Applications of Bioinformatics for Synthetic Biology






Synthetic Biology is a discipline that embraces the emerging ability to design and synthesize novel DNA constructs, new genomes and biomimetic systems. Biomimetic systems are human-made processes, substances, devices, or systems that imitate nature. Therefore, we can define synthetic biology as an emerging field which aspire the usage of synthetic technology in order to create novel molecular machines for the good of human beings and bring insight to current biological questions by providing new approaches and methodologies. In addition, synthetic biology contributes to the accumulation of molecular data. Since 2004, Registry of Standard Biological Parts ((a.k.a Parts Registry) is the only source for the standardized biobricks, which currently harbors 700 available and 2000 defined parts. Annual iGEM competitions continue to help for the accumulation of new biobricks each year. Due to the exponential growth observed in the number of biobricks, application of bioinformatics techniques is urgently needed for the organization, analysis and association of the data in the Registry of Standard Biological Parts and for the prediction of functional device candidates without using wet laboratory.


In this roundtable a brief introduction to synthetic biology will be given and research areas where bioinformatics applications can be applied in synthetic biology will be presented. Following the introduction to the field, discussions on the current topics of synthetic biology research and how bioinformatics can be utilized to address these issues will be conducted. Major discussion topics will be on how bioinformatics can be utilized to aid in organization and presentation of the Registry of Standard Biological Parts, and solutions that can be offered regarding safety, ethics, and ownership in the emerging field of synthetic biology. Although, synthetic biology has scientific and industrial potential, it is hard to foresee and predict potential misuses and dangers. We will be also discussing potential threats of products and publication of these through web-based databases.


Discussions will be organized in to two major topics. Firstly, current applications of bioinformatics in synthetic biology will be discussed. The major aim of the first session is to bring different disciplines together and create an interdisciplinary environment for information exchange and inspiration. Secondly, possible open questions and major discussion subtopics which regard safety and security, ownership and ethics will be included and potential solutions for major problems by using bioinformatics will be discussed as well.


A.  Introduction to the state of the art in Synthetic Biology and current issues of the field.

What are the major literature resources for Synthetic Biology related research? Existing Bioinformatics tools and techniques used in Synthetic Biology.

Synthetic Biology Sector in Turkish Industry

B.  Discussion Session “Applications of Bioinformatics for Synthetic Biology”

1.      How would the application of Bioinformatics methods enhance Synthetic Biology in general ?

2.      Specific areas of synthetic biology new bioinformatics applications are needed to be developed?

a.       selection and design of BioBrick Parts or Devices specific to problem at hand

b.      characterization of BioBrick Parts or Devices

c.       the analysis, modeling, and simulation of BioBrick Parts or Devices

d.      the sharing of BioBrick Parts or Devices as information via the internet.

3.      Human Practice issues of Synthetic Biology that can be addressed  and solutions can be offered  by the design and development of new bioinformatics applications. (ownership, sharing, and innovation, safety, security and ethics and others)

4.      Language of choice for developing software geared for Synthetic Biology. SBML, SBOL and other choices ?

5.      As bioinformaticians which other disciplines we need to collaborate while addressing issues for synthetic biology, such as Biological Sciences, Engineering, and Statistics.

About the Roundtable Organizers


This round table will be presented and moderated by the METU-BIN Team, who will be representing METU at iGEM 2011 in Software Category on November 2011 (


Currently, METU-BIN team has 12 members; Ogün Adebali (METU GENE), İsmail Aslaner (HU, EE), Güngör Budak (METU, BIO), Gökhan Ersoy (METU, BIN), Sassan HashemiKhabir (METU, CENG), Saygın Karaaslan (METU BIO), Gökçe Oğuz (METU BIN), İlim Uğur (METU CENG), Yener Tuncel (METU BIN) , Burcu Yaldız (METU, BIN), Kerem Yıldız (METU, MIN) and two advisors Assist. Prof. Dr. Yeşim AYDIN SON from METU Bioinformatics Program and Assoc. Prof. Dr. Tolga Can from METU Computer Engineering Department.