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informatics for biofuels


along with some key terms to make its old paper notebooks as searchable as possible. ‘It’s not going to be as good as inputting the data directly, but we’re going to go back and input those paper records as well,’ Plack says.


Intellectual property Biofuel R&D can differ drastically from company to company in terms of the organisms and processes involved and there is an emphasis on the informatics packages to protect intellectual property. ‘It’s a very IP-driven business,’ says Dr Othmar Pfannes, CEO of Genedata, a provider of software systems for R&D processes in the life sciences sector. ‘And, new IP is continually generated, which must be protected by the companies developing the IP. This requires sophisticated IT solutions to manage and interpret the biological data resulting from R&D activities.’ Genedata has developed its Selector


platform to manage all biological data required for biofuels R&D – sequence data, gene expression data, metabolic pathway data, mass spectrometry data, and others. Plack at POET agrees: ‘Intellectual


property is extremely important to us. We have several patents available to POET and several that are pending, so it’s very important to our business to protect that intellectual property. With the ELN, you’re getting everything date and time stamped every time data is entered.’


Genedata Selector has been developed for managing and analysing genome sequence and related biological data in industrial biotechnology and biofuels. It includes functionality specifically relevant for microbes and plants


Novel organisms The research work surrounding biofuels has expanded to include novel plants and other organisms that don’t compete with food production. One of Accelrys’ customers, for example, is looking at transgenic mutations in algae to gain increased expression of enzymes that generate more oil and, more importantly, greater quantities of the right kind of oil that needs less processing. This sort of experimentation, and the


biofuel production process in general, is more akin to the fermentation and distillation processes found in the beverage


THE RESEARCH WORK SURROUNDING BIOFUELS HAS EXPANDED


TO INCLUDE NOVEL PLANTS AND OTHER ORGANISMS THAT DON’T COMPETE WITH FOOD PRODUCTION


Furthermore, she says that the data gets


witnessed a lot quicker using the Accelrys ELN: ‘With the paper system, we tried to do monthly lab notebook witnessing, whereas electronically it can be done the next day. You don’t have to get everybody in the same room; you can submit the data and the appropriate researcher can witness it from their ELN immediately.’ The Genedata Selector system covers a


lot of different aspects of R&D, integrating an unlimited amount of sequence and other biological data. It combines proprietary with public domain data, which, according to Dr Pfannes, is specifically important for biofuels R&D work. ‘There is a lot of research happening in the public domain,’ he says. ‘Companies want to take advantage of this research by integrating this data with their corporate database and their proprietary data. Selector provides engines that enable the import and integration of public data.’


10 SCIENTIFIC COMPUTING WORLD


industry, than those employed in classical petroleum production. Colin Thurston, director of product strategy, process industries at Thermo Fisher Scientific, notes a number of differences between the two areas: Biofuels tend to be produced in a batch process, he says, rather than the continuous flow found in petrochemical plants. They also have significantly fewer contaminants to be removed during the process than crude oil, such as sulphur, or methane. In addition, the storage vessels for biofuels require regular monitoring for contamination and the vessels need regular cleaning. ‘All of these attributes mean that


informatics solutions designed specifically for petroleum production are not necessarily a good fit for biofuels,’ Thurston continues. ‘Systems that can support multiple industry disciplines and flexible workflows are much better suited.’


Thermo Scientific provides its LIMS for


biofuels customers to support and manage a changing set of testing processes. Thurston adds that post production testing is often a requirement of biofuels production: ‘Products are susceptible to environmental contamination, such as bacterial growth in biodiesel or water content in bioethanol (bioethanol is strongly deliquescent), which can damage the engines in which these fuels may ultimately be used.’ The informatics systems in general have to


be flexible and adaptable to manage different workflows. John Gabathuler, a director at LIMS provider LabWare, says: ‘From a discussion recently with one of our UK customers involved in bioethanol production, they have found that LabWare LIMS and its configurability is a real asset when it came to integrating bioethanol into their quality environment.’ LabWare LIMS was used to configure


process control and manage remote depot storage and electronic certification at the company. ‘The thing that’s interesting about the biofuels sector is that fundamental questions are being asked about how to create biofuels from other biological entities,’ comments Ted Pawela, senior director product marketing at Accelrys. ‘Researchers are asking fundamental questions about as yet unexplored biological entities and how these can be used to generate biofuels.’ Dominic John, product marketing director


at Accelrys, adds: ‘To date, ELNs have been adopted primarily early on in biofuels research. What we’re likely to see in the future – and this if from experience in the pharmaceutical sector – is the platform to start to be used further downstream in product development and process scale-up. This is what happened with the typical lifecycle of ELNs in pharma and biotech.’


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