Parallel Bio-Computing
September 13-16, 2009
Latest News
26 Jul 2009 - Schedule of the workshop is now available (see below).
08 Jun 2009 - Review process has been completed! By now all authors should have received notification message!
30 Apr 2009 - In response to multiple requests we further extended submission deadline to May 7th.
If you already submitted your paper you still can update it.
04 Apr 2009 - Paper submission system is now open!
03 Apr 2009 - Because of change in PPAM policy
deadline has been extended to April 30th.
01 Nov 2008 - First Call for Papers in now available.
PBC Program
The Workshop will be on Tuesday, September 15.
Time for each presentation is 20 minutes + 5 minutes for discussion.
| 16:40 - 17:05 | M. Terzer, J. Stelling | Parallel Extreme Ray and Pathway Computation |
| 17:05 - 17:30 | S. Pallickara, M. Pierce, Q. Dong, C. Kong | Enabling Large Scale Scientific Computations for Expressed Sequence Tag Sequencing over Grid and Cloud Computing Clusters |
| 17:30 - 17:55 | S. Richardson, B. Olson, J. Dymond, R. Burns, S. Chandrasegaran, J. Boeke, A. Shehu and J. Bader | Automated Design of Assemblable, Modular, Synthetic Chromosomes |
| 17:55 - 18:20 | S.A. Berger, A. Stamatakis | Accuracy and Performance of Single versus Double Precision Arithmetics for Maximum Likelihood Phylogeny Reconstruction |
| 18:20 - 18:45 | P. Steffen, R. Giegerich and M. Giraud | GPU Parallelization of Algebraic Dynamic Programming |
About PBC
PBC has been established in 2005 as a workshop accompanying
PPAM Conference. From the very beginning
its purpose is to provide an open forum for researchers from around
the world to exchange their latest research findings in all aspects
of parallel computational biology and bioinformatics.
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Call for Papers
The first call for papers (announced 01 Nov 2008): PDF version 
and Text version 
.
The second call for papers (announced 03 Apr 2009): PDF version
and Text version .
Bioinformatics is the science of managing, mining, and extracting knowledge
from biological sequences and structures. Since the last PBC workshop in 2007
the field has witnessed two revolutions: the multi-core revolution and the
DNA sequencing revolution due to new sequencing machines such as the 454 or Solexa.
Because of the new data flood in combination with the multi-core revolution,
the application of HPC techniques to solve bioinformatics problems has become crucial
to the success of the field.
The goal of this Workshop is to present the latest research in
high-performance computing applied to bioinformatics. We are
especially interested in parallel and distributed algorithms, memory
efficient algorithms, and design of high-performance software for
clusters, massively parallel systems and grids. Submission of articles
dealing with parallelization of applications on multi-/many-core as
well as accelerator architectures are specifically encouraged. Topics
of interest include but are not limited to:
- Bioinformatics databases
- Computational genomics and proteomics
- DNA assembly, clustering, and mapping
- Gene expression and microarrays
- Gene identification and annotation
- Molecular sequence analysis
- Phylogeny reconstruction algorithms
- Protein structure prediction and modelling
- Parallel algorithms for biological analysis
- Parallel architectures for biological applications
- System tools that support large scale high-performance bio-computing
Paper Submission
The workshop consists of dedicated sessions containing selected
papers. Papers are refereed and accepted on the basis of their
originality, scientific merit and relevance to the Workshop
topics.
Papers presented during the workshop are included into the proceedings
of PPAM Conference and are published after the conference by
Springer-Verlag in the LNCS series.
The only allowed format is Springer LaTeX style. To ensure reasonable
quality and consistency of preparation, please be sure to adhere
closely to the LNCS Author and Volume Editor Instructions. All papers
should be prepared as a PDF or PS file, and should be submitted using
the PPAM Paper Submission link.
Papers should not exceed 10 pages.
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Important Dates
Submission of Papers: May 7, 2009 (23:59 CET) [previously April 30]
Notification of Acceptance: June 8, 2009 [previously May 31]
Camera-Ready Papers: October 31, 2009
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Programme Committee
David A. Bader, Georgia Tech, USA - workshop chair
Denis Trystram, LIG, France - workshop chair
Alexandros Stamatakis, TU Munchen, Germany - programme co-chair
Jaroslaw Zola, Iowa State Univ., USA - programme co-chair
- Dmitry Afonikov, Inst. of Cytology and Genetics, Russia
- Srinivas Aluru, Iowa State Univ., USA
- Wenguang Chen, Tsinghua Univ., China
- Scott Emrich, Univ. of Notre Dame, USA
- Wu-chun Feng, Virginia Tech, USA
- Ananth Kalyanaraman, Washington State Univ., USA
- Bernard Moret, EPF Lausanne, Switzerland
- Pierre Peterlongo, INRIA, France
- Jacques Rougemont, EPF Lausanne, Switzerland
- Bertil Schmidt, Nanyang Tech. University, Singapore
- Evripidis Sotiriadis, Tech. Univ. of Crete, Greece
- Craig Stewart, Indiana University, USA
PBC Archive
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Jaroslaw Zola
Iowa State University
Department of Electrical and Computer Engineering
1126 Coover Hall
Ames, Iowa 50011, USA
Phone: +1 515 294-5498
Fax: +1 515 294-8432
email: zola@iastate.edu
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