can also be imported into MMDS where it can be emailed, exported, tweeted, shared or uploaded to repositories like Dropbox. Datasheets can be linked to dropbox using the MolSync app. Storing data in this way opens up more possibilities for secure or open sharing options. Ekins commented: ‘Alex has created the apps


from the ground up for chemistry. If he can do that for chemistry why can’t people do that for biology and for other areas?’


Where are apps going? However, there comes a point where the processing power of mobile devices cannot keep up with the demands of the computation. Tis is where the use of cloud services to provide computation can be implemented. Ekins sees a time when ‘heavyweight functionality takes place on remote servers which host the data and search algorithms.’ Tis opens up opportunities for more complex computation without the need for drastically improved processing power in mobile devices, as computation can be done remotely by cloud processing and the data sent to the mobile device. Ekins outlined how cloud computing could


be implemented: ‘If you create just a simple docking tool, that would enable you to take a set of compounds and dock them against a small set of target proteins, do that all on the cloud and return the results so that you can visualise them in an app.’ He also suggested a ‘pipelining’ tool similar to Accelrys’s Pipeline Pilot that could automate some of the processes when using mobile apps.


12 SCIENTIFIC COMPUTING WORLD Some of these ideas are only in the concept


stage, but innovative thinking can create some beneficial science apps: ‘You get inspiration in sort of interesting places and come up with some crazy ideas and see what really works. I’m hoping that going to SLAS will inspire other people to think about this.’ When Ekins attended a conference held


by the American Chemistry Society’s Green Chemistry Institute (ACS GCI), the idea for an app that would list environmentally friendly ‘green’ solvents came to him. He realised all the solvent information was freely available as a PDF but that not many people knew about it. It is now featured in the app.


from TB mobile, predict what the activities are likely to be, and then also come back with a prediction for targets that compound may hit as well’. At first these services will probably be limited to searching only one molecule at a time, but Ekins believes that ‘in many ways this could break new ground, show people what an app can do, it’s more than just being able to draw a molecule.’


Security concerns One of the biggest considerations for both vendors and customers in adopting mobile technology is the potential security risks from putting proprietary data into applications for mobile devices. Ekins explained: ‘Security has to be taken into account if you are going to build apps that take advantage of existing business tools.’ But this has been true for mobile devices


such as laptops for a long time and has not stopped the spread of web-based ELN services or other laboratory management soſtware. If similar security features are implemented and technology such as fingerprint scanning on iPhones becomes widespread, the barriers to mobile technology will be lowered, even for proprietary data. Educating people about the potential


EDUCATING PEOPLE ABOUT THE POTENTIAL BENEFITS OF USING MOBILE SCIENCE APPS CAN BE DIFFICULT


Apps against tuberculosis Te primary focus of Ekins’ scientific research is tuberculosis, for which he has created a science app called TB Mobile, which offers access to a database of bioinformatics data and structures of candidate drug molecules. Dr Ekins said: ‘I would like to create a whole


ecosystem of apps for TB and each one has a little functionality.’ He continued: ‘We have TB Mobile to look at targets but it would be useful if we could look at being able to come up with scaffold creations for TB, just give people an idea from known active compounds what might be interesting scaffolds to modify.’ He went on to ask: ‘Could we have an app


that listed the compounds that have been tested in vivo, or we could add models for in vivo, in vitro, and add targets?’ He explains that new features will be


introduced as web services and will be available in the next release of TB Mobile. ‘You will have a molecule of interest and you will go off and,


benefits of using mobile science apps can be difficult and some companies, especially in the pharmaceutical industry, have been slow to adopt the technology, Ekins said. ‘I don’t think that there is really a push from the pharma side to develop these apps. Tey are still very desktop-orientated, and I think they will be for a while unless someone can really disrupt it.’ He went on: ‘You’re paying a million dollars to be able to do this with established soſtware, why can’t you, for a much smaller fee, do this with mobile on the cloud?’ Te pharmaceutical industry is highly


regulated and large companies already have an expensive, existing infrastructure, both of which makes them slow to adopt new technology. However, Ekins believes there are other


factors: ‘Part of it is having strong informatics leadership; part of it is a generational thing – and this is something we always see with technologies. Ultimately there are going to be some people that are the leading edge of it, whether they are small companies or biotechs, and those are the disruptive ones.’ Ekins concluded: ‘Tey [science apps]


present a huge disruption to existing soſtware vendors. We [scientists] had to buy quite expensive soſtware; now we can get free soſtware on these devices, or very cheap soſtware that enable us to do the same kind of things’.


@scwmagazine l www.scientific-computing.com


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