HotTopics: Bioinformatics challenges for Synthetic Biology


October 15, 2012, SURF Utrecht

Synthetic Biology is: (i) the design and construction of new biological parts, devices, and systems, and (ii) the re-design of existing, natural biological systems for useful purposes. It is also applying engineering to biology. This means it applies the ‘design – build – test’ engineering cycle to work on existing and novel biological applications in food, feed, pharma, fuels, but also biobased materials, sensors and novel applications.

Bioinformatics plays an essential role in the ‘design’ phase, and contributes by: knowledge-based systems, understanding of genome structures and its elements, computer-aided design platforms, biobricks-based construction. In the ‘test’ or analysis phase there is a need to handle novel types of data in increasingly large amounts, like (re)sequencing data and all kinds of omics platforms. An to integrate all, models of metabolism, regulation, cellular functions and more – often referred to by Systems Biology.

During this HotTopics meeting we will discuss a number of bioinformatics challenges that arise from synthetic biology:

  • trends in synthetic biology – driven by gene synthesis and genome sequencing
  • to mine (meta)genomes for interesting genes and pathways, refactoring such systems to function in different hosts, known as metabolic engineering
  • to design and create entirely new functionality within and between cells
  • combinatorial design of multi-domain proteins for novel antibiotics
  • computer-aided design platform and biobricks for microbial strain engineering

The aim is to identify key issues and potential avenues of research that arise as we move from understanding biology to designing it.

Keywords: synthetic biology, bioinformatics, microbial genomics, iGEM

Programme October 15th

12:30 – 12:35 Welcome – Marc van Driel
12:35 – 13:10 Lunch
13:10 – 14:00 Synthetic Biology: re-programming cellular behaviour
Vitor dos Santos, WUR Wageningen
14:00 – 14:50 Computer-aided design platform for microbial strain engineering
Hans Roubos, DSM
14:50 – 15:05 3DM protein engineering superfamily systems and smart mutant library design
Henk-Jan Joosten, BioProdict
15:05 – 15:15 Tea break
15:15 – 16:05 Optimizing genes and pathways
Dick de Ridder, TUDelft
16:05 – 16:55 Computational approaches for the design and implementation
of biosynthetic pathways in microbial cell factories
Eriko Takano, Marnix Medema, University of Groningen
16:55 – 17:15 General discussion & Closing


SURFfoundation, Hojel City Center, gebouw D (5e verdieping), Graadt van Roggenweg 340, 3531 AH Utrecht, (max. 25 participants) – Website/route

About HotTopics

NBIC HotTopics are a new series of NBIC meetings committed to bringing scientists together to discuss the concepts and methods on a hot topic in their research field. It should provide a platform to keep in touch with peers in the field and foster sharing of new insights, applications and collaborations. Therefore, the aim of the meeting is not to present the latest results of your own work, but rather to identify new trends and breakthroughs in the field in general.

Four scientists will give a 20 minute lecture followed by 40 minutes of discussion on the important computational concepts:

  • What does a method try to accomplish?
  • What assumptions were made?
  • How does this method compare to similar ones?
  • What are the strengths, weaknesses and pitfalls?
  • Can we apply it in other areas?
  • What are the limitations and challenges for new applications and developments?

Flip over, beamer and laptop are available.

Organising committee

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