----------------------------------------------------
Subject: SMB Digest v13i28
SMB Digest July 9, 2013 Volume 13 Issue 28
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:
Conference: SMB Annual Meeting, Jul 28 - Aug 1, 2014, Osaka
BMB: Complementary Special Issue on "Logical Modelling"
PhD Position: Amyloid Fibril Formation: Imperial College London
PhD Position/Post-doc: Bioinformatics/Comp Bio, UNSW, Australia
Post-doc: Modelling Secondary Contacts..., INRA Angers, France
Post-doc: Neural Simulator, SUNY Downstate, NY
Post-doc: Computational Biology, Arizona State U
Head: CS, Math, Physics, & Stats, UBC, Okanagan Campus, Canada
SMBnet Reminders
----------------------------------------------------
From: Toshiyuki Namba <tnamba@b.s.osakafu-u.ac.jp>
Date: July 5, 2013 11:02:10 PM
Subject: Conference: SMB Annual Meeting, Jul 28 - Aug 1, 2014, Osaka
The Joint Annual Meeting of the JSMB and the SMB will be held
July 28-August 1, 2014, in Osaka, JAPAN
Venue: Osaka International Convention Center, Osaka, Japan.
http://www.gco.co.jp/en/
This is the third joint meeting of the SMB and the JSMB, after the first
at Hiro, Hawaii in 2001, and the second at San Jose, California in 2007.
This time, the joint meeting will be held in Japan, and co-sponsored by
the Chinese Society for Mathematical Biology and the Korean Society for
Mathematical Biology.
We would like to invite you to Osaka in Japan, next July.
The JSMB and all people in the Asian mathematical biology community will
welcome world-wide participants.
Call for mini-symposium proposals for the JSMB/SMB2014 joint meeting
will soon open.
Please visit the website, http://www.jsmb.jp, for details.
CHAIR of the meeting:
Masayasu Mimura (Tokyo, Japan)
PLENARY SPEAKERS (confirmed):
Nanako Shigesada
(2013 Akira Okubo Prize Awardee,
Professor Emeritus of Nara Women's University, Japan)
Carson C. Chow (NIH, USA)
Iain D. Couzin (Princeton University, USA)
Steve A. Frank (Univ. California at Irvine, USA)
Hawoong Jeong (KAIST, Korea)
Laura Miller (University of North Carolina, USA)
Akiko Satake (Hokkaido University, Japan)
Tatsuo Shibata (Center for Developmental Biology, RIKEN Kobe, Japan)
Yanni Xiao (Xi'an Jiaotong University, China)
----------------------------------------------------
From: P.K. Maini <springeralerts@springer.delivery.net>
Date: July 8, 2013 3:00:28 AM
Subject: BMB: Complementary Special Issue on "Logical Modelling"
The Bulletin of Mathematical Biology has launched two significant
initiatives to help our readers keep abreast of the field and stay on
top of the latest research.
We are delighted to announce that Professor James Sneyd, University of
Auckland, has taken up the new position of "Review Editor" and he will
be actively seeking review articles in areas of interest to readers of
the BMB. Please see the journal homepage for further details.
We have also significantly increased our activity in soliciting special
issues and, as detailed below, there are a number of these to appear in
the coming months. The first, "Logical Modelling of Regulatory Networks,
Methods and Applications", co-edited by Claudine Chaouiya and Elisabeth
Remy, presents a number of papers on the analysis of regulatory networks
within the logical framework. Several different approaches are
considered and a number of applications presented and we are pleased to
offer complimentary access to the entire issue.
Read the Special Issue on "Logical Modelling"
Edited by Claudine Chaouiya and Elisabeth Remy
-Remarks on the Respective Roles of Logical Parameters and Time Delays
in Asynchronous Logic: An Homage to El Houssine Snoussi, R. Thomas
-On Circuit Functionality in Boolean Networks, J. Comet, M. Noual,
A. Richard et al.
-Analysis and Characterization of Asynchronous State Transition Graphs
Using Extremal States, T.Lorenz, H. Siebert, A. Bockmayr
-Deconstruction and Dynamical Robustness of Regulatory Networks:
Application to the Yeast Cell Cycle Networks, E. Goles, M. Montalva,
G. A. Ruz
-Probabilistic Approach for Predicting Periodic Orbits in Piecewise
Affine Differential Models, M. Chaves, E. Farcot, J. Gouzé
-Dynamics of Influenza Virus and Human Host Interactions During
Infection and Replication Cycle, A. Madrahimov, T. Helikar, B. Kowal,
G. Lu, J. Rogers
-A Virtual Culture of CD4+ T Lymphocytes, Luis Mendoza
Enjoy complimentary access to the full special issue at
http://link.springer.com/journal/11538/75/6/page/1 until August 15th
Forthcoming Special Issues
-Biomedical Modelling: The role of transport and mechanics' (publishing
August 2013)
-Stochastic Modelling of Reaction-Diffusion Processes' (publishing late
2013/early 2014)
-Spatial moment techniques for modelling biological processes
(publishing mid-2014). The full call for papers can be found here:
https://www.springer.com/?SGWID=0-102-2-1418043-0&utm_campaign=SOC19808_1&utm_medium=newsletter&utm_source=email&wt_mc=email.newsletter.SOC19808_1
-Towards a Quantitative Science of Sustainability: Challenges and
Opportunities (publishing 2014). The full call for papers can be found
here:
https://www.springer.com/?SGWID=0-102-2-1426341-0&utm_campaign=SOC19808_1&utm_medium=newsletter&utm_source=email&wt_mc=email.newsletter.SOC19808_1
Sincerely,
P. K. Maini
Centre for Mathematical Biology, Mathematical Institute, Oxford, UK
Editor
----------------------------------------------------
From: Chiu Fan Lee <c.lee@imperial.ac.uk>
Date: July 4, 2013 6:45:44 PM
Subject: PhD Position: Amyloid Fibril Formation: Imperial College London
PhD studentship available: Theoretical investigations of amyloid fibril
formation
Supervisor: Dr Chiu Fan Lee
(http://www.bg.ic.ac.uk/research/c.lee/index.html)
The three-year PhD studentship is available to start immediately in the
Self-Organisation and Pattern Formation group in the Department of
Bioengineering at Imperial College London. The studentship is fully
funded for UK or EU applicants.
Amyloid formation is intimately related to many diseases, including
Alzheimer's, Parkinson's and other prion diseases. To investigate the
biophysical mechanism of amyloid fibril formation, our group employs
statistical mechanics, soft condensed matter physics, applied
mathematics, and computational methods. We collaborate closely with
experimental biologists. Please see the relevant papers below for more
information.
The candidates must have a good first degree (1st class or good 2:1 in
the UK, or its equivalent) in physics, mathematics, engineering, or
computer science and should have a strong mathematical ability and
interest in interacting with experimentalists. To apply, please submit
an online application at
http://www3.imperial.ac.uk/registry/admissions/howtoapplypg. Informal
enquires to c.lee@imperial.ac.uk are encouraged.
----------------------------------------------------
From: Fabio Luciani <luciani@unsw.edu.au>
Date: July 3, 2013 5:05:56 PM
Subject: PhD Position/Post-doc: Bioinformatics/Comp Bio, UNSW, Australia
PhD position/postdoc - Bioinformatics / Computational Biology
The Evolutionary Dynamics in Infectious Diseases Group at the University
of New South Wales is looking for PhD students to work on research
projects in the area of bioinformatics / computational biology that are
aimed at studying viral evolution in hepatitis B and C viruses, and the
role of host immune response during viral infections. The research work
within the group is based on interdisciplinary projects between
bioinformatics / computational biology/ virology/ immunology and will
involve high-throughput data, such as next-generation sequencing.
PhD
Projects are suited to students with a strong background in quantitative
disciplines such as Bioinformatics, Computer Science, Physics,
Mathematics or similar. Acceptance is competitive, with a first class
honors degree (or equivalent) and a GPA of >87% required. Successful
applicants will join a team of researchers in the Inflammation and
Infection Research Centre, which hosts 70 students and researchers in
various field of Medical Sciences. There is also a great opportunity to
interact with researchers involved in wet-lab activities.
Group's research interests are available at:
http://medicalsciences.med.unsw.edu.au/people/dr-fabio-luciani
and
http://medicalsciences.med.unsw.edu.au/research/groups/inflammation-and-infection-research
Post-graduate scholarships are available to support tuition and living
expenses for domestic (Australian Postgraduate Award APA) and overseas
PhD students to study in Australia. More information on the postgraduate
research scholarships is available at:
http://research.unsw.edu.au/postgraduate-research-scholarships
Postdoctoral fellowships are also available at University of New South
Wales, via the Vice Chancellor scheme, please refer to
http://www.hr.unsw.edu.au/services/recruitment/jobs/14061314.html
Applications close : 23 August 2013.
Interested applicants should contact Dr Fabio Luciani:
luciani@unsw.edu.au.
Please include a cover letter and CV that provide details about research
interests, education, employment history (if any), skills.
----------------------------------------------------
From: sapoukhi <sapoukhi@angers.inra.fr>
Date: July 5, 2013 2:36:07 AM
Subject: Post-doc: Modelling Secondary Contacts..., INRA Angers, France
POSTDOCTORAL POSITION: Modelling secondary contacts between divergent
populations in heterogeneous environments for studying the role of
coupling genetic barriers in disease emergence
The Research Unit of Evolutionary Ecology of Fungal Pathosystems
(EcoFun) at the IRHS (Research Institute of Horticulture and Seeds,
University of Angers, INRA, Agrocampus-Ouest) invites applications for a
one-year postdoctoral position in the field of theoretical spatial
genetics. This position may be renewed for an additional year based upon
the availability of funds. The position is available from the November
2013 (with a flexible start date). The net salary will be approximately
of 24,000 Euros per year.
Global exchanges and climatic changes play a determinant role in the
emergence of human, animal and plant diseases. Secondary contacts
between divergent pathogen populations can favour the occurrence of new
recombinants that are potentially more aggressive or resistant to
treatments. Conventionally, potential for hybridization (and then
recombination) within pathogen populations is linked to the presence of
exogenous (host-dependent) genetic barriers, and the role of
host-independent, so-called endogenous, genetic barriers is less
investigated. Recently, one-dimensional models have shown that such
endogenous barriers are numerous and tend to be spatially correlated.
This process is called coupling. It does not exist any spatially
explicit model which tests whether spatial heterogeneity of habitats can
maximise the coupling. In the case of pathogens, maximising the coupling
effects would reduce the risk of emergence of recombinants. The goal of
the project is to build a parsimonious spatially explicit model of
behaviour of endogenous and exogenous genetic barriers occurring in a
heterogeneous environment. The project constitutes a new conceptual
approach in the understanding of mechanisms of reproductive isolation in
pathogens and the emergence of new infectious diseases.
The successful candidate is expected to develop and validate the model.
The candidate will collaborate with experimentalists working on pathogen
genetics towards designing well-suited strategies of geographical
deployment of resistant cultivars that could prevent rapid pathogen
evolution and spread.
A desirable candidate with a strong (Ph.D.) mathematical background and
experienced in theoretical population genetics will have good computer
programming skills as well as a real interest in evolutionary
epidemiology. The candidate should also have good interaction capability
with experimentalists and a proven record of independent research.
Successful applicants will join an active research team that spans many
areas of plant pathology, genetics, and mathematical biology. Our unit
studies the evolutionary processes of pathogen adaptation to resistant
cultivars carrying quantitative and qualitative resistance, with the aim
to improve the resistance durability.
Applicants should forward, no later than the 15th October, 2013, a cover
letter detailing motivation, training, work experience and future plans,
a curriculum vitae, a publications list, and three references or
recommendation letters to Dr. Christophe Lemaire,
christophe.lemaire@univ-angers.fr and Dr. Natalia Sapoukhina
natalia.sapoukhina@angers.inra.fr.
----------------------------------------------------
From: Bill Lytton <billl@neurosim.downstate.edu>
Date: July 8, 2013 7:35:08 AM
Subject: Post-doc: Neural Simulator, SUNY Downstate, NY
Postdoctoral simulator
Postdoctoral fellowship is available as part of an ongoing project to
add Reaction-Diffusion simulation to the widely-used NEURON neural
simulator (www.neuron.yale.edu). Although this postdoctoral experience
will be highly technical, the context is biology and we ensure that all
of our advances are published and accessible for dissemination to a
biological audience -- i.e., there is ample opportunity for authorship.
Candidates should have a strong background in computer programming, with
demonstrated fluency in C/C++ or Python or some other major programming
language, ideally with a substantial software project to show for it.
Familiarity with cell biology, neurobiology or chemistry simulation is a
plus. Familiarity with Unix is important. Numerical integration,
MPI/HPC, version control (we use hg) nice too.
This position offers an opportunity to link develop novel software tools
that will be widely used by the research community. The postdoc will
receive training in a wide range of interdisciplinary skills from
computer science, applied math, biophysics, cell biology,
electrophysiology, etc. The work is being performed in close
collaboration with experimental laboratories, giving the opportunity to
immediately determine how closely a modeling technique can match the
experimental reality (or in rare cases, how adequately experimental
artifact can be reduced so as to match models). The work is being done
under the auspices of the National Institute of Mental Health and has
substantial clinical translational potential for making linkages
between genomics, proteomics, pharmacotherapy and neuronal/network
outcomes for psychiatric and neurological disorders. The NIH and other
agencies (FDA,NASA,NSF,DARPA,others) have a strong interest in this
multiscale modeling approach, sponsoring an annual meeting for which the
laboratory has taken major initiatives.
Further details: This project offers a number of interfacing and
development challenges. 1. Ion concentrations at the surface determine
driving forces for channels, calculated as a Nernst potential or via
Goldman-Hodgkin-Katz equations. These surface-layer concentrations must
be in placed into equilibrium with diffusing ion concentrations within
cytoplasm. 2. Potential gradients also arise across internal membranes.
It has been hypothesized that the endoplasmic reticulum (ER) exists as a
"neuron within the neuron" that signals both via electrical and calcium
signaling. 3. One cannot simply handle the whole neuron as 1 big
diffusion problem: neurons are too big and have different cytoplasmic
domains that require different types of simulation: stochastic 3D for
spines, deterministic 1D for major dendrites, deterministic 3D for soma.
This requires developing a number of simulators within the simulator and
interfacing all of them properly. 4. Standard neural tracings, which
are quite adequate for electrical simulation, lack the detail required
to produce watertight volumes for reaction-diffusion modeling -- we are
developing algorithms to map the approximate full surface and instrument
both surfaces and the enclosed volumes. 5. Reaction schemes can be
extremely complex, yet often lacking in the kinetic parameters that
would be needed to produce an accurate ODE representation. Therefore
instead of using full kinetic descriptions we may need to use highly
simplified Boolean networks (BNs) or other rule-based representations.
These representations must then be interfaced with kinetic
representations and with diffusion mechanisms.
Applicants should contact Bill Lytton by email
(billl@neurosim.downstate.edu; no snail please) with a CV and cover
letter. SUNY is an equal opportunity employer.
----------------------------------------------------
From: Joseph Zhou <joseph.x.zhou@gmail.com>
Date: July 8, 2013 11:40:24 AM
Subject: Post-doc: Computational Biology, Arizona State U
PostdoctoralFellowship at Arizona State University
The Beyond Center for Fundamental Concepts in Science
(http://beyond.asu.edu) at Arizona State University invites applications
for a postdoctoral research position in origin of life research,
specifically focusing on the physics governing the transition from
nonliving to living matter,to start in Fall 2013. Ideal candidates will
have a background in computational modeling of complex systems,
information theory, and/or dynamical systems. Members of the group
include Paul Davies and Sara Imari Walker. Applicants should send a
cover letter, curriculum vitae, and a statement of research interests,
and should arrange to have 3 letters of recommendation sent to Jeanette
Perez at perezjr@asu.edu by July 15th, 2013 for full consideration.
Application materials in pdf format are preferred. Further enquiries
should be emailed directly to Sara Imari Walker (sara.i.walker@asu.edu)
or Paul Davies (paul.davies@asu.edu).
A background check is required for employment. Arizona State University
is an equal opportunity/affirmative action employer committed to
excellence through diversity. Women and minorities are encouraged to
apply.
----------------------------------------------------
From: Rebecca Tyson <rebecca.tyson@ubc.ca>
Date: July 7, 2013 10:11:57 PM
Subject: Head: CS, Math, Physics, & Stats, UBC, Okanagan Campus, Canada
Irving K. Barber School of Arts and Sciences
Head of Computer Science, Mathematics, Physics and Statistics?Associate
or Full Professor Competition: HEAD UNIT 5?13
The Irving K. Barber School of Arts and Sciences at the University of
British Columbia, Okanagan Campus, invites applications for the position
of Head of Computer Science, Mathematics, Physics, and Statistics. This
administrative Unit is one of eight Units within the Irving K. Barber
School of Arts and Science and has a total of 25 faculty members and 3
staff members. Graduate students have access to graduate programs in
mathematics and interdisciplinary studies. Undergraduate programs
include majors and minors in each of the four disciplines, as well as
specialized interdisciplinary programs in Mathematical Physics and
Mathematical Sciences.
The ideal candidate will be in the early stages of the Full Professor
rank, although a senior Associate Professor may also be considered. The
Head's position includes a faculty appointment. We are seeking a
candidate with demonstrated excellence in research, teaching, leadership
and management skills, with proven ability to lead and motivate faculty,
staff, and students. Field of research specialization can be related to
any area of Computer Science, Mathematics, Physics, or Statistics. We
are especially interested in candidates spanning at least two of these
areas. Desirable attributes include a strong record of published
research and external funding as well as prior experience in academic
administration and undergraduate and graduate education.
The Head will provide administrative, intellectual, and academic
leadership of the Unit and will serve on the Faculty's Leadership Team.
The Head is expected to: (i) oversee the overall operation of the Unit,
including the budget (ii) ensure that courses are suitably staffed
(iii) take an active role in advancing the Unit?s programs and
activities through curriculum and program review, (iv) foster collegial
interaction among faculty members, (v) mentor members of the Unit,
(vi) conduct annual evaluations of each faculty member in the Unit, and
(vii) serve as the advocate for Unit members within the Faculty and the
University. Direct experience with managing reappointment, tenure and
promotion processes and familiarity with budget processes are considered
assets. As a faculty member of the Unit, the Head will be expected to
maintain an active research program in his/her chosen field, to
supervise graduate students, and otherwise contribute to the Unit's
teaching programs.
UBC is one of the world's top universities. The university has two
distinct campuses, one in Vancouver and one in Kelowna. UBC's Okanagan
campus, located in the city of Kelowna, at the heart of the Okanagan
Valley has over 8,400 students in six Faculties, including strong
graduate programs at all levels. Kelowna is connected by direct flights
to major Canadian and USA cities and the region is considered one of the
most desirable regions to live in Canada.
The position will be available July 1, 2014 with a five-year renewable
term. The Head reports directly to the Dean of Irving K. Barber School
of Arts and Sciences.
For more information about the Faculty, see
http://www.ubc.ca/okanagan/academic/welcome.html
How to Apply
Applicants should provide: A cover letter that clearly identifies all
related administrative experience, including a statement of the
candidate's philosophy or approach to leadership; an up-to-date
curriculum vitae; statements of a program of research and of teaching
interests; evidence of teaching ability; and the name, title, and
contact information of three referees. Following the initial review of
applications, candidates selected for further consideration will be
asked to provide letters from the referees.
All documents must be submitted as e-mail attachments and sent to
recruitment.bsas@ubc.ca. Preferred formats are Microsoft Word (.doc) and
Adobe Acrobat (.pdf). Please put the competition title (Head, Unit 5?13)
on the subject line of the e-mail and state whether you are currently
legally entitled to work in Canada.
The closing date for all applications is - September 30, 2013.
Please direct inquiries to: Associate Dean Barbara Rutherford, Irving K.
Barber School of Arts and Sciences (barbara.rutherford@ubc.ca)
All appointments are subject to budgetary approval.
UBC hires on the basis of merit and is committed to employment equity.
All qualified persons are encouraged to apply. We especially welcome
applications from members of visible minority groups, women, Aboriginal
persons, persons with disabilities, persons of minority sexual
orientations and gender identities, and others with the skills and
knowledge to engage productively with diverse communities. Government
regulations require that Canadians and permanent residents of Canada
will be given priority.
----------------------------------------------------
Subject: SMBnet Reminders
To subscribe to the SMB Digest please point your browser at
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Submissions to appear in the SMB Digest may be sent to
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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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