SMB Digest January 28, 2014 Volume 14 Issue 5
ISSN 1086-6566
Editor: Wandi Ding wding1(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,
Access the Bulletin of Mathematical Biology, the official journal
Inquiries about membership or BMB fulfillment should be sent to
membership(at)smb(dot)org .
Issue's Topics:
2014 World Conference on Natural Resource Modeling
StochSS: Stochastic Simulation Service new release
MBL Methods in Computational Neuroscience Course 2014
Infectious Disease Modelling and its Applications-2014
New MBE vol. 11, no. 3 2014 June issue
Postdoc position - INRA Rennes, France
Postdoc position - U of Minnesota
Postdoc position - ENS Paris
Postdoc position - Uppsala University, Sweden
Postdoc position - University of Groningen
SMBnet Reminders
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Date: Fri, Jan 24, 2014 at 5:53 PM
Subject: 2014 World Conference on Natural Resource Modeling
Hosts: Institute of Ecology, Lithuanian State Nature Research
Center (NRC) and Faculty of Natural Sciences, Vilnius University
Dates: July 8 ? 11th, 2014
Venue: Vilnius University
Organizer: Dr Linas Lo?ys (NRC), Dr Harry Gorfine
(NRC, RMA & SIAM representative)
Scientific Advisory Panel: Dr Luc Doyen, Dr Laura Leites,
Dr Linda Nøstbakken
The Resource Modeling Association is an international body of
scientists working at the intersection of mathematical modeling,
environmental science, and natural resource management. Its
annual meetings provide a platform for genuine interdisciplinary
communication and networking. The theme for this conference is
'Modeling our way back to the future' which will be explored
within the UNESCO World Heritage listed setting of Vilnius.
Five keynote speakers will captivate and inspire you with a
diversity of topics: Professor Claire Armstrong - Norwegian
College of Fishery Science, Tromsø University, Faculty of
Biosciences, Fisheries and Economics; Emeritus Professor
Jim Kitchell ? University of Wisconsin, Madison, Department of
Zoology; Professor Martin Quaas - Christian-Albrechts-University
of Kiel, Department of Economics; Professor Steve Railsback
- Lang Railsback & Associates and Humboldt State University;
and Dr Walter Rossing - Farming Systems Ecology, Wageningen
University Plant Sciences. Professor Railsback will also run
a one-day pre-conference introductory workshop on individual
based models on 8th July. In addition Professor Wayne Getz
- Department of Environmental Science, Policy, & Management,
UC Berkeley, will present the NOVA platform for agent-based
modelling.
Registration rates will increase after 31 Mar 2014 and papers
for the first call are due by 31 March 2014.
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Date: Tue, Jan 21, 2014 at 1:22 PM
Subject: StochSS: Stochastic Simulation Service new release
Announcement to the release of StochSS: Stochastic Simulation
Service, Version 1.1.
StochSS is an integrated development environment featuring
state of the art algorithms for discrete stochastic biochemical
simulation. StochSS is designed to enable you to easily scale up
your simulations in complexity, deploying compute resources as
needed. The current version includes algorithms for simulation
of well-mixed systems. Problems can be specified via a graphical
user interface (or imported as StochKit2 models).
New capabilities of Version 1.1 include: simulation of ODE
models, tools for converting ODE models into stochastic models,
support for Windows systems, and enhanced management of cloud
computing resources.
For more details and instructions on how to obtain the code,
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Date: Sat, Jan 25, 2014 at 12:50 AM
Subject: MBL Methods in Computational Neuroscience Course 2014
Applications are open for the Methods in Computational Neuroscience
course at the Marine Biology Laboratory in Woods Hole, MA. The
course will run from July 30 to August 27, 2014, and the online
The course application deadline is March 6.
The course covers a range of topics in computational neuroscience
including neuronal biophysics, neural coding & information
processing, circuit dynamics, learning & memory, motor control, and
cognitive processing & disease. In addition, numerous tutorials and
problem sets will cover a broad range of computational and mathematical
modeling methods. The course strongly emphasizes the collaboration
between theory and experiment in solving neuroscience problems, and
lectures will be given by a mixture of theorists and experimentalists.
The final weeks of the course will primarily be reserved for
development and work on projects that students design in
collaboration with the resident faculty. Further information can
2014 Course Directors:
Michale Fee, MIT
Mark Goldman, UC Davis
2014 Invited Faculty (most confirmed):
Larry Abbott, Columbia University
Steve Baccus, Stanford University
William Bialek, Princeton University
Carlos Brody, Princeton University
Dmitri Chklovskii, HHMI Janelia Farm
Nathaniel Daw, New York University
Bard Ermentrout, University of Pittsburgh
Adrienne Fairhall, University of Washington
Ila Fiete, UT Austin
Loren Frank, UCSF
Jack Gallant, UC Berkeley
Surya Ganguli, Stanford University
David Kleinfeld, UC San Diego
Peter Latham, University College London
Tim Lewis, UC Davis
John Lisman, Brandeis University
Eve Marder, Brandeis University
Bartlett Mel, University of Southern California
Liam Paninski, Columbia University
Jonathan Pillow, UT Austin
David Redish, University of Minnesota
John Rinzel, New York University
Jonathan Rubin, University of Pittsburgh
Nate Sawtell, Columbia University
Maurice Smith, Harvard Univeresity
Sara Solla, Northwestern University
Haim Sompolinsky, Hebrew University
David Tank, Princeton University
Misha Tsodyks, Weizmann Institute
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Date: Mon, Jan 27, 2014 at 5:20 AM
Subject: Infectious Disease Modelling and its Applications-2014
2 week intensive course on:
INTRODUCTION TO INFECTIOUS DISEASE MODELLING AND ITS APPLICATIONS
organized jointly between the London School of Hygiene & Tropical
Medicine and Public Health England
Course dates: 16th? 27th June 2014
Cost: £2,100
Summary:
Mathematical modelling is increasingly applied to predict the
future incidence and control of infectious diseases.
Applications include predicting the impact of control strategies,
such as vaccination or treatment, against pandemic influenza,
measles, HIV, vector-borne diseases and veterinary problems.
Modelling was used extensively in the UK during the swine flu
pandemic to monitor the extent of ongoing transmission and the
potential impact of interventions such as school closures and
vaccination.
This two week intensive course introduces professionals
working on infectious diseases in human or animal populations
to this exciting and expanding area. The emphasis of the course
is on developing a conceptual understanding of the basic
methods and on their practical application, rather than the
manipulation of mathematical equations. The course provides
numerous practical examples, including real-time modelling of
outbreaks, pandemic influenza, sexually transmitted infections,
HIV, vector-borne and animal diseases, as well as tuberculosis,
measles and rubella, and health economics. By the end of the
course, participants will have deepened their current
understanding of infectious disease epidemiology and have
gained an understanding and practical experience of the basics
of infectious disease modelling, which will be important in
their future work.
Who should attend:
The course is designed for individuals interested in expanding
their knowledge of the techniques for analysing and interpreting
epidemiological data on infectious diseases and for predicting
the impact of control programmes, including medical and health
professionals, policy makers, veterinary scientists, health
economists, medical statisticians and infectious disease
researchers.
Specialist mathematical training is not a prerequisite.
However, individuals with degrees in mathematical disciplines
working on some aspect of infectious disease dynamics and/or
control, who wish to learn about the potential of infectious
disease modelling will also benefit.
Further details about the course content and an application
or contact one of the course organizers:
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Date: Fri, Jan 24, 2014 at 4:39 PM
Subject: New MBE vol. 11, no. 3 2014 June issue
Mathematical Biosciences and Engineering (MBE)
Volume: 11, Number: 3 June 2014
1. Derivation and computation of discrete-delay and
continuous-delay SDEs in mathematical biology Pages : 403 - 425
Edward J. Allen doi:10.3934/mbe.2014.11.403
2. Model validation for a noninvasive arterial stenosis detection
problem Pages : 427 - 448 H. Thomas Banks, Shuhua Hu, Zackary
R. Kenz, Carola Kruse, Simon Shaw, John Whiteman, Mark P. Brewin,
Stephen E. Greenwald and Malcolm J. Birch
doi:10.3934/mbe.2014.11.427
3. The global stability of an SIRS model with infection age
Pages : 449 - 469 Yuming Chen, Junyuan Yang and Fengqin Zhang
doi:10.3934/mbe.2014.11.449
4. A metapopulation model for sylvatic T. cruzi transmission
with vector migration Pages : 471 - 509 Britnee Crawford and
Christopher Kribs-Zaleta doi:10.3934/mbe.2014.11.471
5. Optimal sterile insect release for area-wide integrated
pest management in a density regulated pest population
Pages : 511 - 521 Luis F. Gordillo doi:10.3934/mbe.2014.11.511
6. Effect of intraocular pressure on the hemodynamics of the
central retinal artery: A mathematical model Pages : 523 - 546
Giovanna Guidoboni, Alon Harris, Lucia Carichino, Yoel Arieli
and Brent A. Siesky doi:10.3934/mbe.2014.11.523
7. A model of optimal dosing of antibiotic treatment in biofilm
Pages : 547 - 571 Mudassar Imran and Hal L. Smith
doi:10.3934/mbe.2014.11.547
8. A Rao-Blackwellized particle filter for joint parameter
estimation and biomass tracking in a stochastic predator-prey
system Pages : 573 - 597 Laura Martin-Fernandez, Gianni Gilioli,
Ettore Lanzarone, Joaquin Miguez, Sara Pasquali, Fabrizio
Ruggeri and Diego P. Ruiz doi:10.3934/mbe.2014.11.573
9. Modeling and analysis of the San Francisco City Clinic
Cohort (SFCCC) HIV-epidemic including treatment Pages : 599 - 619
Brandy Rapatski and Juan Tolosa doi:10.3934/mbe.2014.11.599
10. Modeling the endocrine control of vitellogenin production
in female rainbow trout Pages : 621 - 639 Kaitlin Sundling,
Gheorghe Craciun, Irvin Schultz, Sharon Hook, James Nagler,
Tim Cavileer, Joseph Verducci, Yushi Liu, Jonghan Kim and
William Hayton doi:10.3934/mbe.2014.11.621
11. Global stability of an age-structured cholera model
Pages : 641 - 665 Jianxin Yang, Zhipeng Qiu and Xue-Zhi Li
doi:10.3934/mbe.2014.11.641
12. Mathematical modeling of Glassy-winged sharpshooter
population Pages : 667 - 677 Jeong-Mi Yoon, Volodymyr Hrynkiv,
Lisa Morano, Anh Tuan Nguyen, Sara Wilder and Forrest Mitchell
doi:10.3934/mbe.2014.11.667
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Date: Wed, Jan 22, 2014 at 9:29 AM
Subject: Postdoc position - INRA Rennes, France
Postdoc position in theoretical population genetics and
evolution of partially asexual species at INRA Rennes, France
Deadline for applications: 2014-01-31
Supervision: Solenn Stoeckel (INRA Rennes) and Sophie
Arnaud-Haond (Ifremer Sète)
Context: Many important species reproduce both sexually and asexually.
While there is an extensive theoretical framework for the population
genetics of both either sexual or asexual species, our ability to
understand the evolution of partial asexuals is still impeded by a
lack of suitable models to analyse and predict changes in their genetic
diversity. Using a variety of stochastic modelling techniques
(Markov chains, SDEs, individual-based numeric simulations) and
statistic approaches (Bayesian, machine learning), our
interdisciplinary workgroup (evolutionary biology, mathematics,
computing) aims to provide the necessary tools for closing this gap.
The task of the postdoc will be to extend the model to spatially
structured populations, synthesizing the consequences of partial
asexuality on their genetic composition and providing new
"null models" for the analysis of field data. The position is part
of a French national research project (ANR Clonix) offering
opportunities to co-author collaborative applied and theoretical
papers. Competences: The candidate should have a strong background
in at least one of the domains of theoretical population genetics,
scientific programming (Unix Batch scripts, C and Python) and/or
mathematics (linear algebra, Markov chains, SDEs). He/she should be
able to work in an interdisciplinary team and to collaborate closely
with scientists from different backgrounds.
Conditions: The position is funded for 16 or 17 months according to
the classical French government contract (1750-1880 EUR net salary
depending on experience, with extra benefits including health
insurance, child care, public transport and lunch contributions).
Though near the sea and situated in a very touristic region, life
in French Brittany is relatively cheap on a European scale. Rennes
is a student city (out of 300.000 inhabitants, ~60.000 are university
students) with a lot of facilities for newcomers.
Application: Candidates should submit their application by email
with the subject "[ANR Clonix Postdoc Application]. It should be
written in English and consist of a CV with a full list of
publications, talks and posters, a motivation letter (2 pages max.)
highlighting their competences relevant to the proposed position and
max. one optional page linking this postdoc position to their
long-term research perspectives. Interviews will be held per
videoconference.
For additional information, please contact Solenn Stoeckel at
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Date: Thu, Jan 23, 2014 at 4:04 PM
Subject: Postdoc position - U of Minnesota
Funding is available for a Postdoctoral Associate/Research Associate
position in the School of Mathematics at the University of
Minnesota-Minneapolis, beginning as early as July 1, 2014.
The position involves mathematical modeling and analysis of cell
and tissue movement. Applicants should have a Ph.D. in Mathematics,
Science or Engineering and have experience in mathematical
modeling in biology, biophysics or medicine. The degree is required
by the beginning date of appointment. Knowledge of Fortran or
C/C++ is also required. The immediate group consists of ten
researchers who are analyzing models of cell movement in single
and multicellular systems, stochastic effects in pattern formation,
and signal transduction and pattern formation in developmental
biology. In addition, the School of Mathematics and the Institute
for Mathematics and Its Applications at Minnesota provide a very
rich research environment for a post-doctoral fellow.
The salary will be commensurate with qualifications and experience.
The initial appointment will be for one year, with continuation
contingent upon performance and availability of funding. Please
submit your CV, research statement and arrange for three letters of
recommendation. Letters could be loaded on the mathjobs website or
be sent to: Professor Hans Othmer, School of Mathematics,
127 Vincent Hall, University of Minnesota, 206 Church St SE
Minneapolis, MN 55455. Any offer will be contingent upon a
successful background check.
The University of Minnesota is committed to the policy that all
persons shall have equal access to its programs, facilities, and
employment without regard to race, color, creed, national origin,
sex, age, marital status, disability, public assistance status,
veteran status, or sexual orientation.
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Date: Tue, Jan 21, 2014 at 10:01 AM
Subject: Postdoc position - ENS Paris
A 2-year post-doc position is available to work on the "Modeling
the spatio-temporal dynamics of Dengue in Cambodia accounting for
viral evolution" at the Department of Ecology and Evolution,
Paris (ENS) under the supervision of Professor Bernard Cazelles.
Today, Dengue fever represents a major challenge in public health
and threatens especially South-East Asia. The objective of DENFRE
knowledge on the ecological and evolutionary dynamics of Dengue
in this area to design innovative public health measures. This
project is strongly interdisciplinary and is composed by
epidemiologists, biologists, computer scientists, statisticians
and mathematicians.
As a part of this research project, the successful candidate
will have to develop cutting-edge models that would be used
synergistically with empirical data on disease incidence, viral
genetic and antigenic variation. These mathematical and/or
computational models of dengue propagation will be supported by
epidemiological and antigenic data from DENFREE consortium, in
close relationship with the Pasteur Institute in Cambodia. In
particularly, the successful candidate will have to account for
heterogeneous and highly interdependent data through a Bayesian
framework. This approach is sufficiently flexible to design
phylodynamic models that account for non-linear disease dynamics,
molecular selection and population structure. This modeling will
in close collaboration with its founders.
The successful applicant will be broadly trained in quantitative
biology and evolutionary biology or a related field (PhD or
equivalent degree required), with expertise in one or more of the
following areas: computer science, mathematics, and computational
biology. A previous experience in biological modeling is expected.
A strong taste for inter-disciplinary research is required.
The appointment is for two years can start between March and June
2014. The net salary will be approximately of 24,000 Euros per
year but can depend on the previous experiences of the candidate.
Applications should include a motivation letter, a CV including a
list of publications, and the address of two-three references. The
applications, as well informal enquiries about the position, should
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Date: Mon, Jan 27, 2014 at 2:22 AM
Subject: Postdoc position - Uppsala University, Sweden
PostDoctoral researcher in Scientific Computing/Computational
Systems Biology at Uppsala University in Sweden.
The research at the Division of Scientific Computing has a broad
scope, ranging from analysis and development of numerical methods,
numerical linear algebra, software development and
high-performance computing to collaborative projects in
computational science and engineering, including computational
systems biology, and industrial applications. To qualify
for the position, the applicant must hold a PhD degree in a
relevant field. The appointment is for two years.
Applications are invited in the general area of Scientific
Computing. For examples of research that is conducted in
For further information about the position and instructions
Deadline for the applications is February 20 2014.
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Date: Mon, Jan 27, 2014 at 5:17 AM
Subject: Postdoc position - University of Groningen
PhD (4 years) position in computational modelling of biological
systems
The behavioural Ecology and Self-organization Group at the
University of Groningen is seeking to recruit a PhD student
to strengthen its research team on Self-organization of Social
systems. The position is full-time and available immediately.
Research environment
The position is part of the project ??Optimisation of navigation
for intercepting prey during aerial hunting by birds?, funded
by a Grant (ALW) from the Netherlands Science Foundation (NWO)
to Prof. dr. Charlotte Hemelrijk. The research project is a
collaborative effort of the research team on Self-organization
of Social systems and the Oxford Flight Group. Predictions
generated by the computational models will be verified with
hunts from real raptors in cooperation with the Oxford Flight
Group. Daily supervision will come from Prof. dr. Hemelrijk
and Dr. Hanno Hildenbrandt. Dr. Graham Tayler (Oxford Flight
Group, UK) will co-supervise the project. The PhD will work in
Groningen in the BESO group which is embedded in the Centre for
Ecological and Evolutionary Studies (CEES), which comprises
several other strong, internationally recognized research groups
in the field of avian and evolutionary biology. The University
of Groningen enjoys an international reputation as a dynamic and
innovative centre of higher education and belongs to the best
research universities in Europe.
Requirements
The successful candidate will have previous research experience
in theoretical modeling, be in good command of the English
language (oral and written) and possess excellent communication
skills (indicated by the ability to write scientific papers and
deliver presentations). Since studies on self-organisation are
highly interdisciplinary, successful candidates are expected to
demonstrate an active and supportive approach to
inter-disciplinary research and collaborate with other group
members. Suitable candidates can be either individuals with a
background in the computational (life-) sciences, with interest
in evolutionary and biological questions, or evolutionary
biologists with experience in computational modeling.
Candidates for the PhD position should have:
MSc in mathematical biology, a MSc in computational science
with focus on biology or an MSc in computational physics with
specialization in biology, MSc in Artificial Intelligence with
a specialization in an area of computational or mathematical
biology or a MSc in Biology, with a specialization in an area
of computational or mathematical biology. Experience with
developing computer simulation code and a sufficient background
in mathematics. A strong interest in biomechanics of flight and
attack, interest in collective, swarming behavior. Candidates
with research experience in these areas are particularly
encouraged to apply.
Conditions of employment
The University of Groningen offers a salary of ? 2,042 (salary
scale 50.0) gross per month in the first year, up to a maximum of
? 2,612 (scale 50.3) gross per month in the final year, based on a
full-time position. The position requires residence in Groningen
and must result in a PhD thesis within the 4-year contract period.
A PhD training program is part of the agreement and the successful
candidate will be enrolled in the Graduate School of Science. The
successful candidate will first be offered a temporary position of
one year with the option of renewal for another three years.
Prolongation of the contract is contingent on sufficient progress
in the first year to indicate that a successful completion of the
PhD thesis within the next three years is to be expected.
How to apply
Applications, including a letter of motivation, a curriculum vitae,
a list of publications (if any), a list of examination marks, and
the contact information of three academic referees, must be
submitted online through the website
The position will remain open until filled. All applications
received by February 15, 2014 will be given full consideration.
For further information, please consult
Informal enquiries can be made to prof. dr. Charlotte K Hemelrijk
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Subject: SMBnet Reminders
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