Be smart – be open: Invest in Innovation, not in routine
Modern drug development is expensive, tedious and very data intensive. One of the most challenging issues is the interoperability of tools and data.
By Thomas Karopka, project manager, BioCon Valley, work group chair at the European Federation of Medical Informatics
Modern drug development is expensive, tedious and very data intensive. With the invent of high throughput technologies and the availability of huge amounts of data over the internet drug development has turned from a lab-dominant to a data-dominant science. One of the most challenging issues is the interoperability of tools and data. Due to the many different sources and tools it is difficult to analyse and compare data. Another pressing demand is the development of new algorithms to analyze and mine the ever increasing amount of data and the linkage of genotype and phenotype data.
The bioinformatics research community has started very early to join forces and develop algorithms in collaboration and share data and tools under a free and open source model. Free/Libre and Open source software (FLOSS) is software that is shared under a that grants the user thr right to study, modify and redistribute the software. Additionally many data sources are available under an open access policy which is actually a prerequisite for effective and efficient research. This has led to a strong open source community in bioinformatics. Already in 2000 an annual conference, the Bioinformatics Open Source Conference (BOSC), was founded and established as a global community for open source in bioinformatics. One of the main advantages of open source is that it allows an evolutionary development process. Developers can focus on the innovative part instead of reinventing the wheel by implementing 80-90% of a software system that are similar in every system.
Being initially driven by researchers motivated to accelerate research in their field the open source philosophy has been adopted also by industry and big pharma recently. One recent example is the tranSMART Foundation which aims at establishing and sustaining an open platform for translational biomedical research based on open source and open data. Translational medicine or translational science is a discipline within biomedical and public health research that aims to improve the health of individuals and the community by “translating” findings into diagnostic tools, medicines, procedures, policies and education. Translational medicine is a highly-collaborative, multi-disciplinary approach and therefore optimally suited for an open approach.
The origins of tranSMART go back to a data management system developed by scientists at Johnson & Johnson and Recombinant Data Corporation. The next generation of tranSMART will be developed in collaboration with developers and users of eTRIKSand TraIT – two informatics/analytics knowledge management systems currently under development and supported by major European translational research initiatives. In bioinformatics and life sciences FLOSS is mainly used in a research context. However, in health care delivery FLOSS has already been used from the very beginning of health informatics development and has gained some attraction over the recent decade. The databaseMedFLOSS lists more than 300 software systems that are available under a FLOSS license. The database also contains a list of references as well as information of professional support providers. A recent meta-review by Karopka et.al. gives a good overview of the development in the field of health care in the last decade.
See also:
Free/Libre Open Source Software in Health Care: A Review
Open Bioinformatics Foundation
Wikipedia list of open source tools in bioinformatics
Open source tools and toolkits for bioinformatics: significance, and where are we?
