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Subject: SMB Digest v13i22
SMB Digest May 30, 2013 Volume 13 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:
CfP: MBMB: Knotted & Random Macromolecule Shapes: Modeling,...
Conference: Math Modelling, JBK@90, Aug 30-31, EPF Lausanne
Conference: Stochastic Models in..., Dec 9-13, Angers, France
PhD Position: Theoretical Ecology, U Groningen, The Netherlands
PhD Position: Neural Field Models, U Reading, UK
Post-doc: Infectious Disease Dynamics, U Notre Dame
Post-doc: Computational Physiology & Biostatistics, U Basel
Post-doc/Programmer Positions: Computational Biology, Okinawa
SMBnet Reminders
----------------------------------------------------
From: Zhao, Shan <szhao@as.ua.edu>
Date: May 27, 2013 4:42:14 PM
Subject: CfP: MBMB: Knotted & Random Macromolecule Shapes: Modeling,...
The journal Molecular Based Mathematical Biology (MBMB) will publish a
special issue entitled "Knotted and random macromolecule shapes:
modeling, analysis, and computation."
The purpose of this special issue is to create a medium for researchers
from mathematical and biological sciences and other related disciplines
to report novel mathematical models, computational algorithms, and
theoretical analysis for knotted and random shapes of macromolecules,
such as DNA, RNA, and proteins.
MBMB is a recently established journal, whose aim is to promote the
mathematical study of biological processes at the molecular scale.
Mathematical research findings which are related to other biomolecular
processes, such as biomolecular structures, function, dynamics and
transport, are also welcome. Original papers and high-quality review
articles on the aforementioned topics are solicited for this special
issue.
Potential topics include, but are not limited to:
-Random knotting and linking in polymers and biopolymers
-DNA topology and enzyme actions
-Knotting in proteins and other open curves
-Ropelength and knot energy constraints on knotting in biological
systems
-Geometric, topological, and algebraic modeling of macromolecules
-Mathematical methods for molecular imaging and visualization
-Biomolecular simulations and software development
Before submission authors should carefully read over the Author
Guidelines, which are located at http://www.degruyter.com/view/j/mlbmb.
All manuscripts are subject to the standard peer review process before
publication. Please note the publisher has waived the Article Processing
Charges for this special issue, but articles will be open-access in
accordance with the overall goals of the journal. Prospective authors
should submit an electronic copy of their complete manuscript via email
to Journal Associate Editor Shan Zhao at szhao@versita.com.
We are looking forward to your submission. If you have any question,
please contact Jason Cantarella at jason@math.uga.edu.
Important Dates
Manuscript Due: August 1, 2013
First Round of Reviews: September 15, 2013
Anticipated Publication Date: December 15, 2013
Guest editors: Jason Cantarella, University of Georgia (lead), Dorothy
Buck, Imperial College London, Heiko von der Mosel, RWTH Aachen, John
Sullivan, Technische Universitat Berlin, Shan Zhao, University of Alabama.
----------------------------------------------------
From: Jaroslaw Glowacki <jaroslaw.glowacki@epfl.ch>
Date: May 29, 2013 5:24:58 AM
Subject: Conference: Math Modelling, JBK@90, Aug 30-31, EPF Lausanne
A Conference to Celebrate Mathematical Modelling on the occasion of the
90th Birthday of Joseph B. Keller
August 30 & 31, 2013, at the EPF Lausanne, Switzerland
Attendance open to all, advance registration is free, but obligatory
Further details at http://lcvmwww.epfl.ch/conferences/JBK90/
----------------------------------------------------
From: sapoukhi <sapoukhi@angers.inra.fr>
Date: May 30, 2013 8:40:25 AM
Subject: Conference: Stochastic Models in..., Dec 9-13, Angers, France
We are pleased to invite you to SMEEG 2013, an international conference
on Stochastic Models in Ecology, Evolution and Genetics to be held in
Angers, France, from December 9 to 13, 2013.
This event will bring together both mathematicians and biologists who
share interests in theoretical or applied aspects of ecology, evolution
and genetic modeling.
Topics will include:
Phylogenetic reconstructions, coalescents
Generalized branching processes
Large-scale behavior and rare events in population dynamics
Spatio-temporal modeling of population dynamics (High dimensional)
Statistical inference in ecology, evolution and genetics.
There will be one keynote presentations in each session delivered by
world-leading scientists. The confirmed speakers to date are:
Linda Allen (Texas Tech University, USA)
Rick Durrett (Duke University, USA)
Amaury Lambert (Université Paris 6, France)
Sylvie Méléard (École Polytechnique, France)
Hans Metz (Leiden University, The Netherlands)
Étienne Pardoux (Université d'Aix-Marseille, France)
Terry Speed (University of California, Berkeley, USA)
Elizabeth Thompson (University of Washington, USA)
In addition, abstracts are invited for oral and poster presentations. To
submit an abstract please visit
http://smeeg2013.math.univ-angers.fr/submission.php.
The conference aims to encourage discussions of the recent
methodological and conceptual advances in these fields and to share
knowledge with young researchers. SMEEG 2013 is organized by a group of
mathematicians and biologists from the University of Angers, Agrocampus
Ouest and INRA, who are involved in MODEMAVE research project on
mathematical models applied to vegetal biology. Please see
http://smeeg2013.math.univ-angers.fr/ for the other details.
For all enquiries contact:
Natalia(dot)Sapoukhina(at)angers(dot)inra(dot)fr
----------------------------------------------------
From: R.S. Etienne <R.S.Etienne@rug.nl>
Date: May 24, 2013 8:27:39 AM
Subject: PhD Position: Theoretical Ecology, U Groningen, The Netherlands
We are looking for a candidate to fill a PhD position in theoretical
ecology.
The project is titled "Competition theory with a dominance/tolerance
trade-off: a mathematical approach to predict species abundances and
distributions. Model development, analysis, and application to data on
salt marsh." The supervisors are Claire de Mazancourt and Bart Haegeman,
Station d'Ecologie Expérimentale de Moulis, and Rampal S. Etienne,
Centre for Ecological and Evolutionary Studies, University of Groningen,
The Netherlands. The student will be based at the Centre for
Biodiversity Theory and Modelling, Station d'Ecologie Expérimentale de
Moulis, Ariège, France, with visits to the University of Groningen, The
Netherlands.
For more information see
http://www.sevab.ups-tlse.fr/fr/popup/detailsSujet.php?id=758 (in
French) or contact Claire de Mazancourt
(claire.demazancourt@ecoex-moulis.cnrs.fr) or Rampal Etienne
(r.s.etienne@rug.nl).
We are looking for a candidate with
- good communication skills in English
- experience in theoretical ecology or a background in
mathematics/physics or similar and affinity for biology
Interested candidates should apply before 31 MAY 2013 by sending a CV
and the names of three references to Claire de Mazancourt
(claire.demazancourt@ecoex-moulis.cnrs.fr) or Rampal Etienne
(r.s.etienne@rug.nl).
----------------------------------------------------
From: Ingo Bojak <i.bojak@reading.ac.uk>
Date: May 30, 2013 5:30:54 AM
Subject: PhD Position: Neural Field Models, U Reading, UK
Dendrites and layers: Neural field models in three dimensions
Prof Ingo Bojak
Cybernetics Research Group, School of Systems Engineering, University of
Reading, UK
Neural field models treat cortical tissue as continuous with emergent
properties. While classical theories consider just a single 2D "cortical
sheet", neurons are actually organized into six anatomical layers and
their connectivity depends systematically on neuron type and depth,
creating "microcircuits" across layers. We will develop a 3D neural
field theory that incorporates synaptic inputs arranged in realistic
depth patterns and produce a software package for their rapid evaluation
(possibly with GPU acceleration). We will fit laminar electrode and/or
EEG data from schizophrenic patients, and explore (speculative)
functional consequences of dendritic processing, like burst-suppression
in anesthesia or acquired epilepsy.
This is a computational neuroscience project, which requires skills and
knowledge in neuroscience, applied mathematics and programming.
Candidates with a good background in at least two of these fields are
encouraged to apply, if enthusiastic about the third. The core of this
project is formed by scientific computing and data analysis, but
according to prior experience and preference of the candidate more
emphasis could be put on mathematical development or biological
experiment, respectively. Concerning the latter the student has the
opportunity to engage with ongoing relevant electrophysiological and
animal experiments of the Co-Supervisor, Dr Ben Whalley (School of
Pharmacy), if they wish.
Eligibility: Applicants should hold a minimum of a UK Honours Degree at
2:1 level or equivalent in a relevant subject. Please note that this
studentship is for UK/EU applicants only.
Funding Details: The studentship will cover Home/EU Fees and pay the
Research Council minimum stipend (13,590 pounds for 2011/12) for up to
3 years. It will begin in October 2013.
How to apply: Please submit an application for a PhD in Cybernetics
(full time) to the University at
http://www.reading.ac.uk/Study/apply/pg-applicationform.aspx.
Please quote the reference GS13-07 in the 'Scholarships applied for' box
which appears within the Funding Section of your online application.
Once you have submitted your application, you should receive an email to
confirm receipt. Please forward this email, along with a covering
letter, to Prof Ingo Bojak (i.bojak@reading.ac.uk) by the application
deadline.
Application Deadline: Friday, 14th June 2013.
Further Enquiries: Please contact Prof Ingo Bojak
(i.bojak@reading.ac.uk).
----------------------------------------------------
From: Brajendra Kumar Singh <brajendra.singh@nd.edu>
Date: May 28, 2013 9:51:09 AM
Subject: Post-doc: Infectious Disease Dynamics, U Notre Dame
POST-DOCTORAL FELLOW POSITION in Infectious Disease Dynamics
An exciting opportunity exists to join the highly innovative,
inter-disciplinary Global Epidemiology and Biostatistics Group led by
Prof. Edwin Michael at the University of Notre Dame in the Department of
Biological Sciences and the Eck Institute for Global Health.
The successful candidate for the Infectious Disease Dynamics position
must be proficient in mathematical model construction and analysis and
interested in the application of these methods to the development,
fitting, and analyses of a suite of infectious disease models, from
compartmental SIR-type models to more complex macroparasitic
transmission models. Our current work encompasses the formulation,
validation, and dynamical analyses of major vector borne,
environmentally-mediated, and multi-pathogen models. Knowledge of the
application of both analytical and numerical methods in model analysis
will be essential. Experience with dynamical systems analysis is highly
desirable. Expertise with individual-based and/or spatially explicit
modeling techniques will be an added advantage. Experience with
data-model assimilation methods will be important as a key focus of our
work is to apply models to data from partners across the world in order
to gain a better understanding of pathogen transmission and control at
both local and global settings. Programming skills in Matlab and C are
essential, and skills in R and parallel computing are an advantage.
The successful candidates for the position should:
-Have completed a PhD or equivalent degree
-Be willing to travel internationally
-Have strong written and oral communication skills, including the
ability to publish research results and make scientific presentations
-Be expected to contribute to and collaborate with faculty and students
within the Departments of Biological Sciences, Applied and Computational
Mathematics and Statistics, Computer Science and Engineering, and the
Center for Research Computing
-Have demonstrated ability to work independently under minimal
supervision, as well as within a team environment with a strong
commitment to team-based processes and outcomes
Location: Notre Dame, Indiana, USA
Tenure: The position has funding available for 2 years in the first
instance
Salary: Based on NIH guidelines for postdoctoral fellow salaries
ABOUT THE UNIVERSITY OF NOTRE DAME
The University of Notre Dame is committed to diversity
(http://diversity.nd.edu/) in its staff, faculty, and student body. As
such, we strongly encourage applications from members of minority
groups, women, veterans, individuals with disabilities, and others who
will enhance our community. The University of Notre Dame, an
international Catholic research university, is an equal
opportunity/affirmative action employer. Information on the Eck
Institute for Global Health may be found at http://globalhealth.nd.edu
APPLICATION PROCESS:
Qualified individuals should send in PDF format a cover letter,
curriculum vitae, statement of research interest, and three letters of
reference to the search committee chair, Dr. Edwin Michael at
eigh@nd.edu. Files must be clearly named and identify the position you
are applying for. There is no deadline and the review of applications
will begin immediately upon receipt and will continue until the position
is filled. For additional information about working at the University of
Notre Dame and various benefits available to employees, please visit
http://hr.nd.edu/employment/working_at_nd.shtml.
----------------------------------------------------
From: Delgado-Eckert, Edgar <Edgar.Delgado-Eckert@ukbb.ch>
Date: May 29, 2013 7:15:39 AM
Subject: Post-doc: Computational Physiology & Biostatistics, U Basel
Post Doc in Computational Physiology and Biostatistics - 60-80%
negotiable
The Clinical Morphology and Biomedical Engineering section of the
Medical Faculty at the University of Basel, together with the University
Children's Hospital of Basel, are offering a Post Doc position within
the Computational Physiology and Biostatistics Group, led by Dr. Edgar
Delgado-Eckert.
One of the main current research activities of this group is the
analysis of time series of physiological signals, such as cardiac
activity, body temperature, movement patterns, and several lung
function parameters. The mathematical and statistical analysis of these
time series is aimed at developing new quantitative approaches of
clinical diagnostic and/or prognostic value, as well as conducting
epidemiological studies within different cohorts.
The mathematical and computational methodology used for the analysis of
these time series comprises techniques borrowed from nonlinear dynamics,
such as the largest Lyapunov exponent, and from statistics and
information theory, including sample entropy, and long range
correlations revealed by detrended fluctuation analysis.
Job Description
The candidate is expected to actively participate in some of the ongoing
projects, by contributing their own ideas, applying their expertise,
mentoring master and PhD students involved in the projects, and
implementing algorithms on the computational platforms we use (mainly
Matlab and R). In addition, the candidate will have the opportunity to
develop their own projects in coordination with the rest of the group.
Profile requirements
-PhD degree in Mathematics, Physics, Statistics, Computer Science,
Bioinformatics, Bioengineering, or a closely related field.
-Evidence of the ability to independently conduct scientific research in
the areas of Computational Physiology or Biology, Biomathematics,
Biostatistics, Bioinformatics or a closely related field is expected,
in the form of peer-reviewed scientific publications in which the
candidate appears as the first author. Submitted but not yet accepted
manuscripts do count.
-Good programming skills and some experience with the environments
Matlab and R.
-Of advantage is basic knowledge in human physiology, particularly
cardiac and respiratory function.
Please send your application to
Applications should include a curriculum vitae and three letters of
reference. The applicant should be aware that referees may be contacted.
Please send application documents by email (with "computational
physiology" in the subject line) to edgar.delgado-eckert@ukbb.ch or via
postal services to:
Dr. Edgar Delgado-Eckert
Studienzentrum Pneumologie
Universitätskinderspital beider Basel (UKBB)
Spitalstrasse 33
Postfach
4031 Basel
Switzerland.
----------------------------------------------------
From: Tatiana Marquez-Lago <tatiana.marquez@oist.jp>
Date: May 28, 2013 3:13:40 AM
Subject: Post-doc/Programmer Positions: Computational Biology, Okinawa
Title: Postdoc / programmer positions - Computational Systems Biology,
Okinawa, Japan
Description:
We are looking for an enthusiastic programmer/postdoc to work in
interdisciplinary projects aimed at developing novel
(1) stochastic/multiscaled simulation algorithms and (2) parameter
estimation techniques. The ideal candidates should have a strong
background in Computer Science and/or Applied Mathematics (numerical
analysis and probability) as well as a strong interest to collaborate
with experimental biologists and theoreticians.
Strong programming skills in Matlab and C/C++ are mandatory, while
additional experience in Perl and Python are desirable. Additionally,
experience with dynamical systems (ODEs, PDEs) is expected, but
experience in biological/chemical reaction modeling and stochastic
simulation (temporal and spatio-temporal) will be considered a plus.
Specific projects will entail constant feedback and cooperation with
experimental and theoretical groups both inside and outside Japan. Thus,
the postdoc/programmer is expected to travel and be able to work in
groups, have excellent personal and communication skills, and a
willingness to communicate research results to interdisciplinary
audiences. Knowledge of Japanese is not required (albeit language
courses will be provided to those interested), but English proficiency
is mandatory. Appointment will be done at the technician (MSc) or
postdoctoral (PhD) level, and will have a remuneration package according
to qualifications.
The successful candidate will join the Integrative Systems Biology Unit
of the Okinawa Institute of Science and Technology Graduate University
(OIST), and will work under the supervision of Assistant Professor
Tatiana T. Marquez-Lago. OIST is a university with no departments,
eliminating artificial barriers between people working in different
fields. Currently, 45 Faculty members and a growing population of over
500 scientists, students, and research support staff are located in OIST
facilities in Onna, Okinawa. English is the language of instruction and
a large segment of the faculty and student population is international.
Further details about the unit can be found on our website
(https://groups.oist.jp/isbu/members).
Further details about the position and application procedure can be
found in
(http://www.oist.jp/careers/simulation-and-parameter-estimation-systems-biology)
-OIST is an equal opportunity and affirmative action employer.
-Information provided by applicants or references will be kept
confidential.
----------------------------------------------------
Subject: SMBnet Reminders
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End of SMB Digest
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