Integrated science opens the road to informatics

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Annabel Sedgwick describes how Applied Biosystems is putting researchers firmly in the driving seat in managing their scientific projects

Bioinformatics is a new science that is growing fast to meet the changing needs of the pharmaceutical industry and laboratories as a whole. Solutions exist or can be created for every researcher and every laboratory, no matter how individual the situation and despite the enormous amounts of various types of data from different sources, different types and different ages of technology.

As biology and related disciplines begin to complement their traditional laboratory research with information-based science, new opportunities exist for technology providers to improve, speed up and lower the cost of life-science discovery and development programmes. A good example of this would be combining genomic, proteomic, metabolic, and other biological information with validated assays at all stages of the drug discovery and development processes. This combination of techniques will help speed up the development of safer, more effective and better-targeted treatments for disease.

Applied Biosystems is in a unique position in that it not only provides instruments and reagents, but also software and expertise in many areas of life science research. As a logical next step, it is concentrating on a new strategy of Integrated Science - iScience - which centres on customer need and the direction of the scientific community as a whole. Bioinformatics will naturally form a large part of this integrated thinking.

Applied Biosystems' business is focused on the following markets: basic research; commercial research (pharmaceutical and biotechnology); standardised testing (including forensic human identification); HIV genotyping; and food testing. The company has an installed base of more than 50,000 instruments in approximately 100 countries.

Basic research includes work at university, government, and other non-profit institutions and represents about half the company's revenue. An additional one third is from pharmaceutical and biotechnology companies that are applying the company's products to molecular medicine in order to discover new drugs more effectively. The remaining revenues come from standardised tests for customers who place priority on precise results from a high volume of automated tests.

Optimising throughput and improving quality are critical success factors for all these laboratories. Applied Biosystems has developed laboratory software flexible enough to meet researchers' needs and solve their problems, whether in a small laboratory or a complex, multi-site research programme.

The company's Informatics Software and Services combine software products and professional services to integrate and automate the laboratory. Its systems track and manage samples, robots, instruments, and data analysis in an integrated manner that will help to increase laboratory throughput and improve the overall quality of results. Implementations based on its core LIMS software are in use in more than 1000 laboratories worldwide, for applications as wide-ranging as high-throughput genotyping, proteomics, gene expression, high-throughput sequencing, pre-clinical testing and forensics.

Integrated science in action
Figure 1 (above) shows how bioinformatics can successfully combine all the different elements relating to laboratory research in a logical way, using the analogy of a car dashboard. It begins when a scientist embarking on research, for example on a certain disease, consults a knowledge database, such as the Celera Discovery System (CDS), to find out information already known about the disease. Resources like the CDS pull together and regularly update information from proprietary, public and third-party databases in one convenient location. They allow, for example, scientists performing genotyping or proteomic experiments to add annotation information quickly, without manually accessing many individual databases or requesting internal bioinformatics assistance.

Having found a potential target, the researcher may use the direct link to the Applied Biosystems on-line store to order validated assays using the Assays-on-Demand product. The advantage of ready-made assays is that they save laboratories time. Rather than having to create them, the assays come in a ready-to-use format, fully validated and checked. There are also a number of direct links to different product areas of Applied Biosystems and partner companies, where researchers can find instruments, reagents, services and anything else they might need, all in one central place.

It is at this stage that data management comes into play, when the experiments are done and the data needs to be installed and properly managed. Results (at the bottom of the circle) create more knowledge about this particular disease and a researcher can then go back to query the knowledge database to validate what has been found, or start again with the next logical target.

This is an example of integration working - coordinating a knowledge database with the assays, the data management, the instrument analysis and research results, and then either repeating the cycle using comparison data or moving onto the next step.

When you want to integrate data, the first step is to make it clear what you want to integrate and why. Going back to the car dashboard analogy, sitting at the wheel you have control of lots of different technologies in front of you. If you push the pedal, the combustion engine goes faster. If you press a button, you turn on the windscreen wiper. Another pedal activates the brakes and another button turns on the radio. You might want to integrate your windscreen wiper with a rain sensor and your combustion engine with cruise control, but this integration is very directed and it would be totally impractical to integrate every component with others. An effective data management solution will allow you to drive the experiment according to the conditions prevailing at the time. Information and controls are pre-selected and a central controlling influence is present throughout the time you are occupied in the specific research required.

Figure 2 (below) shows how a LIMS can make a difference because at every stage the data is being entered into the LIMS database.

 Integrated proteomics LIMS workflow. Click on the image to see a larger version in a new window

Direct links to a knowledge database may be available and integrated in the overall workflow. Due to the integration, there is no need to document all stages manually, allowing researchers to do more laboratory work and less administrative paperwork.

This brings another understanding of the idea of integration. All the data is stored in a centralised repository and is available to anyone with the authorisation to access it, at any time and from any place connected to the network. For projects that are shared between different establishments and even different countries, this kind of system is essential. Consortiums like this are now quite common, where each arm is responsible for a different part of the project but all the information is entered into and is accessible from the same database. Packages such as those from Applied Biosystems have additional features especially geared to this kind of environment, with different levels of secure access and the ability to work in multiple languages simultaneously.

The key point is that integration for integration's sake is not the answer. It takes thorough knowledge - and years of experience of the life science industry - to know exactly when and how integration will work to the best advantage. Pulling together the knowledge and experience of all the component parts of the Applied Biosystems organisation will continue to give customers bioinformatics solutions that work.