SMB Digest Volume 18 Issue 8

February 21, 2018
This issue’s editor:

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Issue’s Topics:

Registration for SMB Annual Meeting in Sydney is open
Tutorial Workshop: Parameter Estimation for Biological Models, NCSU
9th Workshop on Neutron Scattering Applications in Structural Biology
Workshop: Advanced asymptotics of PDEs, modeling … in cell biology
CfP: IWCIA 2018, Porto, Portugal, November 22-24
CfP: Optimization & Decision-Making in Controlling Infectious Diseases
Bulletin of Mathematical Biology, Vol. 80, Issue 3 – New Issue Alert
WIREs Syst Biol Med Content Alert: 10, 2 (March/April 2018)
Letters in Biomathematics announces Carlos Castillo-Chavez co-editor
PhD Position: biological control systems / mathematical modeling …
PhD Positions in Life Sciences, Mathematical Modelling & Image Analysis
SMBnet Reminders


From: Denise Kirschner <>
Date: Tue, Feb 20, 2018 at 8:26 AM
Subject: Registration for SMB Annual Meeting in Sydney is open

REGISTRATION for the annual meeting is now open!! Visit to
register! IF you are not yet a member of the SMB you will want to join first
and experience a SIGNIFICANT decrease in the registration fee! Visit to
join! We hope to see you there!


from: Alun Lloyd <>
date: Wed, Feb 14, 2018 at 11:43 AM
subject: Tutorial Workshop: Parameter Estimation for Biological Models, NCSU

Tutorial Workshop on Parameter Estimation for Biological Models
North Carolina State University, Raleigh, NC
July 25th-28th, 2018
Link for applications:

The NC State Research Training Group on Parameter Estimation for Mechanistic
Biological Models (, funded by the National Science
Foundation (NSF), will run a tutorial workshop on parameter estimation for
biological models between July 25th and July 28th, 2018.

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

This workshop will cover these concepts at an introductory level with a special
emphasis on illustrating their practical application. The meeting will consist
of introductory lectures, research talks and hands-on practical sessions to
provide an opportunity to use the methods on concrete problems. In addition, we
will have a poster session where participants can share their research and get
feedback and advice from presenters and other attendees.

Confirmed speakers include Tom Banks (NC State University), Tyrus Berry (George
Mason University), Marisa Eisenberg (University of Michigan), Dirk Husmeier
(University of Glasgow, UK), Brian Reich (NC State) and Ralph Smith (NC State).

The primary target audience for the workshop is graduate students interested in
learning basic techniques associated with modern methods of identifiability
theory, parameter estimation, and uncertainty quantification in models arising
in biology. We also welcome applications from advanced undergraduates,
postdocs and others who may be interested in these topics.

Individuals wishing to participate should complete the online form at . Full consideration will be given to
applications received by April 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 (requests for support are entered via
the online form).

Further details about the workshop will appear at

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


from: Meilleur, Flora <>
date: Wed, Feb 14, 2018 at 1:40 PM
subject: 9th Workshop on Neutron Scattering Applications in Structural Biology

9th Workshop on Neutron Scattering Applications in Structural Biology
Oak Ridge, TN. June 11 – June 15, 2018

Detailed information can be found on the workshop web page:
Application deadline: April 30, 2018

The workshop on Neutron Scattering Applications in Structural Biology aims at
enabling structural biologists to fully exploit the latest instrumentation and
software development at the SNS and HFIR facilities at Oak Ridge National
Laboratory. Attendees will participate in lectures and tutorials focusing
exclusively on neutron techniques applied in structural biology. The workshop
is designed for graduate students, post-doctoral fellows and faculty new to or
with limited experience of neutron scattering.


date: Thu, Feb 15, 2018 at 7:23 AM
subject: Workshop: Advanced asymptotics of PDEs, modeling … in cell biology

Six workshops (one every week):
Advanced asymptotics of PDEs, modeling and extreme statistics and their
applications to data analysis in cell biology
15 September 2018 – 31 October 2018

1- Probabilistic methods in statistical physics for extreme statistics and
rare events.
2- Advanced asymptotics in PDEs and applications.
3- Multiscale modeling and simulations to bridge molecular and cellular scales.
4- Nanoscale modeling of synaptic transmission, calcium dynamics, transduction
and metabolism in neurons.
5-Reverse mathematical methods for reconstructing single molecular dynamics in
6- Multiscale analysis and reconstruction of chromatin and nuclear

Register before March 15th


from:”João Manuel R. S. Tavares” <>
date:Mon, Feb 19, 2018 at 12:34 PM
subject: CfP: IWCIA 2018, Porto, Portugal, November 22-24

International Workshop on Combinatorial Image Analysis, Porto, Portugal,
Nov. 22-24, 2018


Dear Colleague,

I am pleased to announce IWCIA’18 –,
which is going to be held in Porto, Portugal, in November 22-24, 2018.

IWCIA’18 is the nineteenth of a series of international meetings on
combinatorial image analysis. Image analysis is a scientific discipline
providing theoretical foundations and methods for solving problems appearing in
a wide range of areas, as diverse as medicine, robotics, defense, and security.
As a rule, the processed data are discrete; therefore, the “discrete approach”
to image analysis appears to be a natural one and has an increasing importance.
It is based on studying combinatorial properties of the considered digital data
Combinatorial image analysis often features various advantages (in terms of
efficiency and accuracy) over the more traditional approaches based on
continuous models requiring numeric computation.


Full paper submission due – June 1, 2018
Notification of acceptance – July 15, 2018
Final camera-ready papers – August 15, 2018
Workshop dates – November 22-24, 2018, Porto, Portugal


from: Samit Bhattacharyya <>
date: Fri, Feb 16, 2018 at 2:00 AM
subject: CfP: Optimization & Decision-Making in Controlling Infectious Diseases

Title: Optimization and Decision-Making in Controlling Infectious Diseases

Editors: Samit Bhattacharyya (Shiv Nadar University, India) Tamer F. Oraby
(University of Texas, Edinburg, USA) Gui-Quan Sun (Shanxi University, Shanxi, China)

Publishers: Journal of Optimization, Hindwai publication

Deadline: 31 August 2018

Continuous threat of existing infections and frequent emergence of new
pathogens pose serious challenges to public health. Several control measures
such as vaccination, antibiotics, social distancing, insecticides and bed-nets
are put in line by public health authorities, once an emergence of epidemic is
identified. Whether it is allocation of vaccines of limited supply or school
closures in a city, optimized decision making under uncertain epidemiological
characteristic is essential to mitigate the infection or control the outbreak.
Decision-making even becomes potentially more complex under factors such as
human interference in interventions, like in voluntary vaccination campaigns,
and continuous pathogen evolution. So, designing strategies of targeting
intervention measures that can largely reduce the transmission potential to
group with the highest risk of infection is an optimization problem under a
broad class of assumptions.

This special issue opens up a platform for researchers to showcase their
original work focusing on new advances in modeling and optimization in the
framework of infectious disease control. The special issue focuses on both
mathematical and computational approaches highlighting fascinating results
related to its scope. The discussions and results might benefit researchers and
public health communities in both technical and implementation practices. The
editorial committee welcomes original research papers as well as review
articles that target advanced optimization techniques to address issues in
disease control and mitigation.

Potential topics include but are not limited to the following:
1. Decision-making studies related to designing intervention strategies to
control and mitigate infection
2. Analysis of effectiveness of the intervention strategies
3. Optimization of network epidemic models to control disease transmission
4. Methodological studies (algorithm-based) on optimization techniques applied
to control of disease
5. Optimized management of emergence of an outbreak
6. Modelling on individual behavior towards vaccination and treatment choice
7. Modelling optimal strategies of antibiotic usage to reduce drug-resistance

Papers are published upon acceptance, regardless of the Special Issue
publication date.

Authors can submit their manuscripts through the Manuscript Tracking System at


from: Springer <>
date: Tue, Feb 20, 2018 at 12:25 PM
subject: Bulletin of Mathematical Biology, Vol. 80, Issue 3 – New Issue Alert



from: Wiley Interdisciplinary Reviews <>
date: Fri, Feb 16, 2018 at 4:26 PM
subject: WIREs Syst Biol Med Content Alert: 10, 2 (March/April 2018)

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Volume 10, Issue 2 Pages , March/April 2018


from: Akman, Olcay <>
date: Tue, Feb 20, 2018 at 11:10 AM
resent-from: Amina Eladdadi <>
subject: Letters in Biomathematics announces Carlos Castillo-Chavez co-editor

The Letters in Biomathematics is proud to announce yet another important
milestone for the Letters in Biomathematics.

Dr. Carlos Castillo-Chavez of Arizona State University has joined the journal’s
Editorial Board as co-editor.

Letters in Biomathematics publishes original articles focusing on research,
education, and review in mathematical biology. The journal is listed in DOAJ
and is indexed in major scientific lists. Its double-blind and fast review
policies make the journal stand out for the prospective authors.

To submit a manuscript or for more information, please visit


from: Kristian Thorsen <>
date: Thu, Feb 15, 2018 at 8:44 AM
subject: PhD Position: biological control systems / mathematical modeling …

The University of Stavanger invites applications for a fully funded PhD
I am looking for candidates for the following projects:
1. The control systems behind biomolecular sensing and their connection to
systems for adaptation.
3. Modeling and simulation of antimicrobial resistance in microbial

The applicant should have a master’s degree with specialization in dynamical
systems, mathematical modeling, control theory/engineering, or other related
fields. A background in biology is not required, but certainly a plus,
necessary courses in biology will be offered. The successful applicant will
join an interdisciplinary group with researchers and other PhD students from
both control engineering and molecular biology.

For detailed information about the PhD position and the application process,
please see here:
Remember to specify topic #1 or #3 as your preference.

Application deadline: February 27, 2018


from: Martin Wild <>
date: Tue, Feb 20, 2018 at 8:11 AM
subject: PhD Positions in Life Sciences, Mathematical Modelling & Image Analysis

16 PhD Positions in Life Sciences, Mathematical Modelling and Image Analysis

The joint graduate program of the Excellence Cluster Cells in Motion (CiM) and
the International Max Planck Research School – Molecular Biomedicine
(IMPRS-MBM) offers positions to pursue PhD projects in the areas of biology,
chemistry, physics, mathematics or computer science. We are looking for young
scientists with a vivid interest in interdisciplinary projects to image cell
dynamics from the subcellular to the patient level. PhD projects range from the
analysis of basic cellular processes to clinical translation, from the
application of novel biophysical approaches and the generation of mathematical
models to the development of new imaging-related techniques and compounds.

Research areas:
Cell and Molecular Biology * Developmental and Stem Cell Biology
Vascular Biology * Immunology
Microbiology * Neurobiology
In vivo Imaging * High Resolution Optical Imaging
Biophysics * Chemical Biology
Label Chemistry * Mathematical Modelling
and more.

Applications for the PhD program can be submitted from 13 February – 13 April
Projects start in October 2018 (earlier start possible if desired).
Applications can only be submitted via our online system.

For online application and further information go to

We offer 16 PhD positions. More positions financed by work contracts may be
offered depending on availability. Excellent scientific and transferable skills
trainings, competitive work contracts or tax-free fellowships as well as
support with administrative matters, accommodation, and visas are part of the
program. There are no tuition fees. The program language is English. We invite
applications from highly qualified and motivated students of any nationality
from biological sciences, chemistry, mathematics, computer sciences and
physics. We are looking forward to your application for a PhD position in



Subject: SMBnet Reminders

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