SMB Digest Volume 17 Issue 50

SMB DIGEST ISSN 1086-6566 
VOLUME 17 ISSUE 50
December 8, 2017
This issue’s editor:

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Note:
Information about the Society for Mathematical Biology, including an
application for membership, may be found in the SMB Home Page,
www.smb.org/.

Access the Bulletin of Mathematical Biology, the official journal of
SMB, at www.springer.com/11538.

Inquiries about membership or BMB fulfillment should be sent to
membership(at)smb(dot)org.

Issue’s Topics:
CfA: NRC Research Associateship Programs, Dec 4-Feb 1
Workshop: Dynamics of Ecological Networks, May 14-18, São Paulo
Tutorial: Spatial Data – Ecological Niche, May 16-18, NIMBioS
Summer Course: Brain, Minds, & Machines, Aug 9-30, MA, US
Conference: SIAM, Planet Earth, MPE18, Sep 13-15, Philadelphia
Newsletter: NIMBioS
ToC: BMB, Volume 79, Issue 12
ToC: Wiley, Systems Biology & Medicine, Early View
Books: Modeling of Infectious Diseases, Statistics Handbooks
PhD Positions: Mathematics for Healthcare, U Exeter, UK
Post-doc: Collective Cell Migration, QUT, Australia
Post-doc: Modelling Infection & Immunity, UNSW Sydney
Post-doc: Stochastic Modeling, Gene Regulatory…, U Edinburgh
Tenure Track: Computational Biology, U Dallas, US
NIH Update: Be Careful to Pick the Right Funding Opportunity…
SMBnet Reminders

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From: NASEM NRC Research Associateship Programs <rap@nas.edu>
Date: Mon, Dec 4, 2017 at 11:07 AM
Subject: CfA: NRC Research Associateship Programs, Dec 4-Feb 1

See
mailchi.mp/nas/call-for-applications-nrc-research-associateship-programs-correction?e=caa1f1e465

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From: Jandira Ferreira de Oliveira <jandira@ictp-saifr.org>
Date: Mon, Dec 4, 2017 at 8:57 AM
Subject: Workshop: Dynamics of Ecological Networks, May 14-18, São Paulo

ICTP-SAIFR Workshop on Spatial and Temporal Dynamics of Ecological
Networks

Start time: May 14, 2018
Ends on: May 18, 2018
Location: São Paulo, Brazil
Venue: IFT-UNESP

Description: Network theory has become a fundamental tool to study and
analyze complex systems. In the field of ecology, in particular, the
application of these new methods has led to tremendous progress,
increasing our knowledge of the assembly and dynamics of ecological
communities. Many questions, however, remain open, especially those
requiring the integration of ecological processes that operate over
spatial and temporal scales. This workshop will bring together a diverse
group of scientists spanning the fields of biology, physics, mathematics
and computation to focus on these questions. The group will develop
working hypotheses for factors driving network dynamics based on
empirical patterns; explore case studies of variation across space or
time in ecological networks; develop new models of network dynamics
incorporating coevolution and community ecology; develop models to link
ecology to macroevolutionary processes.

During the workshop participants will be organized in groups to work on
specific projects of common interest. There will be one introductory
talk every morning, before the groups start working, and one more
technical talk in the afternoon. There is no registration fee.

Registration deadline: March 16, 2018

More information: www.ictp-saifr.org/econet18

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From: Catherine Crawley <ccrawley@nimbios.org>
Date: Mon, Dec 4, 2017 at 12:31 PM
Subject: Tutorial: Spatial Data – Ecological Niche, May 16-18, NIMBioS

The National Institute for Mathematical and Biological Synthesis
(NIMBioS) is now accepting applications for its Tutorial, “Applications
of Spatial Data: Ecological Niche Modeling,” to be held May 16-18, 2018,
at NIMBioS.

Objectives: The distribution of a species may be influenced by an array
of factors. The combination of these factors results in the ecological
niche, the set of conditions that allow a species to exist in a
geographic area. However, defining these conditions is difficult, due to
the complexity of natural systems. One approach to characterizing the
ecological niche uses spatial data GIS software. The objectives of this
tutorial are to teach participants the concepts of ecological niche
modeling, introduce them to select analytical techniques (formatting
data in GIS; running Maximum Entropy (MaxEnt) models), and present how
to interpret and apply spatial analyses. Participants will further be
familiarized with several commonly-used and/or newly-available online
spatial data resources. Participants will be provided datasets to use in
hands-on simulations, but can also bring their own data if desired.

This tutorial is intended for advanced graduate students, postdocs, and
faculty who are interested in learning how to incorporate ecological
niche modeling into their research. Some basic knowledge of GIS software
and ecology is preferred. Little to no programming will be involved,
with ecological niche modeling and spatial analysis conducted using
existing applications (MaxEnt) and packages in QGIS and R.

Location: NIMBioS at the University of Tennessee, Knoxville

For more information about the tutorial and a link to the online
application form, go to www.nimbios.org/tutorials/SpatialDataENM

Participation in NIMBioS tutorials is by application only. Individuals
with a strong interest in the topic are encouraged to apply, and
successful applicants will be notified within several weeks after the
application deadline. Lodging, breakfast and lunch will be provided for
tutorial attendees.

Application deadline: February 15, 2018

The National Institute for Mathematical and Biological Synthesis
(NIMBioS) (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, with
additional support from The University of Tennessee, Knoxville.

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From: Gabriel Kreiman <gkreiman@gmail.com>
Date: Wed, Dec 6, 2017 at 8:34 AM
Subject: Summer Course: Brain, Minds, & Machines, Aug 9-30, MA, US

Brains, Minds and Machines Summer Course 2018

A Special Topics Course at MBL Woods Hole, MA

Directors: Gabriel Kreiman, Children’s Hospital, Harvard Medical School;
and Tomaso Poggio, Massachusetts Institute of Technology

Course Dates: August 9 – August 30, 2018

Application Deadline: April 9, 2018

More information: cbmm.mit.edu/summer-school/2018

The basis of intelligence – how the brain produces intelligent behavior
and how we may be able to replicate intelligence in machines – is
arguably the greatest problem in science and technology. To solve it,
we will need to understand how human intelligence emerges from
computations in neural circuits, with rigor sufficient to reproduce
similar intelligent behavior in machines. Success in this endeavor
ultimately will enable us to understand ourselves better, to produce
smarter machines, and perhaps even to make ourselves smarter. Today’s AI
technologies, such as Watson and Siri, are impressive, but their domain
specificity and reliance on vast numbers of labeled examples are obvious
limitations; few view this as brain-like or human intelligence. The
synergistic combination of cognitive science, neurobiology, engineering,
mathematics, and computer science holds the promise to build much more
robust and sophisticated algorithms implemented in intelligent machines.
The goal of this course is to help produce a community of leaders that
is equally knowledgeable in neuroscience, cognitive science, and
computer science and will lead the development of true biologically
inspired AI.

The Center for Brains, Minds and Machines (CBMM) [cbmm.mit.edu] will
also be hosting an Evening Lecture Series, including speakers from both
industry and academia, in the fields of neuroscience, computer science,
and cognitive science.

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From: Frank W. Kunkle <Kunkle@siam.org>
Date: Mon, Nov 27, 2017 at 11:43 AM
Subject: Conference: SIAM, Planet Earth, MPE18, Sep 13-15, Philadelphia

SIAM Conference on Mathematics of Planet Earth (MPE18)
Sponsored by the SIAM Activity Group on Mathematics of Planet Earth.

Location: DoubleTree by Hilton Hotel Philadelphia Center City,
Philadelphia, Pennsylvania, USA
Dates: September 13-15, 2018

The Call for Presentations for this conference is available at:
www.siam.org/meetings/mpe18

SUBMISSION DEADLINES
February 14, 2018: Minisymposium Proposal Submissions
March 14, 2018: Contributed Lecture, Poster and Minisymposium
Presentation Abstracts

TRAVEL FUND APPLICATION DEADLINE
March 2, 2018

Please visit www.siam.org/meetings/mpe18/submissions.php
for detailed submission information.

For additional information, contact the SIAM Conference Department
(meetings@siam.org).

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From: NIMBioS <newsletter@nimbios.org>
Date: Thu, Dec 7, 2017 at 9:05 AM
Subject: Newsletter: NIMBioS

See
myemail.constantcontact.com/Bi-Monthly-News-from-NIMBioS.html?soid=1102610363105&aid=3A2zEyiHSms

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From: Springer <springer@alerts.springer.com>
Date: Tue, Dec 5, 2017 at 10:24 PM
Subject: ToC: BMB, Volume 79, Issue 12

See
link.springer.com/journal/11538/79/12?wt_mc=alerts.TOCjournals

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From: Wiley: Systems Biology and Medicine <WileyOnlineLibrary@wiley.com>
Date: Fri, Dec 1, 2017 at 1:34 PM
Subject: ToC: Wiley, Systems Biology & Medicine, Early View

For the Wiley Interdisciplinary Reviews: Systems Biology and Medicine
Table of Contents, see
onlinelibrary.wiley.com/journal/10.1002/(ISSN)1939-005X/earlyview?campaign=wolearlyview

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From: Anuj Mubayi <anujmubayi@yahoo.com>
Date: Thu, Nov 30, 2017 at 2:19 PM
Subject: Books: Modeling of Infectious Diseases, Statistics Handbooks

Disease Modelling and Public Health, Part A, Volume 36
www.elsevier.com/books/disease-modelling-and-public-health-part-a/srinivasa-rao/978-0-444-63968-4

Disease Modelling and Public Health, Part B, Volume 37
www.elsevier.com/books/disease-modelling-and-public-health-part-b/srinivasa-rao/978-0-444-63975-2

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From: Tsaneva-Atanasova, Krasimira <K.Tsaneva-Atanasova@exeter.ac.uk>
Date: Wed, Dec 6, 2017 at 2:24 PM
Subject: PhD Positions: Mathematics for Healthcare, U Exeter, UK

Open PhD Positions (closing date 10th January 2018)

Developing Gaze Training for Skilled Upper-Limb Prosthetic Use –
Mathematics – EPSRC DTP funded PhD Studentship Ref: 2892
www.exeter.ac.uk/studying/funding/award/?id=2892

Mathematical Modelling of Event-Related Potentials in Semantic
Representation and Memory – Mathematics – EPSRC DTP funded PhD
Studentship Ref: 2891
www.exeter.ac.uk/studying/funding/award/?id=2891

Understanding Emergent Complex Noisy Patterns in Biological Cells –
Mathematics – EPSRC DTP funded PhD Studentship Ref: 2890
www.exeter.ac.uk/studying/funding/award/?id=2890

The Role of the Muscles in Minimising Tibial Stress During Running –
Sports and Health Sciences – EPSRC DTP funded PhD Studentship Ref: 2949
www.exeter.ac.uk/studying/funding/award/?id=2949

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From: Matthew Simpson <matthew.simpson@qut.edu.au>
Date: Wed, Nov 29, 2017 at 9:14 PM
Subject: Post-doc: Collective Cell Migration, QUT, Australia

We are recruiting a full-time postdoctoral fellow to work on an
Australian Research Council funded project that will involve the
development of mathematical and stochastic models of collective cell
migration. The project will involve collaboration with Michael Plank
(Canterbury, New Zealand) and Ruth Baker (Oxford, UK). The applicant
will have a good background in computational mathematics, and a strong
interest in biology and cell biology. The postdoctoral fellow will be
hosted at Queensland University of Technology (Brisbane, Australia).

Information about my research group is at mj-simpson.com/ and the
position description is at
mj-simpson.com/pdf/Simpson_PostdocAd_2017.pdf

Applicants should sent their CV to matthew.simpson@qut.edu.au

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From: Miles Davenport <mdavenport@kirby.unsw.edu.au>
Date: Thu, Nov 30, 2017 at 7:54 PM
Subject: Post-doc: Modelling Infection & Immunity, UNSW Sydney

Research Associate/ Post-Doctoral Fellow/ Senior Research Fellow –
modelling infection and immunity

The infection Analytics team at UNSW Sydney is seeking a post-doc /
research fellow in mathematical biology, to model infection dynamics in
HIV.

The Infection Analytics Program at the Kirby Institute is an
interdisciplinary team including applied mathematicians, physicists, and
computer scientists, who collaborate widely with around 30 experimental
groups around the world to model within-host and epidemiological aspects
of infection and immunity. The group has a high publication output and a
strong history in successful interdisciplinary training. It is an ideal
venue for students with a quantitative background (mathematics / physics
/ statistics) aiming to establish themselves in mathematical biology.

UNSW Sydney is a ‘top 50’ ranked global university, situated 5 km (3
miles) from Central Sydney, and 1.5 km (1 mile) from Sydney’s beaches.

About the role: $72,509 – $141,471 plus 9.5% superannuation and leave
loading; 3 years; Full-time or part-time.

The position of Post-Doctoral Fellow will be responsible for
mathematical modelling of experimental data on viral dynamics of HIV
during treatment and after treatment interruption to better understand
HIV latency. This will involve familiarity with HIV literature and
underlying biology, biostatistical analysis, and ODE and stochastic
modelling.

To be successful in this role you will:
-Demonstrated mathematics and computer programming skills with
experience in modelling experimental health related data
-Proven experience and interest in modelling in immunology and infection
dynamics
-Proven evidence of publications in a related discipline in peer
reviewed journals
-Post graduate degree, preferably PhD, in mathematics / physics or other
quantitative discipline

More information on the group’s work can be found at:
www.researchgate.net/profile/Miles_Davenport

Contact: Professor Miles Davenport, Program Head, IAP
E: mdavenport@kirby.unsw.edu.au
T: (61 2) 9385 0900

You should systematically address the selection criteria listed within
the position description in your application. Please apply online on the
UNSW website – www.jobs.unsw.edu.au/

Position #59644
Applications close: 12 January 2018

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From: GRIMA Ramon <Ramon.Grima@ed.ac.uk>
Date: Mon, Dec 4, 2017 at 9:11 AM
Subject: Post-doc: Stochastic Modeling, Gene Regulatory…, U Edinburgh

Postdoctoral Fellow in Stochastic Modeling of Gene Regulatory Networks

We are looking for a full-time postdoctoral fellow to work on a project
involving stochastic modeling of biochemical reaction networks including
gene regulatory networks in the group of Dr. Ramon Grima
(grimagroup.bio.ed.ac.uk/index.html) located in the Centre for
Synthetic and Systems Biology at the University of Edinburgh. The
project will start in March 2018 and is for 1-2 years. The applicant
must be a citizen of a Commonwealth country, currently not residing in
the UK and have obtained their PhD no more than ten years prior to
1 November 2017. Applications will be accepted until 9th Dec.

Applicants should send full CV’s (plus the names of two to three
referees; one must be the PhD supervisor) to Dr. Ramon Grima
(ramon.grima@ed.ac.uk).

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From: Deanna Soper <dsoper@udallas.edu>
Date: Wed, Dec 6, 2017 at 2:07 PM
Subject: Tenure Track: Computational Biology, U Dallas, US

See chroniclevitae.com/jobs/0000399757-01

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From: NIH Extramural Nexus (NIH/OD) <ExtramuralNexus@mail.nih.gov>
Date: Thu, Dec 7, 2017 at 7:14 PM
Re-sent From: Raymond Mejía <digest.ray@gmail.com>
Subject: NIH Update: Be Careful to Pick the Right Funding Opportunity…

NIH Update: Be Careful to Pick the Right Funding Opportunity
Announcement; Public Posting of Project Outcomes; Retirement of
Grants(dot)gov Downloadable Forms; Single IRB Reminder

Please see:
list.nih.gov/cgi-bin/wa.exe?A2=ind1712&L=extramuralnexus&F=&S=&P=68

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