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[Embl-databank] [Call for Submissions] Biological Systems Design 2012 - BSD-SIG @ ISMB 2012 - July 13, 2012, Long Beach, CA

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Thu Mar 15 09:28:55 EST 2012

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

Homepage: http://bsd2012.bme.jhu.edu/ 
Submission site: https://www.easychair.org/conferences/?conf=bsdsig2012
Email: bsd2012 from jhu.edu


Important Dates:
Paper submission: April 20, 2012
Author notification: May 4, 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 

**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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