Interdisciplinary cooperation, interaction with the private sector, education and training of young scientists and networking – these are the major axes on which the work of SystemsX.ch is based. SystemsX.ch is currently the biggest research initiative in Switzerland to provide financial support and technologies in the field of systems biology research. It is a consortium of twelve Swiss research institutions and universities, but also works with non-Swiss institutions, including the Baden-Württemberg-based company KNIME GmbH, which was established by Professor Michael Berthold from Konstanz. The initiative is interested in expanding its cooperation with other life sciences companies and universities.
SystemsX.ch carries out research in an area that emerged at the end of the 20th century: systems biology. The approach is aimed at collecting data, deriving information on the interactions within an organism and making predictions on potential processes. One example is the sequencing of entire genomes, which has led to a huge amount of data that have not yet been satisfactorily analysed. “The letters of the DNA can be compared to a book written in a known alphabet, but an unknown language,” said Ruedi Aebersold, Professor of Systems Biology at the ETH in Zurich and Chairman of the SystemX.ch Scientific Executive Board, commenting on the ambitious project, whose goal is to learn this language of life and is the reason why SystemsX.ch is particularly interested in interdisciplinary cooperation. “Only around 50% of all scientists involved in the research projects are biologists; the others are engineers, physicists, chemists, mathematicians, computer scientists and medical scientists,” said Jens Selige, scientific coordinator at SystemsX.ch.
The Swiss Initiative in Systems Biology brings together the two Swiss Federal Institutes of Technology (the ETH - Eidgenössische Hochschule - in Zurich, the EPFL - École Polytechnique Fédérale de Lausanne - in Lausanne), seven universities and three Swiss research institutes. More than 300 research groups from academia and industry involving more than 1,000 scientists are working together on 100 projects. The Swiss government has provided a total of 120 million Swiss Francs (CHF) for the projects between 2008 and 2012, with strict requirements attached: funding is based on the “matching funds” principle, which means that an institution only receives funding if it provides a matching amount from its own resources.
Funding is given to different kinds of research projects: 75% is used for so-called “RTD” (research, technology, development) projects, comprising fourteen large integrated projects from different scientific areas. SystemsX.ch also provides funding for interdisciplinary doctoral studies (IPhD) of young scientists. With its interdisciplinary pilot projects (IPP), the initiative is exploring new paths: one-year funding is being provided to ambitious seed and high-risk systems biology projects which might not find funding through traditional channels.
The initiative also attaches great importance to involving companies from both Switzerland and abroad. “It is our declared objective to encourage industry interactions with the initiative’s academic partners and hence contribute to the transfer of technologies between public research and industry,” Selige pointed out. “We are particularly interested in collaborating with universities and companies in Baden-Württemberg, which is our direct neighbour,” Selige added. SystemsX.ch’s transfer projects, which are funded with up to 300,000 CHF for two to three years, are specifically aimed at promoting cooperation between universities and the private sector. “While the annual calls for new projects are specifically addressed at academic research groups in Switzerland, the transfer projects can also involve industrial partners from abroad,” Selige explained.
Such cooperations can take several different forms, including financial support for researchers for participating in research conferences or for working in cooperative research projects. SystemsX.ch was involved in several ways at the “International Conference on the Systems Biology of Human Disease”, held in Heidelberg in May 2012: it was a conference sponsor and also provided speakers. “Our presence at this meeting was not only another important step towards working with international researchers on the scientific level, it was also an important step on the organisational level,” Selige concluded.
SystemsX.ch has plans to continue the existing cooperation between its SyBIT (SystemsBiologyIT) platform, which supports all partners involved in the fields of bioinformatics, analysis software and data management, and the Konstanz-based company KNIME GmbH (www.knime.org). The data mining software KNIME (Konstanz Information Miner), which was developed by Michael Berthold, Professor of Informatics at the University of Konstanz, enables the analysis of huge amounts of data and the identification of new patterns. The cooperation between SyBIT and KNIME GmbH is already bearing fruit: the two partners will jointly design the programme of the 6-day SystemsX.ch Autumn School, which will be held in Engelberg from October 8th to 12th 2012. Training will be provided for students, postdocs and scientists engaged in systems biology research in IT tools and data management.
Projects from a broad range of different areas – cell biology, metabolic physiology, neurobiology and behavioural economics – have already been funded by SystemsX.ch. One project is focused on the investigation of the development of fruitfly wings with the goal to obtain detailed insights into organ development, another project deals with the numerous interactions within the brain with the goal to gain a better understanding of decision processes, and there are many others.
The research carried out by some of the IPPs is a good preview of the potential of systems biology research: researchers from the EPFL in Lausanne are working on the development of a technology that will enable them to grow body tissue in the laboratory. The SystemsX.ch researchers hope that this technology will help them contribute to organ regeneration, and thus help counteract the scarcity of donated organs. “However, this is still a pipe dream, and it will take several decades, rather than just a few years, before our dream comes true,” admitted Matthias Lütolf, professor at the Institute of Bioengineering at the EPFL in Lausanne.
The submission deadline for proposals of the ongoing 6th call is 26th August 2012. The 6th call primarily addresses research groups of SystemsX.ch partner institutions; however, applicants can also work together with partners from Switzerland and abroad (and hence also Baden-Württemberg) in the proposed project. Systems biology research not only requires interdisciplinary cooperation, it also requires cooperation between research institutions in different countries.
Jens Selige, Dr. rer. nat.
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