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Subject: SMB Digest v13i24
SMB Digest June 14, 2013 Volume 13 Issue 24
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:
Workshop: Semantic, Social & Mobil..., Oct 16-18, NETTAB, Italy
Workshop: Analyzing Animal Vocal..., Oct 21-23, NIMBioS, UTK
Workshop: Vectored Plant Viruses, Mar 17-19, NIMBioS, UTK
Newsletter: NIMBioS, UTK
Newsletter: EMBL, Heidelberg
PhD Position: Inverse Problems for Cell Motility, U Sussex, UK
Post-doc: Mathematical Biology, U Oxford
Post-doc: Integrated Math Oncology, Moffitt Cancer Center, US
Post-docs: Computational Biology, INRIA Paris
University Assistant with Doctorate: IMSC, U Graz, Austria
SMBnet Reminders
----------------------------------------------------
From: Paolo Romano <paolo.dm.romano@gmail.com>
Date: June 7, 2013 7:11:00 AM
Subject: Workshop: Semantic, Social & Mobil..., Oct 16-18, NETTAB, Italy
LAST CALL FOR ABSTRACTS FOR ORAL COMMUNICATIONS
NETTAB 2013 Workshop on
"Semantic, Social, and Mobile Applications for Bioinformatics and
Biomedical Laboratories"
October 16-18, 2013, Lido of Venice, Italy
http://www.nettab.org/2013/
NETTAB 2013 will explore mobile, social, and semantic solutions for
bioinformatics and laboratory informatics. A savvy combination of these
technologies could enhance the research outcome of life scientists and
simplify workflows in biomedical laboratories.
KEYNOTE SPEAKERS
+ Barend Mons, Leiden University Medical Center, and Netherlands
Bioinformatics Center, The Netherlands
+ Antony Williams, Royal Society of Chemistry, USA
+ Ross D. King, University of Manchester, Manchester, United Kingdom
TUTORIAL PRESENTERS (confirmed only, more will be announced soon)
+ Andrea Splendiani, IntelliLeaf, United Kingdom, and Digital Enterprise
Research Institute, Ireland
+ Dominique Hazael-Massieux, W3C/ERCIM, Sophia Antipolis, Biot, France
+ Alex Clark, Molecular Materials Informatics, Inc
VENUE
The workshop will be held in the Congress Center "Palazzo ex Casino del
Lido" in Lido of Venice.
DEADLINES
? July 5, 2013: Abstract submission deadline for Oral communications
? July 31, 2013: Abstract submission deadline for Posters
? September 13, 2013: Early registration deadline
TOPICS
We are looking for abstracts on all aspects of the focus theme,
including issues, methods, algorithms, and technologies for the design
and development of tools and platforms able to provide Semantic, Social,
and Mobile applications supporting bioinformatics and the activities
carried out in a biomedical laboratory. An extended list of topics is
available at http://www.nettab.org/2013/call.php .
INSTRUCTIONS
We welcome structured abstracts for oral communications,
industrial-technological communications, and posters. Abstracts for oral
communications and Industrial-technological communications should be
between 3 and 4 pages, including no more than TWO tables / figures.
Abstracts for posters should be between 2 and 3 pages, including no more
than ONE table or figure. All abstracts should include the following
sections: Motivation and Objectives, Methods, Results and Discussion,
Acknowledgements, References. Accepted abstracts will be included in the
Proceedings of the workshop, that will be published in a Supplement of
EMBnet.journal. Full papers from abstracts presented at NETTAB 2013 will
be published in a peer-review, indexed, international journal that will
soon be announced.
SUBMISSION
Structured abstracts must be submitted at
http://conference.embnet.org/index.php/NETTAB/ . Authors must first
register at
http://conference.embnet.org/index.php/NETTAB/NETTAB2013/user/account .
The abstract must be prepared by using the template
http://www.nettab.org/2013/docs/Nettab_abstractTemplate.doc . Full
instructions for the preparation of the abstract are available at
http://conference.embnet.org/index.php/NETTAB/NETTAB2013/about/submissions#authorGuidelines .
----------------------------------------------------
From: Catherine Crawley <ccrawley@nimbios.org>
Date: June 10, 2013 9:53:55 AM
Subject: Workshop: Analyzing Animal Vocal..., Oct 21-23, NIMBioS, UTK
The National Institute for Mathematical and Biological Synthesis
(NIMBioS) is now accepting applications for its Investigative Workshop,
"Multidisciplinary Approaches to Analyzing Animal Vocal Communication
Sequences," to be held October 21-23, 2013, at NIMBioS.
Objectives: The aim of this workshop is to bridge the gap between
mathematical and biological researchers with an interest in the
quantitative analysis of animal vocal sequences. Recent developments in
the mathematical analysis of complex animal communication have
generated opportunities to understand the functional aspects of animal
vocalizations, their role in social organization, and ultimately to
explore the origins and evolution of human language. Until now, however,
the collaboration between mathematicians/computer scientists and
biologists/zoologists in this field has been very limited. We aim to
define the state of the art in this field, explore new horizons for
collaboration, and provide new techniques through a synthesis of the
mathematical and biological approaches to communication analysis. We
will also use this unique gathering to define some of the key questions
that need to be posed to address ultimate and proximate hypotheses about
behavior, in the context of animal vocal communication systems.
Location: NIMBioS at the University of Tennessee, Knoxville
Co-Organizers: Dan Blumstein, Ecology & Evolutionary Biology, Univ. of
California, Los Angeles; Marie A. Roch, Computer Science, San Diego
State Univ.; and Arik Kershenbaum, NIMBioS, Univ. of Tennessee,
Knoxville
For more information about the workshop and a link to the online
application form, go to http://www.nimbios.org/workshops/WS_vocal
Participation in the workshop is by application only. Individuals with a
strong interest in the topic are encouraged to apply, and successful
applicants will be notified within two weeks of the application
deadline. If needed, financial support for travel, meals, and lodging is
available for workshop attendees.
Application deadline: June 24, 2013
The National Institute for Mathematical and Biological Synthesis
(NIMBioS) (http://www.nimbios.org) brings together researchers from
around the world to collaborate across disciplinary boundaries to
investigate solutions to basic and applied problems in the life
sciences. NIMBioS is sponsored by the National Science Foundation, the
U.S. Department of Homeland Security, and the U.S. Department of
Agriculture with additional support from The University of Tennessee,
Knoxville.
----------------------------------------------------
From: Catherine Crawley <ccrawley@nimbios.org>
Date: June 10, 2013 11:11:04 AM
Subject: Workshop: Vectored Plant Viruses, Mar 17-19, NIMBioS, UTK
The National Institute for Mathematical and Biological Synthesis
(NIMBioS) is now accepting applications for its Investigative Workshop,
"Vector Transmission of Plant Viruses," to be held March 17-19, 2014, at
NIMBioS.
Objectives: Plant viruses are among the greatest limiting factors to
modern agriculture. Climate change and the emergence of new viral
strains affect the health and biodiversity of crops and of plants in
general, while the continued growth of the human population emphasizes
the need for sustainable agriculture. This workshop will provide a forum
for discussion of current problems on vectored transmission of plant
viruses, with the goal of identifying mathematical, computational, and
statistical methods, as well as insights derived using these methods. In
addition, this workshop may lead to new collaborations and working
groups on methods for prevention and control of vector transmission of
plant viruses, which promote sustainable agricultural practices and
reduce species invasions. The problems in vector transmission of plant
viruses are not simple; they are multiscale and often are driven by data
from specific crops or fields. This workshop will bring together experts
in plant pathogens, agronomy, and vector and plant virology, physiology,
and ecology with mathematical and statistical modelers to discuss
problems in prevention and control of vector transmission of plant
pathogens.
Some sample breakout sessions envisioned for this workshop include the
following:
-Linking genomics and other molecular information to epidemiological
dynamics
-Evolution of novel virus strains
-Modeling transmission mechanisms (climate effects, environmental
determinants, coinfection)
-Epidemiological consequences of mode of virus transmission
-Spatial spread of vector-borne infection
-Reducing and controlling the rate of spread of emerging virus strains
-Insect dispersal and vector behavior
Location: NIMBioS at the University of Tennessee, Knoxville
Co-Organizers: Linda J. S. Allen, Mathematics and Statistics, Texas Tech
Univ., Lubbock; Vrushali A. Bokil, Mathematics, Oregon State Univ.,
Corvallis; Elizabeth T. Borer, Ecology & Evolutionary Biology, Univ. of
Minnesota, Minneapolis; Alison G. Power, Ecology & Evolutionary Biology,
Cornell Univ., Ithaca, NY; Frank Van Den Bosch, Computational and
Systems Biology, Rothamsted Research, Hertfordshire, UK;
For more information about the workshop and a link to the online
application form, go to http://www.nimbios.org/workshops/WS_plantviruses
Participation in the workshop is by application only. Individuals with a
strong interest in the topic are encouraged to apply, and successful
applicants will be notified within two weeks of the application
deadline. If needed, financial support for travel, meals, and lodging is
available for workshop attendees.
Application deadline: October 28, 2013
The National Institute for Mathematical and Biological Synthesis
(NIMBioS) (http://www.nimbios.org) brings together researchers from
around the world to collaborate across disciplinary boundaries to
investigate solutions to basic and applied problems in the life
sciences. NIMBioS is sponsored by the National Science Foundation, the
U.S. Department of Homeland Security, and the U.S. Department of
Agriculture with additional support from The University of Tennessee,
Knoxville.
----------------------------------------------------
From: NIMBioS <newsletter@nimbios.org>
Date: June 6, 2013 9:27:13 AM
Subject: Newsletter: NIMBioS, UTK
For the bi-monthly newsletter of the National Institute for Mathematical
and Biological Synthesis (NIMBioS), go to
http://archive.constantcontact.com/fs105/1102610363105/archive/1113671969338.html
----------------------------------------------------
From: EMBL Events Newsletter <events@embl-events.de>
Date: June 13, 2013 2:06:39 AM
Subject: Newsletter: EMBL, Heidelberg
For the monthly newsletter of the European Molecular Biology Laborator
(EMBL), go to http://www.embl.de/events/newsletter/2013/june/index.html
----------------------------------------------------
From: Anotida Madzvamuse <A.Madzvamuse@sussex.ac.uk>
Date: June 13, 2013 4:24:07 AM
Subject: PhD Position: Inverse Problems for Cell Motility, U Sussex, UK
EPSRC PhD studentship on inverse problems for cell motility, University
of Sussex, UK
We invite applications for a PhD studentship at the Department of
Mathematics, University of Sussex. The research will focus on inverse
problems for cell motility.
This studentship is jointly funded by EPSRC and the School of
Mathematical & Physical Science, University of Sussex.
The Project in detail:
Modeling the motility of cells is of great importance due to the central
role that it plays in phenomena such as embryonic development, cancer,
tissue development, and immune responses. The complexity of cellular
processes means that the precise mechanisms of cell motility are not
fully understood. Continuum models of cell motility are overwhelmingly
phenomenological and usually couple the mechanics of geometrically
evolving objects describing the cell membrane to partial differential
equations for the involved biochemistry posed either in the cell body or
on the cell membrane. Only recently has it been possible to simulate
model equations using numerical methods. New experimental techniques for
tracking and imaging cells as they migrate now provide high-resolution
reliable time-series data, suitable for use in mathematical modeling.
The goal of this studentship is to work on the blending of experimental
data of migrating cells with mathematical/computational modeling of cell
motility, which leads naturally to inverse problems. Model parameters,
or more generally functions, will be estimated from experimental data
which will drive the future mathematical modeling.
Project objectives:
Extend our existing models for cell motility. Investigate and implement
fast, robust and accurate solvers for the model equations in
multi-dimensions. Develop a methodology for the solution of inverse
problems in cell motility. For suitable simplifications, attempt to
prove theoretical results about the existence of solutions to the model
equations and the convergence of numerical methods. The project will be
jointly supervised by Dr Anotida Madzvamuse (a.madzvamuse@sussex.ac.uk)
and Dr Chandrasekhar Venkataraman (C.Venkataraman@sussex.ac.uk). A
Research Training Support Grant will be made available for additional
training, visits to conferences etc.
Award amount
13726 pounds tax-free maintenance bursary plus fees waived for 3.5
years.
Eligibility
Only UK and EU residents are eligible. UK residents are eligible for
full awards, including fees and maintenance. EU residents are eligible
for awards covering fees only, but EU students who have studied in the
UK for the previous three years may be eligible for a full award. For a
precise statement of eligibility, please consult this EPSRC web page:
http://www.epsrc.ac.uk/skills/students/help/Pages/eligibility.aspx
Applicants must have a Master?s degree at Distinction (first class)
level in mathematics, or a closely-related field, or equivalent
qualifications. A very strong background in PDEs & differential
geometry, or mathematical biology, or numerical analysis & scientific
computing, is essential. Previous experience in the numerical solution
of partial differential equations is also essential.
How to Apply
Apply through the Sussex on-line postgraduate application system:
http://www.sussex.ac.uk/study/pg/applying/2013entry/onlineapplication
In the Other Information/Funding Section state that you are applying for
"The PhD studentship on inverse problems for cell motility with Dr
Anotida Madzvamuse". You should upload a copy of your CV and a personal
statement. The statement should be at least 750 words and should
describe your research experience relevant to the project, and what you
hope to achieve from the PhD. Send an email to Dr Anotida Madzvamuse
(a.madzvamuse@sussex.ac.uk) to confirm that you have applied on-line for
this award.
Timetable
The very latest date we can consider applications is 2nd September 2013.
Early application is advised because the studentship will be awarded as
soon as a suitable candidate is found. The start date of the studentship
is 19th September 2013.
Further information
The PhD student will gain training in state-of-the-art numerical methods
for solving PDEs on and for surfaces, PDEs in time dependent domains, as
well as inverse and optimization problems. The student will also gain
expertise in truly interdisciplinary research that will act as a strong
foundation from which he or she will be able to forge a successful
career in either academia or industry.
Contact details
Informal enquiries should be directed to Dr Anotida Madzvamuse
(a.madzvamuse@sussex.ac.uk) or Dr Chandrasekhar Venkataraman
(C.Venkataraman@sussex.ac.uk).
http://www.maths.sussex.ac.uk/~am328/
http://www.maths.sussex.ac.uk/Staff/CV/
----------------------------------------------------
From: Philip Maini <maini@maths.ox.ac.uk>
Date: June 9, 2013 8:52:50 AM
Subject: Post-doc: Mathematical Biology, U Oxford
Postdoctoral Research Assistant in Mathematical Biology: A
multidisciplinary approach to study crypt-villus homeostasis and
regeneration in the intestinal epithelium
Vacancy Reference: 108193
Grade: 7
Salary Range: Salary in the range 29,541 - 32,267 p.p.a.
Appointment Term: 36 months fixed term
We invite applications for a Postdoctoral Research Assistant, funded by
the BBSRC, to work with Professors Philip K. Maini, Wolfson Centre for
Mathematical Biology, Mathematical Institute, University of Oxford, and
Helen M. Byrne, Oxford Centre for Collaborative Applied Mathematics,
and Computational Biology Group, University of Oxford. This is a 3 year
fixed term position and is available from 1st October 2013.
This is part of a new exciting collaboration between the Wolfson Centre
for Mathematical Biology (WCMB) and the Institute of Food Research
(IFR) at the University of East Anglia. Recent experimental research has
generated fundamental insight into the biology of the gastrointestinal
tract, which is essential for long-term gut health. However, it has also
revealed important questions concerning the mechanisms of regulation of
the small intestinal epithelium in crypts and villi. The purpose of this
project is to combine theoretical approaches with experimental work to
identify the mechanisms that regulate homeostasis in the healthy
intestinal epithelium and those that restore equilibrium after
perturbations. The successful candidate will join a multidisciplinary
team of reseachers from the WCMB and IFR to develop a multiscale
computational framework which can be used to test and generate
biological hypotheses regarding regulation in the gut. Model predictions
will be tested by the experimental group at the IFR (who will employ an
experimental postdoc on this grant - for further details on the
Biologist position in Norwich please visit
http://www.ifr.ac.uk/info/about/vacancies/ or contact
carmen.pin@ifr.ac.uk) and the model refined accordingly. This iteration
between theory and experiment will ensure that the modelling is
biological realistic and that the experiments are designed for maximum
efficiency. As part of general professional training, the successful
candidate may be required to teach up to four undergraduate classes per
year.
With a Ph.D. awarded in applied mathematics, or a related discipline,
the successful candidate will have expertise in modelling (preferably of
biological systems), computing and techniques of applied mathematics.
Applicants should read the job description document before writing their
application. As part of the online application, the applicant will be
required to upload a statement setting out how she or he meets the
selection criteria, a curriculum vitae including a list of publications,
a statement of research interests, and the names and contact details of
two referees.
Please direct informal enquiries to the Administrative Assistant
(email: vacancies@maths.ox.ac.uk), quoting vacancy reference 108193.
Applications for this vacancy are to be made online. To apply for this
role and for further details, including a job description and selection
criteria, please click on the link below:
https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=108193
Only applications received before 12:00 noon UK time on Monday 8 July
2013 can be considered.
Committed to equality and valuing diversity.
----------------------------------------------------
From: Enderling, Heiko <Heiko.Enderling@moffitt.org>
Date: June 10, 2013 9:25:22 AM
Subject: Post-doc: Integrated Math Oncology, Moffitt Cancer Center, US
Applications are sought for the position of Postdoctoral Research Fellow
to work under the supervision of Dr. Heiko Enderling on
inter-disciplinary research projects on modeling stem cells, development
and cancer (http://labpages.moffitt.org/enderlingh/).
We seek a talented individual with a PhD and background in applied
mathematics, physics or a computational discipline to work in the unique
research environment of the Integrated Mathematical Oncology (IMO)
department at Moffitt Cancer Center on the University of South Florida
campus. IMO integrates mathematicians, computer scientists, and
physicists together with imaging specialists as well as clinical and
experimental oncologists to develop novel approaches for the
understanding, treatment and prevention of cancer.
The successful candidate will have a desire to work closely with
experimentalists and clinicians, and have experience in mathematical
modeling of biological systems. Preference will be given to those with
knowledge of stem cells, development and/or cancer. The ideal candidate
will have a history of demonstrated creativity, be highly motivated, and
have good communication skills and experience in developing/ writing
publications in quality peer reviewed scientific journals. Preference
will be given to candidates with the ability to program
(C/C++/Java/Matlab), visualize and analyze numerical/experimental data.
Interested applicants should send a cover letter and C.V. directly to
Heiko[dot]Enderling{at}moffitt.org, and formally apply through the
online recruitment system.
----------------------------------------------------
From: Paul Van_liedekerke <paul.van_liedekerke@inria.fr>
Date: June 11, 2013 4:12:05 AM
Subject: Post-docs: Computational Biology, INRIA Paris
2 Postdoc positions
Summary:
Quantitative mathematical multi-scale modeling are combined to guide
experiments to analyze the organizational principles of multi-cellular
tissues. The mathematical multi-cellular models are either based on
descriptions of each individual cell (agent based) or on local cell
density (PDE?s), and are linked to mechanisms on the molecular scale.
Model applications span lung cancer therapy in-vitro and in-vivo (tumor
modeling), and drug effects on liver cells in bioreactors as well as in
the organ liver. The applications will be developed within
multi-disciplinary research consortia involving mathematicians, computer
scientists, physicists, biologists, clinicians and biotechnologists, and
companies at different locations, mainly within Germany and France.
INRIA is the key applied research institution in France for applied
mathematics and computer science (www.inria.fr). IZBI at University of
Leipzig has an internationally recognized research profile in
multi-cellular tissues (www.izbi.de). Multi-cellular systems biology is
a recently strongly upcoming field with increasing interest from
academics, pharmaceutical companies and clinics. The positions are
within national and EU funded projects.
Candidate Profiles:
We are looking for motivated candidates (mathematician, physicist or
engineer) who fits in either of the following profiles:
1. Agent-based modeling: Compulsory: Experience with programming
languages (C, C++ or similar). Recommended but not compulsory: knowledge
of Ordinary Differential Equations, Stochastic processes.
2. Continuum modeling: Compulsory: Background/Training in numerical
analysis, mathematical modeling (PDEs, solid or fluid mechanics).
Recommended but not compulsory: Programming skills in C/C++.
We offer a scientifically challenging and exciting environment where
there is a strong interaction between different groups (computer
scientists, experimentalists, modelers) located in France (Paris) and
Germany. Salaries are according to local scales and experience
(2500 - 3200 Euros).
Please send your application letter, containing a detailed CV with
recent publications, a statement of current and future career interests,
and names of 3 referees by email to :
Prof. Dr. Dirk Drasdo (Dirk.Drasdo@inria.fr)
Prof. Dr. Irene Vignon-Clementel (Irene.Vignon-Clementel@inria.fr)
Dr. Paul Van Liedekerke (Paul.Van_Liedekerke@inria.fr)
----------------------------------------------------
From: Weiss, Tanja <tanja.weiss@uni-graz.at>
Date: June 12, 2013 8:08:36 AM
Subject: University Assistant with Doctorate: IMSC, U Graz, Austria
Institute of Mathematics and Scientific Computing is filling an
University Assistant with doctorate
(40 hours a week; fixed-term employment for the period of 6 years;
Envisaged Job Starting Date 01 October 2013)
For more information follow the link:
http://jobs.uni-graz.at/en/MB/105/99
----------------------------------------------------
Subject: SMBnet Reminders
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The contents of this publication may be reproduced in whole or in part
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End of SMB Digest
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