Applications of Bioinformatics for Synthetic Biology
METU-BIN
2011iGEM SOFTWARE TEAM
Abstract
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.
Topics
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.
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 (http://metu.edu.tr/~yesim/igem.htm).
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.