SMB Digest July 22, 2015 Volume 15 Issue 29
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:
President's Message to SMB Digest Subscribers
ToC: J Mathematical Neuroscience, Recent Articles
StochSS: Stochastic Simulation Service Version 1.6
Post-doc: Quant. Biol. of Virus-Host interactions, U Wisconsin
Post-doc: Comp. Structured Population Models, UL Lafayette
Post-docs: Biophysics & Computational Biology, U Notre Dame
Post-docs: Systems Biology of Human Microbiome, Korea
Tenure-Tracks: ...Lab. of Experimental Mathematics, Hokkaido U
Faculty Positions: Applied Mathematics, U Bath
SMBnet Reminders
----------------------------------------------------
From: Santiago Schnell <schnells@umich.edu>
Date: July 21, 2015 at 9:55:36 PM
Subject: President's Message to SMB Digest Subscribers
I am writing to you as President of the Society for Mathematical Biology
(SMB) to thank you for subscribing to the SMB Digest, one of our
flagship publications, and to ask you to join or renew your membership
in the Society.
Over the years, I have watched organizations struggle to move with time
while maintaining the focus on their core mission. SMB has always been a
society managing that difficult balancing act thanks to the valuable
service of its members. I am deeply impress with the success and great
value of our SMB Digest, which reaches over 2,500 subscribers. SMB is
also supporting its members in these difficult financial times, through
sponsoring and hosting exciting scientific meetings, and supporting the
attendance of SMB members at meetings through travel awards. SMB is also
advancing career skills and opportunities for both new and established
investigators through its educational and developmental activities. The
Society also publishes an excellent journal: the Bulletin of
Mathematical Biology.
SMB cannot be effective without a large, active and engaged membership -
ranging from undergraduate to senior investigators in academia,
government, and the private sector. The SMB Board of Directors is
presently working on new initiatives to advance and promote the careers
of its members, and to represent and integrate more biological fields at
our annual meetings.
To have an impact on the future vitality of the mathematical and
computational biology community, SMB depends on the membership of
scientists like you. I am asking you to join or renew your membership
today. SMB membership fees are among the lowest in scientific societies.
To join online go to http://smb.org/membership/application.shtml. To
renew online go to http://smb.org/membership/memberprofile.shtml. For
more information, email onlinemembership@smb.org.
I hope the SMB can count on your continue support through your
membership!
Sincerely,
Santiago Schnell
President, Society for Mathematical Biology
----------------------------------------------------
From: Stephen Coombes <Stephen.Coombes@nottingham.ac.uk>
Date: July 20, 2015 at 9:30:02 AM
Subject: ToC: J Mathematical Neuroscience, Recent Articles
The Journal of Mathematical Neuroscience publishes research articles on
the mathematical modeling and analysis of all areas of neuroscience. The
current list of journal articles is available at
http://www.mathematical-neuroscience.com/ :
Conditions for Multi-functionality in a Rhythm Generating Network
Inspired by Turtle Scratching
Snyder AC and Rubin JE
http://www.mathematical-neuroscience.com/content/5/1/15
The Minimal k-Core Problem for Modeling k-Assemblies
Wood CI and Hicks IV
http://www.mathematical-neuroscience.com/content/5/1/14
Stochastic Synchronization in Purkinje Cells with Feedforward Inhibition
Could Be Studied with Equivalent Phase-Response Curves
Verduzco-Flores S
http://www.mathematical-neuroscience.com/content/5/1/13
Orientation Maps in V1 and Non-Euclidean Geometry
Afgoustidis A
http://www.mathematical-neuroscience.com/content/5/1/12
On the Effects on Cortical Spontaneous Activity of the Symmetries of the
Network of Pinwheels in Visual Area V1
Veltz R, Chossat P and Faugeras O
http://www.mathematical-neuroscience.com/content/5/1/11
and see also the recent Special Issue on Stochastic Network Models in
Neuroscience
http://www.mathematical-neuroscience.com/series/SNMN
----------------------------------------------------
From: From: Linda Petzold <petzold@engineering.ucsb.edu>
Date: July 18, 2015 at 5:35:36 PM
Subject: StochSS: Stochastic Simulation Service Version 1.6
We are pleased to announce the release of StochSS Version 1.6!
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 models.
New capabilities of Version 1.6 include:
-Spatial visualization now supports animation, wireframe rendering, and
mesh slicing
-FlexCloud: run 'cloud' jobs on dedicated hardware (in addition to using
EC2)
-Import SBML models
-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 Lotstedt and Andreas Hellander
Uppsala Universiteit
----------------------------------------------------
From: John Yin <yin@engr.wisc.edu>
Date: July 20, 2015 at 10:12:22 PM
Subject: Post-doc: Quant. Biol. of Virus-Host interactions, U Wisconsin
Post-doctoral Opening
Quantitative Biology of Virus-Host Interactions
A position is available immediately for a highly motivated individual to
develop methods that advance our mechanistic and systems-level
understanding of virus and host processes during virus infections. Our
approach combines single-cell measures of viral and cellular processes,
within-cell readouts of viral and anti-viral intermediates, use of
established and novel culture systems, mathematical modeling, and
quantitative imaging of infection spread. Our studies focus on RNA
viruses relevant to human health and technology development, including
human rhinovirus and vesicular stomatitis virus. This NIH-supported work
involves close collaboration among biological and physical scientists,
including molecular biologists, engineers and clinicians. Applicants
with a strong background in data-driven mathematical modeling, computer
simulation, microscopy, quantitative imaging, microbiology, immunology,
are especially encouraged to apply.
We pursue our research at the Wisconsin Institutes for Discovery, a
major public- and private-sponsored initiative, housed in an
award-winning facility, that promotes cross-disciplinary training and
research, as well as public outreach, for societal benefit (see
discovery.wisc.edu). Madison is an attractive and affordable city
surrounded by beautiful lakes. Among U.S. cities, Madison routinely
ranks among "best places to live," and residents thrive on its diversity
of educational, cultural and outdoor opportunities.
Interested candidates should submit by email a single PDF that includes
a letter of interest, curriculum vitae, and contact information for at
least three references to:
Professor John Yin
Systems Biology Theme, Wisconsin Institute for Discovery Chemical and
Biological Engineering Department University of Wisconsin-Madison
Madison, WI 53715, USA
Email with a subject line that states "Postdoc Application" to:
john.yin@wisc.edu
----------------------------------------------------
From: Grace I Bouillion <graceb@louisiana.edu>
Date: July 21, 2015 at 10:57:40 AM
Subject: Post-doc: Comp. Structured Population Models, UL Lafayette
Position: Post-Doctoral Research Associate
Affiliated Dept: Ray P. Authement College of Sciences
Effective Date: August 19, 2015, or as soon as selected candidate is
available.
Qualifications: Ph.D. degree required. Applicants must possess a Ph.D.
degree in Mathematics or Applied Mathematics with substantial knowledge
of statistics and experience in developing and analyzing discrete and
continuous structured population models and in developing and
implementing numerical methods for solving such models. Also, experience
in writing and publishing papers is required and a history of
presentations at professional meetings is desired.
Duties: The selected candidate will be a member of the consortium
"Littoral Acoustic Demonstration Center - Gulf Ecological Monitoring and
Modeling (LADC-GEMM)" working closely with Dr. Ackleh and his graduate
students and the rest of the UL Lafayette LADC-GEMM Team. Current
research projects focus on modeling and monitoring marine mammals in the
Gulf of Mexico. For more details go to the following site:
http://www.ladcgemm.org/ and click on "Research".
Applications: We will review applications as they are received and
continue until the position is filled. Send letters of application with
vitae and a list of three (3) references to: graceb@louisiana.edu
----------------------------------------------------
From: Kathy Phillips <Kathy.Phillips@nd.edu>
Date: July 17, 2015 at 11:23:48 AM
Subject: Post-docs: Biophysics & Computational Biology, U Notre Dame
Postdoctoral Fellow Positions: Interdisciplinary Projects between
University of Notre Dame, University of Pennsylvania and Argonne
National Laboratory
Applications are invited for two NIH and NSF funded postdoctoral
research positions to participate in two interdisciplinary projects in
Prof. Mark Alber's group at the University of Notre Dame. This work will
be carried out in close collaboration with computational modelers and
experimentalists from the University of Pennsylvania and Argonne
National Laboratory. The group's work spans fields ranging from
biophysics and computational biology to high-performance computing and
image processing.
We are seeking highly motivated, driven and curious applicants with a
strong background in computational methods and modeling, strong
communication skills, and an ability to work independently and
collaborate effectively. Experience with computational implementation of
numerical algorithms for solving partial differential equations or Monte
Carlo models, programming with C or C++, and parallelizing simulation
code using MPI or GPUs is desirable.
The goal of the first project is to develop multi-scale computational
models to study blood clot formation and mechanical properties of fibrin
networks that will be calibrated using specific experiments. The second
project will combine computer simulations with new biophysical methods,
live imaging, and advanced organ culture techniques to investigate
intercellular signaling in intact epithelial organs within a controlled
microenvironment. Success in this project will lead to a better
understanding of how exogenous factors impact the endogenous regulation
of organ growth and differentiation.
We are offering a highly interactive and exciting interdisciplinary
research environment with strong mentoring and career development
support. Positions will involve regular visits to the University of
Pennsylvania and Argonne National Laboratory. We will also provide
support for participation in conferences. The University of Notre Dame
is located 1.5 hours from downtown Chicago and Argonne National
Laboratory.
Recent selected publications:
Anyan et al. Proc. Natl. Acad. Sci. USA vol. 111, no. 50, 18013-18018
(2014),
Kim et al., Biomaterials 35, 6739-6749 (2014),
Wu et al., Philosophical Transactions of the Royal Society A 372:
20130380 (2014),
Gupta et al., Proc. Natl. Acad. Sci. USA, 2013 Dec 17;110(51): 20449-54
(2013),
Kim et al., Computational Biology 9 (6), e1003095 (2013).
Positions are for 1 year with possible extension for up to two more
years. To apply, please send CV and cover letter explaining your
interest in the position to malber@nd.edu. Also, arrange for at least
three letters of recommendation to be sent to the same email address.
The evaluation of candidates will begin immediately and continue until
the positions are filled.
----------------------------------------------------
From: Pan-Jun Kim <pjkim@apctp.org>
Date: July 19, 2015 at 11:50:24 PM
Subject: Post-docs: Systems Biology of Human Microbiome, Korea
Postdoctoral Positions in Systems Biology of Human Microbiome
(Asia Pacific Center for Theoretical Physics)
The Junior Research Group (JRG), "Emergent Dynamics of Complex Living
Systems" led by Dr. Pan-Jun Kim at the Asia Pacific Center for
Theoretical Physics (APCTP, http://apctp.org) in Korea, invites
applications for postdoctoral positions in the area of computational and
systems biology. JRGs at the APCTP are supported by the Korean
government and POSTECH.
The research will focus on the computational study of biological
networks of microbial communities inside the human gut. The ideal
candidates are expected to have experience/interest in the areas of
systems biology, bioinformatics, data analysis, and/or complex networks.
Previous experience with nonlinear dynamics, and/or computer simulation
would be a plus.
Screening of applications begins immediately and will continue until the
position is filled. Salary will be commensurate with qualifications and
experience. To apply, please e-mail curriculum vitae along with a brief
statement of your research interests to Pan-Jun Kim at pjkim@apctp.org
and arrange to have three letters of recommendation e-mailed to the same
address.
----------------------------------------------------
From: tn078 <nakagaki@es.hokudai.ac.jp>
Date: July 21, 2015 at 1:42:59 AM
Subject: Tenure-Tracks: ...Lab. of Experimental Mathematics, Hokkaido U
Hokkaido University invites applications for Six Tenure-Track positions
at the Assistant Professor level, beginning in January, 2016. We seek
accomplished young individuals who can enhance the research capabilities
of the university and display extraordinary leadership as new generation
of leaders.The tenure-track selection process evaluates not only
research skills, but also comprehensive abilities as leaders
(administration, motivation, planning skills, analytical skills and
internationality).
One of six positions is in Research Center of Mathematics for Social
Creativity/Laboratory of Experimental Mathematics. Please see the
details NO. 27-1 in the following web site:
http://tenure-track.cris.hokudai.ac.jp/en/opencall/fy2015-international-open-call-for-tenure-track-positions/
----------------------------------------------------
From: Nicholas Britton <N.F.Britton@bath.ac.uk>
Date: July 22, 2015 at 11:27:24 AM
Subject: Faculty Positions: Applied Mathematics, U Bath
Department of Mathematical Sciences, University of Bath, UK
Faculty Positions in Applied Mathematics
The Department wishes to make two appointments in Applied Mathematics.
Applications are welcome in any area of Applied Mathematics which
complements and enhances existing activity at Bath, which includes
Mathematical Biology.
Appointments may be made at Lecturer, Senior Lecturer or Reader level,
equivalent to Assistant or Associate Professor.
Further information is available from
https://www.bath.ac.uk/jobs/Vacancy.aspx?ref=FY3282
----------------------------------------------------
Subject: SMBnet Reminders
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