Subject: Society for Mathematical Biology Digest

SMB Digest      March 30, 2016   Volume 16  Issue 13
ISSN 1086-6566

Editor: Amina Eladdadi eladd.digest(at)gmail(dot)com

Send submissions to appear in this Digest to
SMBnet(at)smb(dot)org .

Information about the Society for Mathematical Biology, including an
application for membership, may be found in the SMB Home Page,

Access the Bulletin of Mathematical Biology, the official journal of SMB, at

Inquiries about membership or BMB fulfillment should be sent to

Issue's Topics:     
    Vacancies for the Society for Mathematical Biology Elections 2016
    Call for Proposals - CBMS Regional Research Conferences
    CFP: Molecular Bioscience & Biophysics: Models, Methods ...
    The release of StochSS Version 1.7
    NetIMP 2016 Symposium on Biological Networks
    ICMNS 2016: Early Registration Deadline March 31
    VCell 6.0 beta and Annual VCell Workshop
    Workshop: Param. Estimate for Biological Models, NCSU, July 28-31
    PhD: Math Modeling in Animal/Vet. Science, U. of Newcastle, UK
    Postdoc: Cancer Multiscale Computational Systems Biology, JHU, USA
    Postdoc: Applied Math, U. of Waterloo, Canada
    Postdoc: Plant Modeling, INRA Avignon, France
    Assistant Director for Mathematical and Physical Sciences (AD/MPS)
    SMBnet Reminders


From: Santiago Schnell <schnells@umich.edu>
Date: Mon, Mar 28, 2016 at 10:25 AM
Subject: Vacancies for the SMB Elections 2016

Vacancies for the Society for Mathematical Biology Elections 2016

The Elected Board of Directors, and Officers of the Society for
Mathematical Biology are essential to the implementation of the
Society?s stated purpose to promote the development and dissemination
of research at the interface between the mathematical and biological

The Society for Mathematical Biology is seeking nominations for:

The President-Elect Office.  The President-Elect will serve for a one
year at the closing of the Annual Business Meeting, held at the 2016
Annual Meeting in Nottingham, United Kingdom.  Then, The
President-Elect automatically becomes President for two years.

The Elected Board of Directors.  Three elected board members will be
appointed at the closing of the Annual Business Meeting, held at the
2016 Annual Meeting in Nottingham, United Kingdom.  Each Elected
Member of the Board serves a term of four years.

Society members interested in serving the Society for Mathematical
Biology in a leadership role of President-Elect or member of the
Elected Board of Directors must submit a CV and a nomination statement
(300 words or less). The statement should describe why you would be a
valuable addition to the Officers or Board of Directors, include
specific strengths and areas of expertise, and how they fit the role.
The statement should also include your vision on what you would seek
to achieve for the Society for Mathematical Biology during the period
of office. The Officers (President-elect or Past-President,
President), and Elected Board of Directors must be current members of
the society.

Please submit your material electronically to the Society Secretary,
Amina Eladdadi (E-mail: eladdadi@gmail.com) by April 15th, 2016.

Santiago Schnell, DPhil (Oxon), FRSC,
President of the Society for Mathematical Biology


From: Santiago Schnell <schnells@umich.edu>
Date: Mon, Mar 28, 2016 at 10:08 PM
Subject: Call for Proposals - CBMS Regional Research Conferences

CBMS (Conference Board of the Mathematical Sciences) is seeking
proposals for the 2017 NSF-CBMS Regional Research Conferences in the
Mathematical Sciences, broadly conceived.  To stimulate interest and
activity in mathematical research, NSF will support up to 10 such
conferences in 2017.  Each five day conference features a
distinguished lecturer who delivers ten lectures on a topic of
important current research in one sharply focused area of the
mathematical sciences. The lecturer subsequently prepares an
expository monograph based upon these lectures, which is normally
published as a part of a regional conference series. Depending upon
the conference topic, the monograph is published by the American
Mathematical Society, the Society for Industrial and Applied
Mathematics, or jointly by the American Statistical Association and
the Institute of Mathematical Statistics.  Support is provided for
about 30 participants at each conference and the conference organizer
invites both established researchers and interested newcomers,
including postdoctoral fellows and graduate students, to attend.

Details about the conference series and how to submit proposals are at

Proposals for 2017 conferences are due to NSF by April 29, 2016.


From: Zhao, Shan <szhao@ua.edu>
Date: Wed, Mar 23, 2016 at 5:26 PM
Subject: CFP: Molecular Bioscience & Biophysics: Models, Methods ...

The journal Molecular Based Mathematical Biology (MBMB) will publish a
special issue entitled ?Molecular Bioscience & Biophysics: Models,
Methods and Applications?. 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 biological applications in the
fields of molecular level biosciences and biophysics.

More information on this special issue can be found here:

We are looking forward to your submission. If you have any questions,
please contact Dr. Zhan Chen at zchen@georgiasouthern.edu.

Guest editors: Dr. Emil Alexov, Clemson University, USA; Dr. Jaydeep
Bardhan,   Northeastern University, USA; Dr. Zhan Chen, Georgia
Southern University, USA (Lead); Dr.  Xinqi Gong, Renmin University of


From: Linda Petzold <petzold@engineering.ucsb.edu>
Date: Sun, Mar 27, 2016 at 6:25 PM
Subject: The release of StochSS Version 1.7

We are pleased to announce the release of StochSS Version 1.7!

StochSS: Stochastic Simulation Service, is an integrated development
environment for modeling and simulation of discrete stochastic
biochemical systems.  An easy to use GUI enables researchers to
quickly develop and simulate biological models on a desktop or laptop,
which can then be expanded or combined to incorporate increasing
levels of complexity.  As the demand for computational power
increases, StochSS is able to seamlessly scale up by deploying cloud
computing resources.  The software currently supports simulation of
ODE and well-mixed discrete stochastic models, parameter estimation of
discrete stochastic models, and simulation of spatial stochastic

New capabilities of Version 1.7 include:
Volume rendering visualization for spatial jobs.
StochSS-launcher uses docker containers to run StochSS. Includes
support for newest OSX and Windows operating systems.
Added RSS feed to front page
Many bug fixes and stability enhancements

For more details and instructions on how to obtain the code, visit us
at www.StochSS.org.

Linda Petzold and Chandra Krintz,
University of California Santa Barbara
Per Lötstedt and Andreas Hellander,
Uppsala University


From: Pan-Jun Kim <pjkim@apctp.org>
Date: Fri, Mar 25, 2016 at 8:00 AM
Subject: NetIMP 2016 Symposium on Biological Networks

We would like to bring your attention to the NetIMP symposium, "I am
My Phenotypes: Bringing Biological Networks into Phenotypic Contexts
(NetIMP 2016)", which is the satellite symposium of the International
Conference on Network Science (NetSci2016; http://netsci2016.net/).

Date: Monday, May 30 , 2016
Venue: The K-Hotel, Seoul, Korea

The detailed information of the NetIMP symposium is available at this
URL: https://www.apctp.org/plan.php/netimp2016

We cordially invite you to submit a 200~300-word abstract (along with
title, authors, and affiliations) for contributed talks of this
symposium by April 6, 2016 to this email address:

The NetIMP symposium is the satellite symposium of NetSci2016. The
main conference of NetSci2016 (http://netsci2016.net) will take place
in the same venue on the dates right after satellite symposia. NetSci
is the premier and largest general international conference on the
broad interdisciplinary area of network science, established by the
Network Science Society in 2005. Now in its 11th incarnation, NetSci
conference is aimed at providing the current overview and showcasing
the latest development in the network science and complex systems
science at large, bringing hundreds of researchers worldwide annually.

Best regards,
Pan-Jun Kim


From: Zachary Kilpatrick <zpkilpat@math.uh.edu>
Date: Sun, Mar 27, 2016 at 4:02 PM
Subject: ICMNS 2016: Early Registration Deadline March 31

Deadline for Early Registration is March 31, 2016

International Conference on Mathematical Neuroscience (ICMNS 2016)
at the Congress Center in Juan-les-Pins on the French Riviera
May 29 to June 1, 2016
Tutorials: May 29
Main Conference: May 30 - June 1
A detailed schedule is forthcoming.

The goal of this event is to provide an interdisciplinary conference
to bring together theoretical neuroscientists and mathematicians
interested in using and extending mathematical concepts and methods
for solving problems in neuroscience. In turn, we expect the
connections and insights gleaned through mathematics can pose future
questions to experimental neuroscience.

For more information check out the conference website:

Conference Chairs:
Romain Veltz (INRIA - Sophia Anitpolis)
Zachary Kilpatrick (U Houston)
Evelyn Buckwar (Johannes Kepler Universitat Linz)


From: <GWeatherby@uchc.edu>
Date: Fri, Mar 25, 2016 at 3:08 PM
Subject: VCell 6.0 beta and Annual VCell Workshop

Dear Virtual Cell users (or future users),

1. The annual Virtual Cell Short Course will take place June 20-22.
Applications, due on April 30, consist of a short proposal explaining
how you feel VCell will help your research project. For more details
see: http://www.ccam.uchc.edu/events/ShortCourse2016.pdf.

2. VCell 6.0 beta is now available at
http://vcell.org/vcell_software/login.html. This new version has
extensive support for rule-based modeling including a new gui for
visually expressing the structures of multi-state molecules and for
specifying reaction rules. It allows users to intermix explicit
reaction network specifications with reaction rules. To allow users to
simulate systems that have too large a number of species, the
network?free (agent-based) simulator NFSim has been added to the
choice of ~12 pre-existing ODE, PDE and stochastic solvers. New
features are explained in Help (within VCell), and described in a
quick tutorial available at

Please share this with potentially interested colleagues.

The VCell Team


From: Alun Lloyd <allloyd@ncsu.edu>
Date: Thu, Mar 24, 2016 at 4:34 PM
Subject: Workshop: Param. Estimate for Biological Models, NCSU, July 28-31

Tutorial Workshop on Parameter Estimation for Biological Models
North Carolina State University, Raleigh, NC
July 28th-31st, 2016

The NC State Research Training Group on Parameter Estimation for
Mechanistic Biological Models (http://rtg.math.ncsu.edu), funded by
the National Science Foundation (NSF), will run a tutorial workshop on
parameter estimation for biological models between July 28th and July
31st, 2016.

Mathematical modeling of biological systems is a rapidly growing area
of research. Typically, some (and often many) of a model?s parameters
and/or states are unknown and have to be inferred from the available
data. However, for many systems only partial observations are
available. Much effort has been devoted to solving this problem. Some
key questions considered in this context are: How sensitive is a
model?s output to changes in its parameters (sensitivity analysis)?
Which parameters can be estimated uniquely from a model?s input and
output (identifiability analysis)? What are the uncertainties of
parameters estimated by fitting a model to data? How are predictions
of a model impacted by uncertainties in its parameters (and structure)
(uncertainty quantification)?

Individuals wishing to participate should contact Mette Olufsen
(msolufse@ncsu.edu). Full consideration will be given to applications
received by May 1st, although applications received after that date
will be considered if space permits. Financial support is available
for a limited number of US students and postdocs. If you wish to
request financial support, please attach a copy of your CV and ask
your advisor to email a letter of recommendation to us.

Further details about the workshop will appear at

On behalf of the co-organizers: 
Andrea Arnold, Franz Hamilton, Alun Lloyd and Mette Olufsen.


From: Joao Filipe <Joao.Filipe@newcastle.ac.uk>
Date: Wed, Mar 23, 2016 at 3:02 PM
Subject: PhD: Math Modeling in Animal/Vet. Science, U. of Newcastle, UK

PhD studentship: Mathematical modeling in Animal/Veterinary Science,
University of Newcastle, UK

School of Agriculture, Food and Rural Development, University of Newcastle
Funding per year: £16,557 (with Industrial Enhancement) + tuition fees
Start and duration: 1 October 2016 for 4 years
Closing date for applications: 14 May 2016
Sponsors: BBSRC, KTN, AB Vista

This project will use a range of mathematical and statistical modeling
techniques to predict the digestion and metabolism of two
macro-minerals essential in livestock feeding: Calcium and Phosphorus.
The ultimate goal is to incorporate the model into a user-targeted
tool. The project has both theoretical and applied training components
and focuses on learning quantitative skills as well as the relevant
context of nutrition and metabolism, offering a practical perspective
of modeling and opportunities for gaining research experience linked
to the agri-food industry.

For further details see:
or contact Professor Ilias Kyriazakis at ilias.kyriazakis@newcastle.ac.uk


From: Aleksander Popel <apopel@jhu.edu>
Date: Thu, Mar 24, 2016 at 10:10 AM
Subject: Postdoc: Cancer Multiscale Computational Systems Biology
Postdoctoral Position in Cancer Multiscale Computational Systems Biology
Departments of Biomedical Engineering and Oncology
Johns Hopkins University

Seeking an independent and motivated Postdoctoral Researcher in Dr.
Aleksander Popel's laboratory in the Departments of Biomedical
Engineering and Oncology, The Johns Hopkins School of Medicine.

The successful candidate will join a team that combines computational
and experimental researchers using computational modeling and
computational systems biology tools to discover and elucidate
mechanisms of tumor angiogenesis and metastasis, immuno-oncology,
tumor microenvironment, and perform drug discovery research.

Specific skills include strong computational modeling of signaling
pathways and multiscale modeling from signaling pathways to tumor

Applicant must have a doctoral degree with a demonstrated record of
innovative scientific accomplishments as evidenced by first-author
papers published or accepted in premier journals.

Qualified candidates must be able to work independently, demonstrate
outstanding communication skills, have a strong commitment to science,
and work well within a group.

US citizens, permanent residents or holders of an F1/OPT visa with
at least six months of work authorization left.

Johns Hopkins University is an Equal Opportunity Employer with a
commitment to diversity. All individuals are encouraged to apply.

How to apply: Email curriculum vitae and names of three references to:
Dr. A.S. Popel, Dept. of Biomedical Engineering, School of Medicine,
Johns Hopkins University, Baltimore, MD 21205. E-mail apopel@jhu.edu


From: Chris Bauch <cbauch@uwaterloo.ca>
Date: Thu, Mar 24, 2016 at 1:13 PM
Subject: Postdoc: Applied Math, U. of Waterloo, Canada

Department of Applied Mathematics, University of Waterloo
Postdoctoral Fellowship in Applied Mathematics

Applications are invited for a postdoctoral fellowship in the
Department of Applied Mathematics at the University of Waterloo, with
an anticipated start date of September 1, 2016. This is a one-year
fellowship with the possibility of renewal for another year.

In addition to engaging in research close collaboration with a faculty
member or members in the department, the successful candidate will be
responsible for teaching two, one-term courses. Candidates should
indicate in their cover letter the names of faculty member(s) they
propose to work with. Selection will be based on the candidate's
research potential, availability of a supervisor, fit with a research
area in the department and teaching ability. All interested recent
PhDs are encouraged to apply.

The Department of Applied Mathematics has 22 regular faculty and two
lecturers. Research interests include scientific computing, control
theory, differential equations and dynamical systems, fluid dynamics,
mathematical biology and medicine, and mathematical physics. The
department has a substantial graduate program with over 80 graduate
students pursuing Masters or PhD degrees, and strong undergraduate
programs in applied mathematics and mathematical physics. More
information about the department can be found at

Application for this fellowship is through the website MathJobs.org.
Candidates should submit a cover letter, curriculum vitae and a
one-page research statement to www.MathJobs.org. Applicants should
also arrange for three letters of recommendation, with at least one
letter addressing the candidate's teaching abilities, to be submitted
through www.MathJobs.org website.

The application deadline is April 1, 2016.

We appreciate all replies to this advertisement, but only applicants
under consideration will be contacted.

The University of Waterloo is strongly committed to employment equity
within its community, and to recruiting a diverse faculty and staff.
The University encourages applications from all qualified candidates,
including women, members of visible minorities, Aboriginal persons,
members of sexual minorities, and persons with disabilities.

This position is contingent upon funding.

Chris Bauch, PhD
Professor and University Research Chair


From: valentina baldazzi <valentina.baldazzi@paca.inra.fr>
Date: Fri, Mar 25, 2016 at 4:55 AM
Subject: Postdoc: Plant Modeling, INRA Avignon, France

Two-years Postdoc on plant modeling at INRA Avignon in France

The INRA GAFL and PSH units are seeking a highly-qualified
post-doctoral researcher to work on a project on genotype-phenotype
kinetic modeling, in France. The successful candidate should hold a
PhD with a background in modeling, and also have experience in
optimization paradigm is needed moving from the optimization of
individual parameters to the optimization of the combination of
alleles involved in the control of the genotype- dependent parameters
of the model. For this purpose, the optimization algorithm has to be
adapted to explore a discrete, binary, solution space describing the
presence or absence of each QTL effect on the value of each model
parameter. In a second step, genetic constraints describing linkage
and interactions between genes (pleiotropy and epistasis) among QTLs
could be added to the algorithm, further reducing the allowable search

At term, an improved optimization strategy together with the
mechanistic nature of the model have the potential to facilitate the
discovery of new genes of interest for the modification of sugar

Valentina Baldazzi


From: Henry Warchall <hwarchal@nsf.gov>
Date: Mon, Mar 28, 2016 at 12:32 PM
Subject: Assistant Director for Mathematical and Physical Sciences (AD/MPS)

Dear Colleague:

We are initiating a national search for the National Science
Foundation's Assistant Director for Mathematical and Physical Sciences
(MPS) and seek your assistance in the identification of candidates.
Dr. Fleming Crim has served in this position, with distinction, since
January 2013.

The Assistant Director, MPS, leads a directorate comprised of five
divisions ? Astronomical Sciences (AST), Chemistry (CHE), Materials
Research (DMR), Mathematical Sciences (DMS), Physics (PHY) ? and the
Office of Multidisciplinary Activities (OMA). Enclosed is an
information sheet that summarizes the directorate's activities and the
responsibilities of the position, together with the criteria that will
be used in the search.

We are very pleased to announce that Dr. Saul Perlmutter, Franklin W.
and Karen Weber Dabby Professor at the University of California,
Berkeley, will head the search committee. We seek your help in
identifying candidates with the following qualifications: outstanding
leadership; a deep sense of scholarship; a grasp of the issues facing
the mathematical and physical sciences in the areas of research and
education; experience developing and overseeing complex scientific
facilities; and the ability to serve effectively as a key member of
the NSF management team. Recommendations of individuals from any
sector ? academic, industry, or government ? are welcome. The National
Science Foundation is an equal opportunity employer committed to
employing a highly qualified staff that reflects the diversity of our

Please send your recommendations, including any supporting information
that you can provide, to the AD/MPS Search Committee via e-mail
(mpssrch@nsf.gov) or at the following address: National Science
Foundation, Office of the Director, Suite 1205, 4201 Wilson Boulevard,
Arlington, VA 22230. We would appreciate receiving your
recommendations by May 13, 2016.

Your assistance in this very important task is appreciated.

/// signed ///
France A. Córdova
National Science Foundation

The full letter can be accessed here:


Subject: SMBnet Reminders

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