C4SYS is a priority infrastructure project on the national roadmap, and currently builds on close collaboration between the Academy of Sciences (Center for Nanobiology and Structural Biology, Nove Hrady, Institute of Microbiology, Prague, Global Change Research Institute, Brno), the University of South Bohemia and Masaryk University, Brno.
C4SYS has the ambition to concentrate the knowledge potential in the field of systems biology in the Czech Republic and to connect the diverted systems biology research at the Academy of Sciences and various universities in the Czech Republic to the ESFRI infrastructure ISBE (Infrastructure for Systems Biology Europe), which aims to establish, and enable access to an integrated, distributed infrastructure of state-of-the-art facilities for systems biology across Europe.
The C4SYS infrastructure in accordance with ISBE aim offers academia and industry at the national level easy and rapid access to expertise in the broad field of systems biology.
(i) a spectrum of approaches to build and exploit predictive maps and models of complex biological systems that range from the molecular (genetic networks, snRNA, ion homeostathis, protein interaction networks etc) to the whole organism (yeast, bacteria, cynaobacteria, ticks) level,
(ii) the design of experimental approaches (bioreactors, two-photon polarization microscopy, ion fluxes, metagenomics, isotope fingerprinting, stopped-flow, rapid-quench flow, ITC and DSC microcalorimetry, microfluidics, CD-spectroscopy, robotic GC spectrometry, ChIP techniques) to efficiently collect data that are fit for modelling and
(iii) stewardship of relevant data, models and maps.
C4SYS services comprise
(b) support through contract activities
(c) development of standards and
(d) teaching and training.
Also, C4SYS will reach out to laymen that are interested in or need information about model-driven life sciences.
a. Stewardship and standardisation: To make the results of research projects re-usable and combinable/additive it is essential to link protocols, data, models and tools using efficient and well-accepted standards that are easy to implement and widely accepted by the life sciences communities. To make that possible, C4SYS will ensure that SB-related data, models and maps are preserved by creating established dedicated archives and repositories. These activities will be coordinated and harmonised at the European level.
b. Modelling and data integration: A wide range of modelling approaches are being used, ranging from the molecular to the physiological level. Choices depend on the system under investigation and the type of model that is needed specifies what data are required but will link biological systems to theory and models. Therefore, C4SYS will design workflows based on the user needs which encompasses experimental design, data acquisition, modelling, simulations and validation ensuring integration of diverse experimental data with literature data and theory.
c. Data generation: To make data sets useful for systems biology their acquisition must be planned and carried out in such manner that they are fit for incorporation in predictive models. Data generation services specified in Appendix II. are present in-house while others will be linked to the respective national technological core facilities or infrastructures. C4SYS will develop and implement community SOPs and other standards for the acquisition, handling and formats of data. These will be particularly valuable if data are generated outside C4SYS.
An important task of the data generation expertise of C4SYS is providing the availability of expertise, equipment and personnel for the acquisition of high-, medium- and low-throughput data sets that are tuned to model building as is planned in the experimental design phase. Also we will provide advice in the experimental design phase, about data storage and data analysis. Lastly C4SYS develops user-specified applications (methodology development) when appropriate. The portfolio based services will be revised during the operationg phase based on actual biological domains, requests and aquires from previous phase. There is a possibility that portfolio will mature and change a bit durign the operational phase. For example, the CMP-based services portfolio will focus on currently targeted biological domains (cyanobacteria and photosynthesis) and will generalize to other biological domains (signallig pathways, gene regulation) during the operating phase.