BioSCENTer @ iGEM 2013BioSCENTer - Research objectives
Build the tetrahedron
We view BioSCENTer as a tetrahedron, the edges of which are the 4 clusters. First of all, clusters themselves have to be consolidated, before we can start building out the edges, in the form of bilateral research topics and projects. True interdisciplinarity and multiscale projects will cover the facets of the tetrahedron. Of course, research projects will be set up with external partners too.
Activate cross-disciplinary fertilization
We briefly describe some potential cross-challenges between the 4 clusters, that might serve as an inspiration for further research topics, to be consolidated in research proposals. The main research lines of each cluster can be found below in the detailed description of the clusters.
Cluster Bioinformatics and Systems Biology
| Supply | Demand | |
|---|---|---|
| Bioi & Syst.Biol. | ||
| Virtual Life | Pathway analysis top-down | Modeling biofilm Integrate flux analysis in transcriptional networks |
| BioMint | Pathway analysis Preprocessing/analysis techniques | High resolution microscopy for pathway analysis Protein-DNA interaction data Metabolomics data |
| iCEB | Between species pathway comparison | Cases for pathway comparison |
Cluster Virtual Life
| Supply | Demand | |
|---|---|---|
| Bioi & Syst.Biol. | Advance algorithms for identification and parameter estimation of metabolic pathway models Integration of omics data Relation between regulatory pathways at different organizational levels | Mechanistic metabolic pathway models Bioreactor and fermentation facilities |
| Virtual Life | ||
| BioMint | Mechanistic metabolic pathway models Microtomography Multiscale modeling techniques Bioreactor and fermentation facilities | High-throughput metabolomics and proteomics facilities High resolution microscopy and optical techniques |
| iCEB | Population dynamic models In silico simulation of evolutionary and environmental stress adaptations | Host-pathogen interactions |
Cluster Biomint
| Supply | Demand | |
|---|---|---|
| Bioi & Syst.Biol. | Heterogenous data sets Data on protein-protein, protein-DNA, protein-ligand interactions | Integration of omics data Network inference Evolutionary distance prediction Modeling cellular behavior |
| Virtual Life | Data on cell-cell communication in multicellular organisms | Mathematical models of microbial dynamics Bioreactor experiment design for microbial dynamics |
| BioMint | ||
| iCEB | Host-pathogen interaction models | Cross-species regulator and enzyme comparison |
Cluster iCEB
| Supply | Demand | |
|---|---|---|
| Bioi & Syst.Biol. | Phylogenetic footprinting | |
| Virtual Life | Population dynamics Biodiversity | |
| BioMint | ||
| iCEB |
Integrate multiscale research projects
One of the important research objectives, is that we would formulate research topics, the coverage of which ‘spirals’ over different order or magnitudes in space and time (‘multiscale’). Indeed, an as of yet largely unexplored
Create a stimulating and inspiring research environment for new ideas and challenges
BioSCENTer will also be the platform to find new research opportunities. As an example, take synthetic biology. Synthetic biology is the creation of novel (i.e. non-existing in the natural world) biological functions and tools by modifying and integrating well-characterized components ('bio-parts') into higher-order systems. This requires advanced mathematical modeling and simulation tools, wet-lab experiments and lots of systems biology know how. The idea is to design biological systems from a list of a priori defined 'macroscopic' specifications, just like the design of microelectronics systems. The key challenge is in the design engineering of the system, dealing with the several layers of complexity so that the resulting biological organisms functionally implements the specifications. While systems biology is largely devoted to (detailed multiscale) analysis of biological systems, synthetic biology concentrates on the design thereof, in a hierarchical, functional component based methodology. There is a wealth of potential applications in pharmaceuticals, health, environment and energy, among others. To enable synthetic biology in practice, we need to strive for four basic objectives:
- 1. Scalable manufacturing (component standardization, cost-effectiveness, reproducibility, fault tolerant);
- 2. A scalable hierarchical design methodology and supporting basis libraries of components ('bioparts', e.g. 'MIT biobricks').
- 3. Reliable and fast computational biology methods for 3D simulation over multi-time and space scales (e.g. Berkeley's BioSpice).
- 4. Wet lab facilities to produce 'biological prototypes'.
All of these ingredients are in one way or another available at BioSCENTer, platform in which we could decide to define a synthetic biology road map.
Leverage platform for funding
The creation of interdisciplinary opportunities within BioSCENTer, must also be reflected in the research funding we try to acquire. BioSCENTer must function as a platform where joined proposals can be formulated, where we attempt to generate co-publications, and by sharing best practices, increase the opportunities and effectiveness of our research funding.
BioSCENTer also seems the right platform for international benchmarking with similar initiatives and institutes elsewhere in the world.
