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BSD-SIG 2012 : Biological Systems Design 2012


When Jul 13, 2012 - Jul 13, 2012
Where Long Beach, CA USA
Submission Deadline Apr 30, 2012
Notification Due May 10, 2012
Categories    synthetic biology   bioinformatics   computer science   biology

Call For Papers

Apologies for cross-posting


Intelligent Systems for Molecular Biology (ISMB 2012)
July 13, 2012 - Long Beach, CA USA

Submission site:


Important Dates:
Author notification: May 10, 2012
Workshop: July 13, 2012


**General Information**

The complexity of the genomic structure and our limited understanding of biological processes
require new computational methods to investigate the huge number of possible designs for circuits,
pathways, and entire genomes, with the ideal being the ability to model, simulate and redesign a
biological system in-silicon prior to fabrication, similar to CAD/CAM for physical devices.

Synthetic Biology aims to establish a standard and effective biological design flow,
where biological systems are designed and verified computationally, before in vitro synthesis and
in vivo experiments. Each phase of this process has multiple challenges ranging from managing
high-throughput laboratory operations to developing new software and defining accurate and
interoperable computational models.

The Special Interest Group in Biological Systems Design (BSD-SIG 2012) aims to provide a broad view
of the current state-of-the-art for scientists from biology, chemistry, computer science, mathematics
and engineering.


**Keynote Speakers**

- Jef D. Boeke, Johns Hopkins University
- Christodoulos A. Floudas, Princeton
- Dan Gusfield, UC Davis
- Nathan J. Hillson, Joint BioEnergy Institute
- Christina Smolke, Stanford

**Invited Speakers**

- Jake Beal, BBN Technologies
- Michal Galdzicki, University of Washington School of Medicine
- Sarah Richardson, Joint Genome Institute



BSD-SIG is structured in four sessions:

* Genome Design
* Protein Design
* Computer Aided Design Tools
* Data management & standards

**Genome Design**
The availability of high-fidelity techniques for the synthesis of long DNA strands constitutes the
starting point for effective pathway engineering. The aim of this session is to present state-of-the-art
methods for genome design, focusing, but not limited to, on the following topics: oligo-nucleotides
design, Probe and watermark design, High-throughput techniques, theoretical aspects of DNA design.

**Protein Design**
An important purpose of synthetic DNA is to express non-native or human-designed proteins.
Protein expression and design introduce additional complexities. This session provides a forum
to discuss the recent advances in this field, with particular emphasis on the design of
therapeutic peptides and proteins.

**Computer Aided Design Tools**
The design of biological systems is often characterized by ad hoc, human-centric procedures,
which limit applications to small-scale problems. While Computer-Aided-Design (CAD) tools are
standard in many engineering fields, CAD capabilities for synthetic biology are at a
very early stage. This session gives a broad view of some emerging approaches in Biological
Design Automation (BDA), with the aim of finding and discussing new areas where CAD tools can
improve and accelerate the synthesis of living matter.

**Data management & standards**
The enormous amount of data generated by high-throughput techniques and synthesis processes
requires the introduction of new and specific representation schemes, along with efficient and
open standards for interfacing different data sources. New systems are also required to collect
information and performing on-line data analysis. The aim of this session is twofold: first,
exploring data structures and representations for synthetic biology; second, promoting and
discussing use-case scenarios for the Synthetic Biology Open Language (SBOL).



We encourage submissions in the form of oral and poster presentation; authors must submit a
1 page abstract specifying the track and the form of the contribution.

Two blind reviewers will review each submission, and suggest the most appropriate form for
presentation. All the accepted abstracts will be published on the hands-out materials of BSD-SIG.

Contributions must be submitted through EasyChair:


We are looking forward to see you in Long Beach:

Joel Bader, Doug Densmore, Swapnil Bathia and Giovanni Stracquadanio

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