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A Foundation for Synthetic Biology in Europe

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EMERGENCE (FP6) cooperates intimately with TARPOL (FP7) on all issues of Synthetic Biology. For more information on TARPOL click here

To all users of  Synthetic Biology:

Do you want to organize a SB-relevant workshop and would like to get support from EMERGENCE, then click here.

Contact  Imprint

Workpackages

1. General networking activities
WP leader: HZI (Vitor Martins dos Santos)

The activities in this WP aim at: a) establishing a networking platform for current and future synthetic biology projects bundling the diverse competencies and concertedly working towards the translation of this joint know-how into scientific, technological and economical developments; b) setting a European-wide, cross-disciplinary framework for discussion on the possibilities, needs, boundaries, implications and advancements of synthetic biology. This framework will transcend its European-wide nature by promoting relations between European and non-European researchers. A special emphasis will be put on fostering focused interactions with top Mid- and Far-East research institutions; and c) maintaining a communication channel, jointly with the four running SSAs (SYNBIOL, SYNBIOCOMM, SYNBIOSAFE, TESSY) on synthetic biology, pertaining societal (e.g. risk, safety, ethics), dissemination (e.g. public awareness, perception, etc.) and funding (synthetic biology in the context of national funding agencies, establishing a roadmap) issues.

2. Attracting talents to Synthetic Biology in Europe
WP leader: ETHZ (Sven Panke)
Other partners: EP (Alfonso Jaramillo), UCAM (Jim Haseloff)

WP2 addresses educational aspects in Synthetic Biology. We have at the moment three core topics:

  1. Summer schools: The Emergence team has committed to organizing 2 summer schools to distribute cutting edge knowledge and technology to the community. We are currently defining place, topics, and time. Any suggestions here are highly appreciated, please contact Sven Panke (leader WP2).
  2. Evaluating the case for a European Master in Synthetic Biology: Synthetic Biology is a challenging discipline on the interface of biology and engineering. It requires a combination of skills that are typically not available in students from one of the “standard” master programs. Therefore, we are evaluating the case to unit several schools in putting together a Synthetic Biology curriculum.
  3. Web resource for educational material: New students and workers are coming into the field from very diverse areas, and need to come to grips with the details of unfamiliar biological systems, engineering tools and computer sciences. There is a demand for specialized coverage of this new field, including educational and review materials. In cooperation with the Institute of Engineering and Technology (http://www.theiet.org), we plan to construct an integrated web resource for educational material. The web resource will include downloadable teaching materials, video presentations, online reviews and technical articles.

3. A European IT infrastructure for Synthetic Biology
WP leader: CNIO (Alfonso Valencia)
Other partners: ETHZ (Jörg Stelling), CRG (Luis Serrano), HZI (Vitor Martins dos Santos)

The key element for an IT infrastructure in synthetic biology consists of the 'Registry of Standard Biological Parts' hosted at MIT. The registry provides a database of composable parts, devices and systems, including the specification of corresponding DNA sequences, functional annotations, and - in too few cases - quantitative characterizations of their functions.
However, in terms of integrated workflows for synthetic biology, several critical elements are missing: (i) tools for automatic information integration, e.g. from literature and existing bioinformatics databases, (ii) tools for function prediction at the parts and systems level, and (iii) methods and tools for model-based systems design, analysis and optimization.
The objective of this work-package is hence to provide all these critical elements for an expanded IT infrastructure for synthetic biology aiming at integrated workflows as they are established, for example, in electrical engineering and the corresponding industries. In close collaboration with the groups at MIT, we will provide a European mirror of the registry and augment it with a set of computational tools for rational systems design. This will involve (i) integration of available software tools in bioinformatics and in biocircuit modeling and simulation, and (ii) development and implementation of novel methods for function prediction and rational systems design. For a proof-of-concept study, this CA (through collaboration of WP3 and WP4) will focus on in silico design tasks with transcriptional regulators and genetic circuits built thereof. The methods and tools, however, will be adaptable to other circuits and their elements, in particular, because the efforts for developing the IT infrastructure will be closely coordinated with standardization tasks as described in WP4.

4. Towards a consensus language for synthetic biology: Conceptual and hermeneutical tools for formatting and categorization of transcriptional working states
WP Leader: CSIC (V. de Lorenzo)
Other partners: UCL (Nicolas Szita)

Description and re-design of biological functions, in particular those involving regulatory actions brought about by promoters and transcription factors is currently afflicted by the dearth of adequate conceptual, linguistic and numerical tools to represent biological transactions in an absolute, unambiguous form. This is due not only to the current diversity of methods for assessing promoter strength e.g. using reporter systems, but also caused by the vagueness of the language employed by experimentalists to describe to what are otherwise intrinsically quantitative events executed by molecular devices. While the gene expression route from the DNA sequence to the cognate biological activity encompasses a multi-step development with multiple regulatory checks, it is possible to disclose or de-compress such a complex progression in discrete sub-processes. These can be separately formatted or, for the sake of simplicity, have some of them fixed in a constant working state, so we can draw a linear relationship between promoter strength and gene expression. Under this simplification, the core of the standardization-by-formatting effort is the absolute description of promoter output under the effect of the core components, physico-chemical conditions and small molecules. This, as argued above, will be the essence for the standardization of key components in synthetic genetic circuits.
Once this definition process has been finished, the stage is set for the application of the now vigorous concepts to the task of engineering gene circuits to desired behavior. This requires three sets of information: [i] quantitative information on the behavior of existing gene regulatory systems to extract the values of the parameters that characterize the various interactions (such as DNA/protein interactions, protein/protein interactions, etc); [ii] a method to evaluate the suitability of the existing information and to design experiments to obtain this information in the future; and [iii] information on how to manipulate the existing system into the desired behavior by changing a suitable set of the core interactions identified before.

5. Building the Academia-Industry Interface (including Intellectual Property Rights)
WP-leader: Royal DSM (Markus Wyss)
Other partners: Geneart (Ralf Wagner), ETHZ (Sven Panke)

Adoption by industry of the emerging scientific discipline of synthetic biology depends on three main factors: (i) that the concepts and tools developed by synthetic biology research programs help to address major bottlenecks in industrial R&D, that (ii) key players in industrial R&D are familiarized, trained and convinced by the opportunities and achievements of synthetic biology, and that (iii) a competitive environment is created for start-up companies in this field. Therefore, proper management of the academia-industry interface is a critical success factor for maximal return-on-invest in this field. To address these topics, several lines of activities are planned:

  1. Two workshops among major European industries to define the primary needs and interests of industry in synthetic biology.
  2. Linked to major industry-relevant scientific conferences in Europe (e.g., Metabolic Engineering VI in October 2006), workshops in synthetic biology will be organized to familiarize and train industry representatives in the concepts and tools of synthetic biology.
  3. Participation of industry representatives in student workshops and academic conferences in the field of synthetic biology will help to improve understanding of the industrial needs and will help to spot talents who may help to (i) adopt and develop synthetic biology in industry, and (ii) prevent drain of the still few talents in this emerging discipline to competing fields which, in turn, would slow development of the synthetic biology competence in Europe.
  4. For securing the competitiveness of the European industry in synthetic biology, building an effective IP position that rewards industrial research and innovation efforts but does not stifle broad exploitation will be crucial, as the latter point is intrinsic to the concept of Synthetic Biology.
  5. The activities in this WP (e.g., IP landscape), together with concepts developed in the other WPs as well as in other European synthetic biology projects will help to prioritize most attractive business areas for start-ups and SMEs. Depending on the evaluations and progress in this CA, a workshop will be held on either the opportunities for start-ups in the field of synthetic biology, or with potential investors to evaluate their priorities and interests in synthetic biology.

6. Project management
WP leader: ETHZ (Sven Panke, Frauke Greve)

Project Management has the objective to coordinate the overall technological progress, administration and finances of the project, to communicate with the EU commission and to coordinate and supervise the multi-disciplinary team of 10 European partners to realize the deliverables and milestones according to the Work Plan.
The second objective is to establish a framework for the efficient dissemination of the results of EMERGENCE, to generate wide visibility for the project and its results, and to establish the conditions and network for the larger European Synthetic Biology community to prosper
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