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Subject: SMB Digest v12i22
SMB Digest May 30, 2012 Volume 12 Issue 22
ISSN 1086-6566
Editor: Richard Schugart richard(dot)schugart(at)gmail(dot)com
Note:
Information about the Society for Mathematical Biology, including an
application for membership, may be found in the SMB Home Page,
http://www.smb.org/ .
Access the Bulletin of Mathematical Biology, the official journal of
SMB, at http://www.springer.com/11538 .
Inquiries about membership or BMB fulfillment should be sent to
membership(at)smb(dot)org .
Issue's Topics:
Cf Poster Presentations: SMB 2012, July 25-28, U Tennessee
Workshop: Hybrid Systems & Biol, Sep 3, Newcasle upon Tyne, UK
ToC: BMB, Volume 74, Issue 6
PhD Position: Multi-scale Inference of Foot-and-..., U Warrick
Post-doc: UC Santa Cruz/NOAA Fisheries' Santa Cruz Laboratory
Post-doc: Mathematical Immunology, Imperial College London
Tenure-tracks: Bioinformatics & Systems Biology, Oregon State U
SMBnet Reminders
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From: Catherine Crawley <ccrawley@nimbios.org>
Date: May 25, 2012 10:24:39 AM
Subject: Cf Poster Presentations: SMB 2012, July 25-28, U Tennessee
Call for Poster Presentations: Society of Mathematical Biology
2012 Annual Meeting
The 2012 Annual Meeting and associated research and education conference
for The Society for Mathematical Biology is still accepting submissions
of poster presentations, and strongly encourages undergraduates involved
in summer research projects to submit a poster. The conference, with its
theme of Mathematics and Biology: Interdisciplinary Connections and
Living Systems, will be held in Knoxville, Tennessee, July 25-28, 2012.
Deadline for Contributed Poster Sessions: June 15, 2012.
For more information and the online abstract submission form, visit
http://nimbios.org/SMB2012.
----------------------------------------------------
From: Luca Bortolussi <luca@dmi.units.it>
Date: May 26, 2012 8:44:06 AM
Subject: Workshop: Hybrid Systems & Biol, Sep 3, Newcasle upon Tyne, UK
First International Workshop on Hybrid Systems and Biology
Newcasle upon Tyne, UK, September 3, 2012
Colocated with CONCUR 2012
http://hsb2012.units.it/
The goal of systems biology is to provide a system-level understanding
of biological systems by unveiling their structure, dynamics and control
methods. The intrinsic multi-scale nature of these systems, both in
space, in organization levels, and in time, makes extremely difficult to
model all of them in a uniform way, e.g. by means of differential
equations or discrete stochastic processes. Furthermore such models are
often not easily amenable to formal analysis and simulation at the organ
or even the cell level is frequently impractical. Indeed, an important
open problem is finding appropriate computational models that scale well
for both the simulation and formal analysis of biological processes.
Hybrid modeling techniques, combining discrete and continuous processes,
are gaining more and more attention in systems biology, and they have
been applied to successfully capture the behavior of several biological
complex systems, ranging from genetic networks, biochemical reactions,
signaling pathways and cardiac tissues electrophysiology.
This workshop aims at collecting scientists working in the area of
hybrid modeling applied to systems biology, in order to discuss about
current achieved goals, current challenges and future possible
developments.
Topics of interest include, but are not limited to:
- Hybrid models of biological systems (case studies of genetic, cellular
networks, models of tissues, etc.)
- Models of biological systems with hybrid behavior
- Computational and mathematical analysis techniques for hybrid systems
(i.e. reachability, model checking, abstract interpretation, bifurcation
theory for hybrid dynamical systems, stability analysis, etc.), with
applications in Systems Biology
- Hybrid system identification techniques (learning the model from the
experimental data)
- Efficient simulation techniques for hybrid systems
- Hybrid modeling languages for biological systems
- Hybrid systems coping with incomplete and uncertain information
- Hierarchical Hybrid Systems for multi scale analysis
- Stochastic Hybrid Systems
- Hybrid simulation (stochastic/deterministic) methods for biological
systems
- Abstraction and Approximation techniques
- Hybrid Systems modeling for Synthetic Biology
- Hybrid Control of biological systems
- Sensitivity analysis for hybrid systems
- Behaviour-driven parameters identification for hybrid systems
- Analysis and simulation tools
We solicit the submission of unpublished results that address on both
theoretical and applied aspects of hybrid modeling techniques in systems
biology.
The proceedings will be published in the Electronic Proceedings in
Theoretical Computer Science (EPTCS) series.
There will be a following special issue on Information and Computation,
based on selected papers of the workshop.
Paper submission
Full papers should be no more than 15 pages long, typesetted in the
EPTCS-style.
Electronic submissions of abstracts and of full-length papers (in PDF
format), can be done through the online submission system:
https://www.easychair.org/conferences/?conf=hsb2012
Special Issue
There will be a special issue on Information and Computation, based on
selected papers of the workshop.
Registration
The registration can be done via the CONCUR 2012 web site.
Important dates
June 15, 2012 - Abstract submission deadline
June 22, 2012 - Full paper submission deadline
July 30, 2012 - Notification of paper acceptance
August 7, 2012 - Camera-ready of accepted papers
Invited Speaker
Radu Grosu, TU Wien, Austria
Program co-chairs
Ezio Bartocci, TU Wien, Austria
Luca Bortolussi, Univerity of Trieste, Italy
Program committee
Marco Antoniotti, University of Milano Bicocca
Gregory Batt, INRIA Paris-Rocquencourt, France
Alberto Casagrande, University of Trieste, Italy
Edmund Clarke, Carnegie Mellon, USA
Thao Dang, VERIMAG Lab, Grenoble, France
Alexandre Donzé, UC Berkley, USA
James R. Faeder, University of Pittsburgh, USA
Jasmin Fisher, Microsoft Research, Cambridge, UK
Vashti Galpin, University of Edinburgh, UK
Colas Le Guernic, NYU, USA
Oded Maler, VERIMAG Lab, Grenoble, France
Emanuela Merelli, University of Camerino, Italy
Bud Mishra, NYU, USA
Carla Piazza, University of Udine, Italy
Alberto Policriti, University of Udine, Italy
Scott A. Smolka, University of Stony Brook, USA
Gouhei Tanaka, University of Tokyo, Japan
Verena Wolf, Saarland University, Germany
Paolo Zuliani, Carnegie Mellon, USA
----------------------------------------------------
From: Springer <springeralerts@springer.delivery.net>
Date: May 26, 2012 7:07:21 AM
Subject: ToC: BMB, Volume 74, Issue 6
Volume 74 Number 6 is now available on SpringerLink
http://www.springerlink.com/content/119979/
IN THIS ISSUE:
A Multiscale Hybrid Model for Pro-angiogenic Calcium Signals in a
Vascular Endothelial Cell
Marco Scianna
Cross-Strain Quorum Sensing Inhibition by Staphylococcus aureus.
Part 1: A Spatially Homogeneous Model
Sara Jabbari, John R. King & Paul Williams
Cross-Strain Quorum Sensing Inhibition by Staphylococcus Aureus.
Part 2: A Spatially Inhomogeneous Model
Sara Jabbari, John R. King & Paul Williams
Age or Stage Structure?
Arild Wikan
On the Probability of Random Genetic Mutations for Various Types of
Tumor Growth
Cristian Tomasetti
Effects of Time-Dependent Stimuli in a Competitive Neural Network Model
of Perceptual Rivalry
Suren Jayasuriya & Zachary P. Kilpatrick
Modeling of Biocide Action Against Biofilm
Tianyu Zhang
Impact of Directed Movement on Invasive Spread in Periodic Patchy
Environments
Kohkichi Kawasaki, Keisuke Asano & Nanako Shigesada
----------------------------------------------------
From: Leon Danon <leon.danon@gmail.com>
Date: May 24, 2012 3:26:19 AM
Subject: PhD Position: Multi-scale Inference of Foot-and-..., U Warrick
"Multi-scale Inference of Foot-and-Mouth Disease Spread in the UK and
Japan"
3/4 years PhD Funding at standard RCUK rates is available for a
collaborative PhD Project with the University of Warwick and the
Institute of Animal Health, starting in September/October 2012. The
University of Warwick has an established track record in the development
of large scale stochastic models to simulate the potential for spread of
animal diseases such as FMD and avian influenza. Pirbright Institute for
Animal Health has a unique understanding of transmission and the
pathogenesis of FMD. In collaboration, researchers have developed a
state-of-the-art model that predicts how disease spreads at a national
level based directly upon experimental data of how disease is
transmitted between individual animals. In this project the model will
be further developed to incorporate recent data on contacts between
sheep and cattle on farms, and future results pertaining to viral
transmission amongst vaccinated cattle. To properly quantify the
uncertainties in available data and knowledge the system will be
implemented in a fully Bayesian framework. The model will be applied to
two scenarios: the 2001 outbreak in the UK and, in collaboration with
the University of Miyazaki, the 2010 outbreak in Japan. The aim of this
project is to develop and validate a model that can then be used to
determine optimal control strategies for future outbreaks in the UK,
Japan and elsewhere.
For more information on eligibility, closing dates, how to apply and a
full project outline please visit the apply online link below or e-mail
M.J.Tildesley@warwick.ac.uk or L.Danon@warwick.ac.uk . See also:
http://www.jobs.ac.uk/job/AEK512/3-4-year-funded-phd-for-a-home-or-eu-candidate-in-multi-scale-inference-of-foot-and-mouth-disease-spread-in-the-uk-and-japan/
(Editor's note: The link may need to be copy and pasted into your web
browser.)
The deadline for applications is Thursday, 31 May 2012, and we are
hoping to hold interviews on the 8th of June.
----------------------------------------------------
From: steve munch <steve.munch@noaa.gov>
Date: May 23, 2012 5:31:59 PM
Subject: Post-doc: UC Santa Cruz/NOAA Fisheries' Santa Cruz Laboratory
We (Stephan Munch, Alec MacCall and Marc Mangel) are seeking a candidate
to fill a postdoctoral position in the Center for Stock Assessment
Research, Department of Applied Mathematics and Statistics at UC Santa
Cruz in conjunction with NOAA Fisheries' Santa Cruz Laboratory. This
position is part of a NOAA-funded project to improve assessment methods.
The successful candidate will work with us to develop semi-parametric
Bayesian tools for nonlinear time-series modeling and non-parametric
approaches to optimal harvest policies that implicitly account for
multi-species dynamics.
The ideal candidate should have experience with hierarchical Bayesian
data analysis, Gaussian process regression, and nonlinear time-series
modeling, and have the ability to work effectively with both applied
mathematicians and ecologists or fisheries scientists. Familiarity with
stochastic dynamic programming is beneficial but not required. Please
direct inquiries and applications (please include a CV with any initial
application) to Steve Munch (steve.munch@noaa.gov).
Closing Date: June 20, 2012
----------------------------------------------------
From: Asquith, Becca <b.asquith@imperial.ac.uk>
Date: May 28, 2012 7:36:57 AM
Subject: Post-doc: Mathematical Immunology, Imperial College London
Postdoctoral Research Associate in Mathematical Immunology
Department of Medicine
Section of Immunology
Imperial College London
Salary 31,300 - 39,920 pounds per annum
An exciting opportunity has arisen for a Postdoctoral Research Associate
in the Mathematical Immunology group in the Immunology Department at
Imperial College London.
You will join a dynamic, productive group headed by Becca Asquith
carrying out research on the human cellular immune response.
Our group is working to identify the factors that constitute a
protective CD8+ T cell response. Recently we have found that the gene
encoding a particular receptor (namely KIR2DL2) is strongly associated
with enhanced control of two unrelated viruses. The aim of this 3 year
MRC-funded project is to identify the mechanism underlying this
observation and to test whether a similar KIR2DL2-enhancement is
observed in virus-associated leukemia. The successful applicant will
model and analyze experimental data generated by other group members and
collaborators. The experimental data will include ultra-deep virus
sequence data, immunogenetics data from a cohort of leukemia cases and
controls as well as basic cellular data.
Applications must have a PhD degree in Bioinformatics, Physics,
Mathematics, Computer Science or equivalent (or be within three months
of having completed the period of study required for a PhD). Previous
experience of bioinformatics or modeling immunological data will be a
strong advantage.
The post is full-time and available for three years from September 2012.
Informal enquiries are welcome and should be addressed to Dr Becca
Asquith (b.asquith@imperial.ac.uk).
For more information and to apply please go to
http://www3.imperial.ac.uk/employment
and search for post reference HM2012083.
Closing date: June 11
----------------------------------------------------
From: Cropley, Jeannine <Jeannine.Cropley@cgrb.oregonstate.edu>
Date: May 23, 2012 1:25:38 PM
Subject: Tenure-tracks: Bioinformatics & Systems Biology, Oregon State U
THREE FACULTY POSITIONS IN BIOINFORMATICS AND SYSTEMS BIOLOGY
Oregon State University is conducting three open rank searches for
collaboratively-minded faculty who demonstrateenthusiasm for research
and teaching at the interface of the quantitative and life sciences, to
join our strong growing genomics and systems biology community.
NUCLEIC ACID SEQUENCE BIOINFORMATICS
The appointee will execute a strong research and teaching program at the
interface of computer and life sciences that advances the use of
nucleic acid sequence data to understand the functions of biological
systems at any scale. This is a tenure-track, 9-month, full-time faculty
position at any rank that will reside jointly in the School of
Electrical Engineering and Computer Science, and in a life science unit
depending on the appointee?s expertise and interest.
SYSTEMS BIOLOGY OF HOST-MICROBE INTERACTIONS
The appointee will conduct research addressing host-microbe interactions
through integrating experimental life science and quantitative methods.
The context of the research may be infectious disease, allergic or
chronic disease in humans, animals or plants, or mutualistic
interactions at the level of individuals or communities. This is a
tenure-track, 9-month, full-time faculty position at any rank that will
reside jointly in a life science department and in a quantitative
science department depending on the appointee?s expertise and interest.
APPLIED DISCRETE MATHEMATICS IN SYSTEMS BIOLOGY
The appointee will execute a strong research and teaching program at the
interface of applied discrete mathematics and molecular, cellular or
organismal systems biology. The context of research may include, but is
not limited to, areas of discrete mathematics centered around data
integration, network inference, or modeling in systems biology. This is
a tenure-track, 9-month, full-time faculty position (Associate or Full
Professor) that will reside jointly in the Department of Mathematics,
and in a life science unit depending on the appointee's expertise and
interest.
More information and application procedures can be found at
http://www.cgrb.oregonstate.edu/faculty-positions
----------------------------------------------------
Subject: SMBnet Reminders
To subscribe to the SMB Digest please point your browser at
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and complete the subscription information. Alternatively, if you prefer
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After you subscribe, you will receive a greeting with additional
information.
Submissions to appear in the SMB Digest may be sent to
SMBnet(at)smb(dot)org .
Items of interest to the mathematical biology community may be submitted
for inclusion in the SMBnet archive. See instructions at:
http://smb.org/publications/SMBnet/pubs/fyi .
The SMB Digest is also available on the SMB Home Page at
http://smb.org/publications/SMBnet/digest/
The contents of this publication may be reproduced in whole or in part
with attribution.
End of SMB Digest
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