Call For Papers and Abstracts
in Multi-Scale Modeling in Biology
Pacific Symposium on Biocomputing
The Big Island of Hawaii -- January 5-9, 2009
The fourteenth Pacific Symposium on Biocomputing (PSB), will be held January 5-9, 2009 at the Fairmont Orchid on the Big Island of Hawaii. PSB will bring together top researchers from North America, the Asian Pacific nations, Europe and around the world to exchange research results and address open issues in all aspects of computational biology. The session is organized jointly by researchers from NBCR (http://nbcr.net) and Simbios (http://simbios.stanford.edu/).
Developing tools, techniques, algorithms, and mathematical theory to integrate modeling and simulation from the micro to the macro-scale is important in biocomputing. This session aims to foster the interactive environment for researchers working across different scales of biological problems, so that more collaborations and activities to bridge multi-scales will be initiated. The overall focus of our session is on challenges to be overcome in computational approaches to multiscale modeling in biology, with a specific focus on mechanistic (i.e. biophysics-based) patient-specific modeling crossing different scales from proteins, cells, tissues, organs, up to the whole-organism level.
Since the last few decades, novel diagnostic and therapeutic medical technologies have been developed. This resulted in an increasing knowledge of pathophysiology from gene to organ systems. Together with ever increasing computer power, it is becoming feasible to design biophysically detailed multi-scale patient-specific models to guide and predict the response to therapy in many aspects of medicine. Modeling from a biophysical base would not only provide predictions of specific therapies or surgical interventions, but also insight into the degree of success or failure. To rely on the predictive capabilities of these types of models, efficient methods and computational tools are of the utmost importance.
We cordially invite submissions of papers or abstracts that will address physics-based modeling activities focused on encompassing at least two levels of physiology. Submission topics can include, but are not limited to:
Methods for making the connection between continuum macroscale models and discrete molecular phenomena
Model reduction and systems identification for multiscale dynamical systems
Algorithmic tools for multi-scale modeling systems using optimization and simulation in time and space
Mesoscale methods to bridge microscales and macroscales
Multi-level finite element methods
From genotype to phenotype
Molecular biology of ion channels and transporters
Excitation-contraction coupling and mechanoelectric feedback in normal and diseased cells
Dynamic simulation of neuromuscular systems
Real-time patient-specific modeling during surgery
Pharmacological (toxicological) effects on physiologic function
Acquisition of patient-specific material properties
Automation of patient-specific modeling
University of California San Diego
National Biomedical Computation Resource (NBCR)
University of Washington
National Center for Physics-based Simulation of Biological Structures (Simbios)
The core of the conference consists of rigorously peer-reviewed full-length papers reporting on original work. Accepted papers will be published in a hard-bound archival proceedings, which is indexed by PubMed. Researchers wishing to present their research without official publication are encouraged to submit a one page abstract by November 7, 2008.
Paper submissions due: July 21, 2008 (extended deadline for this session only)
Notification of paper acceptance: September 8, 2008
Final paper deadline: September 22, 2008 at midnight PDT
Abstract deadline: November 7, 2008 at noon PST
Meeting: January 5-9, 2009
Papers must be submitted to the PSB 2009 paper management system at
Please click the "Not a user? Create an account with this site" link to create an author account and upload your paper.
All papers must be submitted in electronic format to the paper management system.
The file formats we accept are: postscript (*.ps) and Adobe Acrobat (*.pdf). Attached files should be named with the last name of the first author (e.g. altman.ps or altman.pdf). Hardcopy submissions or unprocessed TEX or LATEX files or electronic submissions not submitted through the paper management system will be rejected without review.
Each paper must be accompanied by a cover letter. The cover letter must state the following:
Submitted papers are limited to twelve (12) pages in our publication format. Please format and submit your paper according to instructions found at http://psb.stanford.edu/psb-online/psb-submit/. If figures can not be easily resized and placed precisely in the text, then it should be clear that with appropriate modifications, the total manuscript length would be within the page limit.
Color pictures can be printed at the expense of the authors. The fee is $500 per page of color pictures, payable at the time of camera ready submission.
Contact Russ Altman (psb.hawaii @ gmail.com) for additional information about paper submission requirements.