----------------------------------------------------
Subject: SMB Digest v13i46

SMB Digest      November 12, 2013   Volume 13  Issue 46
ISSN 1086-6566

Editor: Ray Mejía ray(at)smb(dot)org

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:
   JSMB-SMB Joint Meeting 2014, July 28 - August 1, Osaka
   Course on Mathematical Modelling in Infectious Disease Epidemiology
   CfA: Predictive Models for ERA, NIMBioS Investigative Workshop
   CfA: Modeling Contamination of Fresh Produce, NIMBioS Invest. Workshop
   CfP: ANTS 2014 Ninth International Conference on Swarm Intelligence
   BICOB-2014 Bioinformatics and Computational Biology 6th Int'l Conf.
   News from Journal of Biological Dynamics
   PhD Position: Auckland Cancer Society Research Centre
   Postdoc Positions: Cardiovascular Modeling & Simulation UNC-Chapel Hill
   Interdisciplinary Postdoc: EMBL-EBI and MRC-Imperial College London
   Postdoc Positions: Computer Science & Population Genetics
   Assistant Professor Position: Ecoinformatics, UC Berkeley
   Selected NIH Intramural Research Positions - November Update
   SMBnet Reminders


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From: Toshiyuki Namba <tnamba@b.s.osakafu-u.ac.jp>
Date: Fri, 8 Nov 2013 13:56:47 +0900
Subject: JSMB-SMB Joint Meeting 2014, July 28 - August 1, Osaka

Dear Colleagues,

The Japanese Society for Mathematical Biology will hold
a joint meeting with the Society for Mathematical Biology
July 28 - August 1, 2014, in Osaka, JAPAN

VENUE: Osaka International Convention Center, Osaka, Japan
http://www.gco.co.jp/en/
TERM: July 28 (Mon) - August 1 (Fri), 2014

The meeting is co-sponsored by the Chinese Society for Mathematical Biology
and the Korean Society for Mathematical Biology.

The JSMB and all people in the Asian mathematical biology community will
welcome world-wide participants.

Please visit the website, http://www.jsmb.jp, for details.


----------------------------------------------------

From: Althaus Christian <calthaus@ispm.unibe.ch>
Date: Thu, Nov 7, 2013 at 8:19 AM
Subject: Course on Mathematical Modelling in Infectious Disease Epidemiology

Dear colleague,

I would like to draw your attention to the three day course on "Mathematical
Modelling in Infectious Disease Epidemiology" that takes place as part of
the Swiss Epidemiology Winter School in Wengen, Switzerland, on January 23 -
25, 2014.

Course objectives:
- To understand the role of infectious disease dynamics for research
  and health care
- To become familiar with the basic concepts of mathematical models of
  infectious diseases
- To use simple mathematical models to study disease transmission and
  control interventions

Lecturers:
- Prof. Sebastian Bonhoeffer, Institute of Integrative Biology, ETH Zurich,
  Switzerland
- Dr. Christian Althaus, Institute of Social and Preventive Medicine (ISPM),
  University of Bern, Switzerland
- Prof. Nicola Low, Institute of Social and Preventive Medicine (ISPM),
  University of Bern, Switzerland

The course is aimed at students, academics and people from the public
health industry who would like to be introduced into the basic concepts of
infectious disease modelling.

More information can be found on the following website:
http://epi-winterschool.org

I would be grateful if you could circulate this announcement among your
interested co-workers and colleagues.

Thank you very much.


----------------------------------------------------

From: Catherine Crawley <ccrawley@nimbios.org>
Date: Thu, Nov 7, 2013 at 10:17 AM
Subject: CfA: Predictive Models for ERA, NIMBioS Investigative Workshop

The National Institute for Mathematical and Biological Synthesis (NIMBioS) is
now accepting applications for its Investigative Workshop, "Predictive Models
for Ecological Risk Assessment," to be held April 28-30, 2014, at NIMBioS.

Objectives: A major challenge in assessing the impacts of toxic chemicals
on ecological systems is the development of predictive linkages between
chemically-caused alterations at molecular and biochemical levels of
organization and adverse outcomes on ecological systems. This investigative
workshop will bring together a multi-disciplinary group of molecular and
cell biologists, physiologists, ecologists, mathematicians, computational
biologists, and statisticians to explore the challenges and opportunities
for developing and implementing models that are specifically designed to
mechanistically link between levels of biological organization in a way
that can inform ecological risk assessment and ultimately environmental
policy and management. The focus will be on predictive systems models in
which properties at higher levels of organization emerge from the dynamics
of processes occurring at lower levels of organization.

Location: NIMBioS at the University of Tennessee, Knoxville

Co-Organizers: Valery Forbes, School of Biological Sciences, Univ. of
Nebraska, Lincoln, and Richard Rebarber Mathematics, Univ. of Nebraska,
Lincoln

For more information about the workshop and a link to the online application
form, go to http://www.nimbios.org/workshops/WS_era.html

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: January 20, 2014

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: Fri, Nov 8, 2013 at 2:57 PM
Subject: CfA: Modeling Contamination of Fresh Produce, NIMBioS Invest. Workshop

The National Institute for Mathematical and Biological Synthesis (NIMBioS)
is now accepting applications for its Investigative Workshop, "Modeling
Contamination of Fresh Produce," to be held April 24-25, 2014, at NIMBioS.

Objectives: Food borne diseases associated with fresh produce continue
to cause serious difficulties for public health in North America. As
globalization has broadened the food supply chain and increased its
complexity, more sophisticated methods of surveillance are needed at key
links to ensure the safety of fresh produce. In particular, recent studies
have identified the sanitization juncture as well as packaging and shipping as
important players that can promote contamination or even cross-contamination
of produce. Focusing on each of these areas, our investigative workshop
will pursue four goals:
 * Develop novel models that capture contamination and pathogen growth
   dynamics involved in sanitization, packaging and shipping.
 * Discuss and develop multi-scale models that connect these supply chain
   links to form a global picture.
 * Explore how these new models can aid in more relevant data collection to
   test and inform model predictions at both the local and global levels.
 * Provide a venue for collaboration among mathematical modelers, food
   technologists, statisticians, microbiologists, and industrial and
   government agency representatives in order to synthesize knowledge in
   a way that establishes modeling as an indispensable tool for pathogen
   surveillance and control in the fresh produce industry.
Location: NIMBioS at the University of Tennessee, Knoxville

Co-Organizers: Yaguang Luo, Environmental Microbial and Food Safety Lab,
USDA, and Daniel Munther, Mathematics, Cleveland State Univ.

For more information about the workshop and a link to the online application
form, go to http://www.nimbios.org/workshops/WS_produce.html

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: January 20, 2014

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: Dorigo Marco <mdorigo@ulb.ac.be>
Date: Thu, Nov 7, 2013 at 3:25 AM
Subject: CfP: ANTS 2014 Ninth International Conference on Swarm Intelligence

ANTS 2014
Ninth International Conference on Swarm Intelligence
September 10-12, 2014. Brussels, Belgium

Call for papers prepared on October 28, 2013
More details and up-to-date information at
http://iridia.ulb.ac.be/ants2014


----------------------------------------------------

From: Nurit Haspel <nurit.haspel@umb.edu>
Date: Fri, Nov 8, 2013 at 12:49 AM
Subject: BICOB-2014 Bioinformatics and Computational Biology 6th Int'l Conf.

6th International Conference on Bioinformatics and Computational Biology
BICoB-2014
March 24-26, 2014 - Las Vegas, Nevada, USA
Conf website:   http://www.cs.umb.edu/bicob/

Paper Submission Deadline: November 30, 2013  ***EXTENDED***
Notification of Acceptance: December 30, 2013
Paper submission site:
https://www.easychair.org/conferences/?conf=bicob2014


----------------------------------------------------

From: Gray, Helen <Helen.Gray@tandf.co.uk>
Date: Wed, Nov 6, 2013 at 4:29 AM
Subject: News from Journal of Biological Dynamics

Visit the news page for Journal of Biological Dynamics, with calls for
papers, special issues, key articles and more:
http://explore.tandfonline.com/content/est/tjbd

Journal of Biological Dynamics is an open-access journal published by Taylor
& Francis. For more information on submitting your article, please see here:
http://mc.manuscriptcentral.com/tjbd


----------------------------------------------------

From: "Gib Bogle" <g.bogle@auckland.ac.nz>
Date: Mon, 11 Nov 2013 12:29:26 +1300 (NZDT)
Subject: PhD Position: Auckland Cancer Society Research Centre

PhD Project: Tumour Spheroid Modelling

A stipend for this project will be paid under Marsden Grant funding:
Tuition fees will be covered and the successful applicant will receive
$25,000 p.a.

Background
The tumour spheroid, which is grown in vitro from human tumour cells, is
a very powerful cell culture model in cancer research. All tumours are
initially avascular, and as the cells multiply the tumour core becomes
hypoxic. Bill Wilson's team at the Auckland Cancer Society Research Centre
(ACSRC) develops hypoxia-activated prodrugs (HAPs), compounds that have
cytotoxic activity switched on when taken up by a hypoxic cell. Spheroids
provide an important way to test these drugs, and to explore the influence
of the factors that determine their effectiveness.

Agent-based spheroid model
In the agent-based approach each cell in the aggregation is simulated as a
separate entity that responds to its microenvironment. A preliminary agent-
based model (ABM) for tumour spheroids has been developed, simulating cell
growth, division and death taking into account the diffusion and consumption
of oxygen and nutrients.

Project aims
The first goal is to calibrate and validate the ABM on the basis of data from
tumour spheroid growth experiments with a range of medium conditions. Once
the model has been shown to be capable of reliably predicting the results of
these growth experiments, it will be extended to incorporate drug effects,
again validating against experiments. Since radiotherapy is ineffective
against hypoxic cancer cells, we are very interested in exploring therapeutic
protocols that combine radiation and HAPs, and killing by radiation will
also be implemented in the model. At this point we will be able to design
(and test through experiment) optimal combined treatment protocols.

Importance
This project will break new ground in cancer modelling - there are currently
no published studies on the 3D agent-based simulation of drug-induced
killing of tumours. Those models of drug therapy that have been published
are continuum-based, incapable, we believe, of achieving the level of
detail and realism that the agent-based approach provides. Our opinion
seems to be shared by the Marsden reviewers, one of whom wrote: "This
proposal is original and has significant merit: Developing a pre-clinical
'in vitro-in silico' drug/RT testing platform would have obvious benefit for
integrative oncology research as well as, potentially, for the development
of new treatment paradigms; this would be an accomplishment beyond Auckland
or NZ, rather it would have an impact on the cancer modeling field itself."

Requirements
We are looking for a very good student, someone with strong mathematical,
computational modelling, and programming skills. Interest in and willingness
to learn basic cell biology is also important - this project is highly
interdisciplinary, and will involve working closely with Dr Kevin Hicks
and Professor Bill Wilson at the ACSRC.

Contact:
Gib Bogle
g.bogle@auckland.ac.nz
09-837-7186


----------------------------------------------------

From: Boyce Griffith <boyceg@email.unc.edu>
Date: Tue, Nov 5, 2013 at 2:32 PM
Subject: Postdoc Positions: Cardiovascular Modeling & Simulation UNC-Chapel Hill

Applications are invited for up to two postdoctoral positions in
cardiovascular modeling and simulation. These positions will be part of a
new cardiovascular modeling research group being established in 2014 at the
University of North Carolina at Chapel Hill in the Applied Mathematics Program
and the McAllister Heart Institute at UNC School of Medicine. This group will
also interact with the UNC/NCSU Joint Department of Biomedical Engineering,
the new Department of Applied Physical Sciences at UNC, and others.

One of these positions is expected to be funded by a recently awarded NIH
grant to develop large-scale computational models of aneurysmal, dissecting,
and dissected aortas. Consequently, applicants are sought with experience
in damage and fracture mechanics, simulating tissue growth and remodeling,
and/or high-performance scientific computing. Prior experience in a specific
area is not required, however, and any applicant with a relevant background
and interests will receive full consideration.

Please provide via http://www.mathjobs.org/jobs/jobs/5398: (1) a vita; (2) a
research statement; and (3) at least three letters of reference. In addition,
applicants must also apply online at http://unc.peopleadmin.com/postings/34254
to be considered for this position.

The University of North Carolina is an Equal Opportunity Employer.

For further information, please contact:
Boyce Griffith
boyce.griffith@unc.edu
http://griffith.web.unc.edu


----------------------------------------------------

From: Santos, Silvia <silvia.santos@csc.mrc.ac.uk>
Date: Thu, Nov 7, 2013 at 12:05 PM
Subject: Interdisciplinary Postdoc: EMBL-EBI and MRC-Imperial College London

Dear colleagues

We are very happy to announce an interdisciplinary post-doctoral
position coordinated by the Beltrao group at the European Bioinformatics
Institute (EMBL-EBI) and the Quantitative Cell Biology group, at the
MRC-Clinical Sciences Centre in Imperial College London.

We are looking for a highly motivated candidate who enjoys working in a
multi-disciplinary and highly collaborative environment. 

For more details please
see http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jj&id=51933&aid=15470
and any informal inquires can be directed to silvia.santos@imperial.ac.uk.

I would be extremely grateful if you could pass on this information to
colleagues who might be interested in applying.


----------------------------------------------------

From: Per Kristian Lehre <PerKristian.Lehre@nottingham.ac.uk>
Date: Tue, Nov 5, 2013 at 2:57 PM
Subject: Postdoc Positions: Computer Science & Population Genetics

FOUR POSTDOC POSITIONS IN COMPUTER SCIENCE AND POPULATION GENETICS Speed
of Adaptation in Population Genetics and Evolutionary Computation (SAGE)
http://www.project-sage.eu

Four outstanding postdoctoral candidates are required to support the
2M euro EU-funded project 'Speed of Adaptation in Population Genetics
and Evolutionary Computation' (SAGE). This project brings together four
European research institutions - University of Nottingham, University of
Sheffield, Friedrich Schiller University Jena, and IST Austria - to develop
world-leading research at the interface between Population Genetics and
Computer Science. Specifically, SAGE aims at bringing together these two
research fields to develop a new quantitative theory of the efficiency of
evolutionary processes in natural and artificial evolution.

Applications are invited from highly skilled researchers in Computer Science,
Mathematics, Physics, Theoretical Biology or related areas (at the interface
between computer science and biology). A good understanding of evolutionary
computation and/or population genetics will be an advantage. In addition,
strong mathematical and analytical skills are essential. The applicants must
have (or be very close to completing) a PhD in Computer Science, Biology,
Mathematics, Physics or related disciplines. The successful candidates
will be working on the development of a generalised theory of evolution
covering both artificial evolution, such as in evolutionary algorithms,
as well as natural evolution, and integrating methods and tools from
both fields, including runtime analysis and the diffusion approximation,
amongst others. They should be able to work independently as well as in
multidisciplinary teams. Good communication and presentation skills are
crucial. The candidates are expected to disseminate research results in
peer-reviewed journals and conferences.

These posts offer a competitive salary and are available from January 2014,
for a period of up to 36 months. Applications should include a CV, names
of references and a letter of motivation.

Applications should be submitted to individual sites as follows:

 - University of Nottingham, UK:
   Applicants should apply online through
   http://www.cs.nott.ac.uk/~pkl/sage-ad.html
   Informal enquiries to Per Kristian Lehre,
   perkristian.lehre@nottingham.ac.uk

 - Friedrich Schiller University Jena, Germany:
   http://www.theinf.uni-jena.de/en/SAGE.html
   Applications and informal enquiries should be emailed
   to Tobias Friedrich, friedrich@uni-jena.de

 - University of Sheffield, UK:
   Applicants should apply online through
   http://www.dcs.shef.ac.uk/~dirk/sage-ad.html
   Informal enquiries to Dirk Sudholt, d.sudholt@sheffield.ac.uk

 - Institute of Science and Technology Austria:
   http://ist.ac.at/research-groups-pages/barton-group/positions/
   Applications and informal enquiries should be emailed
   to Tiago Paixao, tiago.paixao@ist.ac.at.

For more information, please see http://www.project-sage.eu


----------------------------------------------------

From: Wayne Getz <wgetz@berkeley.edu>
Date: Thu, Nov 7, 2013 at 8:28 PM
Subject: Assistant Professor Position: Ecoinformatics, UC Berkeley

ASSISTANT PROFESSOR IN ECOINFORMATICS IN THE DEPARTMENT OF
ENVIRONMENTAL SCIENCE, POLICY, AND MANAGEMENT
UNIVERSITY OF CALIFORNIA, BERKELEY

The Department of Environmental Science, Policy, and Management's (ESPM)
Division of Organisms and Environment at the University of California,
Berkeley is recruiting for a tenuretrack (academic year), assistant
professor position in the field of Ecoinformatics, with an expected start
date of July 1, 2014. This position includes a joint appointment with the
California Agricultural Experiment Station. The department seeks candidates
whose research, teaching and service position them to develop a world class
ecoinformatics program that connects with one or more related programs on the
Berkeley campus, such as the Berkeley initiative on Global Change Biology
(BiGCB), the College of Natural Resources Geospatial Innovation Facility
(GIF), or the Center for Computational Biology (CCB). We are seeking a
candidate either with exceptionally strong computational and modeling skills
or with extensive data mining and manipulation, and information management
experience. We are particularly interested in candidates capable of linking
physical and biological processes to obtain a comprehensive understanding
of environmental and ecosystem processes. The successful candidate will
be expected to offer an upper division undergraduate course in management
and analysis of ecological data and develop a cutting edge ecoinformatics
course for graduate students in their sub-area of expertise. Candidates are
also expected to contribute to diversity and equal opportunity in higher
education through their teaching, research, and service.

The minimum requirement to be considered as an applicant for this position is
the completion of all doctoral degree requirements except the dissertation in
an applicable area of research. The Ph.D. or equivalent is required by the
date of hire. Post-doctoral experience in the ecological and environmental
sciences demonstrating an ability to manage, visualize and analyze large
sets of data is desired. Women and under-represented ethnic minorities are
especially encouraged to apply.

Applications will be accepted through January 10, 2014. Applicants should
submit the following materials online at
http://aprecruit.berkeley.edu/apply/JPF00268: 1) a cover letter, 2)
a curriculum vitae, 3) a statement of research and teaching interests,
4) pdf copies of three peerreviewed publications, and 5) three letters of
recommendation (requested directly through our online application system).
All letters will be treated as confidential per University of California
policy and California state law. Please refer potential referees, including
those submitting letters via a third party (i.e., dossier service or career
center), to the UC Berkeley statement of confidentiality:
http://apo.chance.berkeley.edu/evalltr.html.

Applicants may direct questions to ESPM_recruit@berkeley.edu. Additional
information on this position can be found at
http://ourenvironment.berkeley.edu/Ecoinformatics.pdf .  For additional
information on the Department and the campus visit
http://ourenvironment.berkeley.edu, and http://berkeley.edu.

The University of California is an equal opportunity, affirmative action
employer.


----------------------------------------------------

From: "Owens, Roland (NIH/OD) [E]" <owensrol@mail.nih.gov>
Date: Fri, 8 Nov 2013 17:51:44 +0000
Resent-from: Raymond Mejía <mejiar@helix.nih.gov>
Subject: Selected NIH Intramural Research Positions - November Update

Tenure Track
Laboratory of Chemical Physics, NIDDK
(deadline:  December 15)

A tenure track position is available for a biophysical scientist to establish
an independent research program in the Laboratory of Chemical Physics,
NIDDK, NIH.  Current research in this Laboratory is primarily concerned
with experimental, theoretical and computational problems in the structure,
dynamics, and function of biological macromolecules. Experimental techniques
include solution and solid-state nuclear magnetic resonance spectroscopy,
time-resolved X-ray crystallography and optical spectroscopy, and single
molecule spectroscopy.  Development of fundamental aspects of experimental
and theoretical techniques is an active area in the Laboratory.

The Laboratory is located on the main intramural campus of the NIH in
Bethesda, Maryland, just outside Washington, D.C.  The Principal Investigators
in the Laboratory are: Philip Anfinrud, Ad Bax, Robert Best, Marius Clore,
William Eaton, Attila Szabo, and Robert Tycko (Scientists Emeriti are Edwin
Becker and Robert Zwanzig).  Applicants must have a Ph.D. or equivalent degree
and have demonstrated expertise and a record of achievement. Interested
applicants should submit (as a single .pdf file) a Curriculum Vitae and
list of publications, copies of no more than 5 publications, a summary
of research accomplishments, and a plan for future research. Applicants
should also have three letters of reference submitted.  The application and
reference letters should be emailed to Reed Wickner, Chair, Laboratory of
Chemical Physics Search Committee, c/o Mrs.  Nancy Moser, mosern@niddk.nih.gov

Deadline for receipt of applications and reference letters is December
15, 2013.  DHHS and NIH are equal opportunity employers.


The NIH Intramural Research Program
http://irp.nih.gov/
http://irp.nih.gov/careers/tenured-and-tenure-track-scientific-careers

Link to Fellowships and Positions of Interest to fellows
https://www.training.nih.gov/
https://www.training.nih.gov/career_services/jobs


----------------------------------------------------

Subject: SMBnet Reminders

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End of SMB Digest
****************************************************

----------------------------------------------------