SMB Digest August 13, 2014 Volume 14 Issue 33
ISSN 1086-6566
Editor: Richard Schugart richard(dot)schugart(at)gmail(dot)com
Note:
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Issue's Topics:
Workshop: Stochastic & Multiscale Problems, Sep 1-2, Oxford U
CfP: Morphogenic Collective Systems, Dec 1-3, Boston
Workshop: Lymphoid Cells in Acute..., Jan 15-16, NIMBioS
Keystone Symposia: Immunology & Infectious Disease Conferences
Newsletter: NIMBioS, U Tennessee
MSc and PhD Positions: Math Biology, Memorial U of Newfoundland
PhD Position: Neural Fields & Movement Control, U Reading, UK
Post-doc: Agent-based Modelling of Vascular...,U Stuttgart
Post-doc: Infectious Diseases, Weill Medical College, Qatar
Post-doc: Computational Neuroscience, IUPUI & Purdue U
Research Associate: Spatiotemporal..., Imperial College London
New NSF Funding Opportunity: Designing Materials to...
SMBnet Reminders
----------------------------------------------------
From: Duncan, Andrew <a.duncan@imperial.ac.uk>
Date: August 7, 2014 1:13:37 AM
Subject: Workshop: Stochastic & Multiscale Problems, Sep 1-2, Oxford U
Workshop - Stochastic and Multiscale Problems, 1-2 September 2014,
Mathematical Institute, Oxford University.
The aim of this two-day workshop is to bring together mathematicians,
biologists and researchers from other disciplines whose work involves
stochastic and multiscale phenomenon, to identify common methodologies
to studying such systems, both from a numerical and analytical
perspective. Relevant topics include asymptotic methods for PDEs;
multiscale analysis of stochastic dynamical systems; mean-field limits
of collective dynamics. Numerical methods, mathematical theory and
applications (with a specific focus on biology) will all be discussed.
The workshop will take place on the 1st and 2nd of September, at the
Mathematical Institute, Oxford University. Please visit
https://sites.google.com/site/stochmultiscale2014/
for more information and to register.
----------------------------------------------------
From: Hiroki Sayama <sayama@binghamton.edu>
Date: August 6, 2014 8:40:58 AM
Subject: CfP: Morphogenic Collective Systems, Dec 1-3, Boston
Call for Papers:
BICT 2014 Special Track on Morphogenetic Collective Systems (MCS)
December 1 - December 3, 2014
Boston, MA, USA
http://bionetics.org/2014/show/workshop-mcs
Real-world biological collectives show various kinds of complex
phenomena, such as multi-cellular organisms' morphogenesis and
physiological control, colony building and maintenance by termites, and
growth and self-organization of human social systems. These systems
operate with emergent, yet highly sophisticated, internal regulation
mechanisms that typically involve (1) heterogeneity of components,
(2) dynamic differentiation/re-differentiation of components, and
(3) local information sharing among components. These features are often
omitted in traditional models of collective behaviors, yet the dynamics
and capabilities of such morphogenetic collective systems have high
relevance to scientific inquiries and great potential for applications
in engineering, computer science and ICT.
This special track seeks high-quality, original contributions on a wide
variety of topics relevant to morphogenetic collective systems. Topics
of interest include (but are not limited to):
-Theories and models of morphogenetic collective systems
-Pattern formation, self-organization and self-repair
-Biological examples of morphogenetic collective systems
-Socio-economical examples of morphogenetic collective systems
-Novel behaviors of morphogenetic swarms
-Evolution of morphogenetic collective systems
-Design and programming of morphogenetic collective systems
-Algorithms based on or inspired by morphogenetic collective systems
-Applications to computational problem solving
-Applications to information and communication network design
-Applications to robotics and engineering
-Applications to biology/biomedicine
IMPORTANT DATES:
Regular paper submission due: September 1 (EXTENDED)
Notification for regular papers: September 22
Short, work-in-progress paper submission due: September 22
Notification for short, work-in-progress papers: October 6
Camera ready due: October 13
PAPER SUBMISSION:
Authors are invited to submit regular papers (up to 8 pages each), short
papers (up to 4 pages each) or poster/demo papers (up to 2 pages each)
in ACM format. Up to two extra pages are allowed for each paper with
extra page charges. See
http://bionetics.org/2014/show/initial-submission for more details.
PUBLICATION:
All accepted paper will be published by ACM and submitted for indexing
by SI, EI Compendex, Scopus, ACM Library, Google Scholar and many more.
Selected papers will be considered for publication in leading journals
including:
ACM/Springer Mobile Networks and Applications
Elsevier Information Sciences
International Journal of Software Engineering and Knowledge Engineering
Elsevier Nano Communication Networks Journal
Cloud-integrated Cyber-Physical Systems (Springer book)
TRACK CHAIR:
Hiroki Sayama
Binghamton University, State University of New York
Binghamton, NY, USA
PROGRAM COMMITTEE MEMBERS:
Jacob Beal (BBN Technologies, USA)
Sylvain Cussat-Blanc (University of Toulouse, France)
Rene Doursat (CNRS/Ecole Polytechnique, France)
Sebastian von Mammen (University of Augsburg, Germany)
For more information, contact the track chair (sayama@binghamton.edu).
----------------------------------------------------
From: Catherine Crawley <ccrawley@nimbios.org>
Date: August 11, 2014 2:56:53 PM
Subject: Workshop: Lymphoid Cells in Acute..., Jan 15-16, NIMBioS
The National Institute for Mathematical and Biological Synthesis
(NIMBioS) is now accepting applications for its Investigative Workshop,
"Lymphoid Cells in Acute Inflammation," to be held January 15-16, 2015,
at NIMBioS.
Objectives: The Acute Inflammatory Response (AIR) to infection or
traumatic injury has largely been characterized by the actions of
complement, immune cells such as macrophages and neutrophils, and the
inflammatory mediators they produce. Recent advances have highlighted
the early and important role of regulatory T cells and innate lymphoid
cells in the AIR, and these findings have begun to alter the perception
that effects on lymphoid cells occur later in the response to infection
or injury. Along with the biological advances in the area, mathematical
modeling studies have highlighted the dynamic nature of the AIR, and
have pointed toward the need to consider lymphoid cells in order to
explain key biological phenomena as well as impacting clinical
translation. This workshop aims to survey and organize what is currently
known about the role of lymphoid cells and their mediators in the AIR,
how the role of lymphoid cells may differ in acute inflammation due to
infection versus traumatic injury, and efforts at computational modeling
of the AIR. Implicit in this aim is the goal of determining what
relevant experimental datasets are available and how best to use them
for the modeling efforts.
This workshop will inspire new primary research collaborations between
those who have not had the opportunity to work closely with researchers
developing and using computational methods to investigate biological
questions. Likewise, those whose expertise is in modeling and
computational methods will be able to establish connections with
experimental or theoretical immunologists. The workshop should foster
new collaborations by highlighting the benefits of interdisciplinary
efforts in answering fundamental questions in immunology.
Location: NIMBioS at the University of Tennessee, Knoxville
Co-Organizers: Judy Day (Mathematics and Electrical Engineering and
Computer Science, Univ. of Tennessee) and Yoram Vodovotz (Director,
Center for Inflammation & Regenerative Modeling, Univ. of Pittsburgh)
For more information about the workshop and a link to the online
application form, go to http://www.nimbios.org/workshops/WS_lymphoid
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: September 30, 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: keystonesymposia <keystonesymposia@keystonesymposia.org>
Date: August 11, 2014 8:39:17 AM
Subject: Keystone Symposia: Immunology & Infectious Disease Conferences
For information regarding Keystone Symposia on Immunology and Infectious
Disease Conferences, go to
http://www.keystonesymposia.org/index.cfm?e=Web.Meeting.List&tab3#Cat11
----------------------------------------------------
From: NIMBioS <newsletter@nimbios.org>
Date: August 7, 2014 10:30:57 AM
Subject: Newsletter: NIMBioS, U Tennessee
For the bi-monthly newsletter from the National Institute for
Mathematical and Biological Synthesis, go to
http://archive.constantcontact.com/fs105/1102610363105/archive/1118125603188.html
----------------------------------------------------
From: Amy Hurford <ahurford@mun.ca>
Date: August 10, 2014 5:55:21 PM
Subject: MSc and PhD Positions: Math Biology, Memorial U of Newfoundland
M.Sc. and Ph.D. positions: Mathematical biology ? Memorial University of
Newfoundland
I invite applicants for M.Sc. and Ph.D. studies in mathematical biology.
Possible research topics include the ecology and evolution of infectious
disease, animal movement models, and disease spread in changing
environments.
The salary for these positions is $20,000 per year with additional
funding available for conference travel. Applicants should email Dr. Amy
Hurford (ahurford@mun.ca). This email should include: (i) 1-2 paragraphs
describing your research interests and any relevant past experience,
(ii) your CV, and (iii) transcripts pertaining to your previous or
ongoing studies (if possible). I will consider applications as they are
received. For full consideration applicants should indicate their
interest before September 1, 2014. Applicants should be able to begin
their studies in January, May or September, 2015.
Interdisciplinary training in biology, mathematics and/or experience in
computer programming is ideal, but only proficiency in one of these
areas is necessary where there is an interest to develop further skills
in the other areas.
Memorial University is located in St John?s, Newfoundland, Canada. The
city offers many unique experiences with a vibrant arts community,
stunning coastline, and proximity to a variety of outdoor activities
(hiking, fishing, cross-country skiing, etc:
http://www.newfoundlandlabrador.com).
----------------------------------------------------
From: Ingo Bojak <i.bojak@reading.ac.uk>
Date: August 7, 2014 7:41:00 AM
Subject: PhD Position: Neural Fields & Movement Control, U Reading, UK
Frog in silico: Understanding hand-eye coordination
Profs Ingo Bojak & William Harwin
Systems Neuroscience Research Group, School of Systems Engineering,
University of Reading, UK
Hand-eye coordination has been extensively studied as paradigm for the
neural control of movement. We wish to elucidate how movement patterns
emerge from neural models coupled with biomechanics. In particular,
spinal stimulation in bullfrogs leads to "force fields" at the limb, but
it is unknown how the kinematics of the limb link with the spinal
reflexes to generate these forces. Furthermore, higher centres must
control these force fields to allow ballistic and repetitive motor
plans. This project will combine neural models of cognitive control with
models of the muscular-skeletal system to explain how brain and body
dynamically interact to produce coordinated movement.
Once we can reverse-engineer actual motion into the observed force
fields, our research will turn to the neural control that assembles
these building blocks. In particular, we will establish likely
mechanisms for the required signal to arise and be maintained from
visual stimuli. Different delays after a visual stimulus should result
either in a singular motor pattern, such as a jump reflex, or in
tracking motor patterns, such as the frog?s pursuit of a mate.
We will build classical robotic models of the frog using the
biomechanics library Opensim and populate them with simplified
actuators. Neural dynamics will be considered in terms of
interconnecting patches of neural fields separated by fixed time delays.
A simplified eye and retinal structure will be used to inject visual
stimuli into the model and track possible pathways determining motor
actions.
This project will be a combination of theoretical studies and computer
simulations based on biological models and experimental data. The ideal
candidate has a good working knowledge of dynamical systems and
numerical analysis, as well as consummate programming abilities. Prior
understanding of the neural control of movement is highly desirable, but
may be acquired during the project.
Eligibility: Applicants should have a Bachelors (at least 2.1) or
Masters degree in neuroscience, physics, engineering, computer science
or a related discipline. Good analytical and programming skills are
necessary; experience in neuroscience and/or movement studies is
desirable.
Funding Details: The studentship will cover UK/EU/International fees and
pay the Research Council maintenance (2013-14 at £13,726 p.a. tax free)
for up to 3 years. It will begin in October 2014, though a delayed start
is negotiable.
How to apply: Please submit an application for a PhD in Cybernetics
(full time) to the University at
http://www.reading.ac.uk/Study/apply/pg-applicationform.aspx.
Please quote the reference GS14-099 for funding and identify Prof Ingo
Bojak as potential supervisor. Once you have submitted your application,
you should receive an email to confirm receipt. Please forward this
email, along with a covering letter, to Prof Ingo Bojak
(i.bojak@reading.ac.uk) by the application deadline.
Application Deadline: 01 September 2014, or until position filled.
Further Enquiries: Please contact Prof Ingo Bojak
(i.bojak@reading.ac.uk).
----------------------------------------------------
From: Holger Perfahl <holger.perfahl@gmail.com>
Date: August 11, 2014 3:33:17 AM
Subject: Post-doc: Agent-based Modelling of Vascular...,U Stuttgart
Post-doc position in Systems-Medicine: Agent-based Modelling of Vascular
Tumour Growth and Comparison to Imaging Data
A postdoctoral position is available at the Stuttgart Research Center
Systems Biology (SRCSB). The successful candidate will work in the
development and implementation of agent-based models of vascular tumour
growth and their comparison to experimental imaging data from the
medical hospital in Tübingen. Therefore, candidates from the fields of
mathematical modelling and image analysis are welcome to apply. The
fellowship is part of the Federal Ministry of Education and Research
(BMBF) funded e:Bio initiative and the salary will be in group TVöD 13.
Applicants should possess a Ph.D. degree in Engineering, Physics,
Computer Science, Mathematics, or a related field. The candidate should
have a strong knowledge in mathematical modelling, image analysis and
C++/MatLab programming.
Please send your motivation letter and CV to:
Prof. Dr.-Ing. Dr.h.c. Matthias Reuss / Dr. Holger Perfahl
perfahl@ibvt.uni-stuttgart.de
Stuttgart Research Center Systems Biology (SRCSB)
University Stuttgart
Nobelstr. 15
70569 Stuttgart
----------------------------------------------------
From: Adona Canlas <apc2003@qatar-med.cornell.edu>
Date: August 11, 2014 11:53:39 PM
Subject: Post-doc: Infectious Diseases, Weill Medical College, Qatar
Postdoctoral Position
In a pioneering international initiative, Cornell University and Weill
Cornell Medical College established the Weill Cornell Medical College in
Qatar (WCMC-Q) through a unique partnership with the Qatar Foundation
for Education, Science and Community Development. Located in Doha,
Qatar, and entering its eleventh year of operation, WCMC-Q seeks
candidates for a postdoctoral associate position in:
Mathematical Modeling of Infectious Diseases
The Infectious Disease Epidemiology Group (IDEG) at WCMC-Q invites
applications for a postdoctoral position in the area of mathematical
modelling of the transmission dynamics of sexually transmitted
infections. The position is full-time and is available for up to three
years subject to satisfactory progress.
IDEG is a renowned research group in quantitative methods of infectious
diseases, and is at the forefront of infectious disease research
internationally. IDEG research has been published in prestigious
scientific journals such as Science, Proceedings of the National Academy
of Sciences, PLoS Medicine, Lancet, Lancet Infectious Diseases, Physical
Review Letters, and Science Translations Medicine. A number of IDEG
studies have had high impact in terms of understanding the epidemiology
of diseases and assessing the impact of public health interventions.
IDEG research work has been key in the formulation of public health
policy at the national, regional, as well as international levels.
Findings of IDEG research work have received global coverage in
national, regional, and international mass and print media through
numerous articles and news stories.
Major duties:
-Conduct project-related research on the biomedical and behavioural
aspects of the population dynamics of HIV and other sexually transmitted
infections (STIs).
-Develop mathematical models describing HIV and other STI epidemiology
and the impact of HIV and other STI interventions using deterministic
models, stochastic compartmental models, and individual-based models.
-Review and validate different approaches and existing models.
-Publish research findings in scientific journals and present them at
major medical/scientific meetings.
Qualifications:
-A Ph.D. degree in a quantitatively-oriented field, such as mathematical
epidemiology, theoretical physics, or applied mathematics.
-Robust research experience in mathematical modelling and building
deterministic and individual-based models.
?-Experience in analytical and quantitative methods, including
deterministic and stochastic differential equations, integral equations,
nonlinear dynamics, probability theory, and stochastic processes.
-Extensive experience in scientific computing involving programming,
numerical analysis, symbolic and logical analysis, Monte Carlo
simulations, and computer graphics.
-Experience in Berkeley Madonna, Matlab, Mathematica, C or C++, Fortran,
Microsoft Office, LaTex, and Windows.
-Working knowledge of the biology and epidemiology of infectious
diseases, especially HIV and other STIs.
-Experience with statistical data analysis and related packages, such as
SPSS and R.
WCMC-Q is located in Education City among other American universities in
Doha, which is a rapidly growing research hub. The WCMC-Q research
program offers a collaborative, multidisciplinary team environment,
endowed with a comprehensive support infrastructure. Details regarding
the WCMC-Q research program and facilities can be accessed at
http://qatar-weill.cornell.edu/research/index.html.
WCMC-Q postdoctoral associates are appointed by the academic departments
at Weill Cornell Medical College in New York. Salary is commensurate
with experience and is accompanied by an attractive foreign-service
benefits package, including paid housing and a car allowance.
Qualified applicants are invited to submit a letter of application,
which should outline their interest in the position, along with their
curriculum vitae including the names and contact details of three
referees, to http://job.qatar-med.cornell.edu
Positions are open until filled. Please note that, due to the high
volume of applications, only short-listed candidates will be contacted.
Applications may also be sent to Adona Canlas
(apc2003@qatar-med.cornell.edu)
Cornell University is an equal opportunity, affirmative action educator
and employer.
----------------------------------------------------
From: Leonid Rubchinsky <leo@math.iupui.edu>
Date: August 12, 2014 11:48:02 AM
Subject: Post-doc: Computational Neuroscience, IUPUI & Purdue U
Postdoctoral opening in computational neuroscience
The Department of Mathematical Sciences at Indiana University-Purdue
University Indianapolis (IUPUI) invites applications for a postdoctoral
position in the area of mathematical and computational neuroscience. The
position is with a collaborative group of scholars from the Department
of Mathematical Sciences at IUPUI, Weldon School of Biomedical
Engineering at Purdue University and the Department of Neurosurgery of
the Indiana University School of Medicine. The current research project
is aimed at the development of adaptive deep brain stimulators for
Parkinson's disease. Part of the duties may also include some teaching
in the Mathematical Sciences. The position offers excellent
interdisciplinary training possibilities in mathematical biology and
computational neuroscience.
Qualifications: Applicants are expected to have a Ph.D. in mathematics,
physics, neuroscience, biomedical engineering, computer science or other
related field. Applicants should have strong quantitative skills in data
analysis and modeling and a strong interest in neuroscience
applications. Experience in nonlinear dynamics/control theory/
neurophysiology is a plus.
How to apply: Send your CV with a list of publications, research
statement, and arrange two-three recommendation letters to be sent to
Dr. Leonid Rubchinsky via e-mail: leo@math.iupui.edu. Address all your
inquiries to the same e-mail. Alternatively send your application by
regular mail to: Dr. Leonid Rubchinsky, Department of Mathematical
Sciences, IUPUI, 402 N. Blackford Street, LD 270, Indianapolis, IN
46202. Screening of applications will continue until position is filled.
IUPUI is an EEO/AA Employer, M/F/D.
----------------------------------------------------
From: Isalan, Mark <m.isalan@imperial.ac.uk>
Date: August 7, 2014 5:25:28 AM
Subject: Research Associate: Spatiotemporal..., Imperial College London
Spatiotemporal Network Modeller - NS 2014 157 AB
https://www4.ad.ic.ac.uk/OA_HTML/OA.jsp?page=/oracle/apps/irc/candidateSelfService/webui/VisVacDispPG&OAHP=IRC_EXT_SITE_VISITOR_APPL&OASF=IRC_VIS_VAC_DISPLAY&akRegionApplicationId=821&transactionid=1592972582&retainAM=Y&addBreadCrumb=RP&p_svid=44158&p_spid=1678198&oapc=10&oas=V_WMZk6xhv0RtdllueK54A
We are seeking a computational modeller who has strong experience in
spatiotemporal dynamical modelling of biological networks. The project
will involve modelling the phenomena associated emergent gene expresion
under a fitness selection pressure. Suggested reading: Mol Syst Biol.
2011 May 24;7:493. A second project will involve modeling
reaction-diffusion genetic networks. Suggested reading: ACS Synth Biol.
2014 May 16;3(5):264-72.
----------------------------------------------------
From: Henry Warchall <hwarchal@NSF.GOV>
Date: August 7, 2014 8:52:02 PM
Reply-To: dmsnews <DMSNEWS@LISTSERV.NSF.GOV>
Subject: New NSF Funding Opportunity: Designing Materials to...
A new NSF program solicitation (NSF 14-591) is now available:
Designing Materials to Revolutionize and Engineer our Future (DMREF)
Please see
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=505073
for details.
Full Proposal Window: January 5, 2015 - January 29, 2015
From the program solicitation:
DMREF is the primary program through which the National Science
Foundation participates in the national Materials Genome Initiative
(MGI) for Global Competitiveness. MGI recognizes the importance of
materials science to the well-being and advancement of society and aims
to "deploy advanced materials at least twice as fast as possible today,
at a fraction of the cost."
DMREF seeks to promote activities that significantly accelerate
materials discovery and development by building the fundamental
knowledge base needed to progress towards designing and making materials
with specific and desired functions or properties from first principles.
Also of interest is research that seeks to advance fundamental
understanding of materials across length and time scales to elucidate
the effects of microstructure, surfaces, and coatings on the properties
and performance of materials and devices.
Controlling material properties through design requires understanding
the interrelationships of composition, processing, structure,
properties, performance, and process control. The approach envisioned in
DMREF to achieve this goal involves modeling, analysis, and
computational simulations, validated and verified through measurement,
experimentation, or device demonstration. DMREF aims to support
collaborative and iterative research wherein theory guides computational
simulation, computational simulation guides experiments, and experiments
further guide theory.
This requires efforts spanning topics in materials science, chemistry,
mathematics, statistics, computer science, and engineering to develop
new data analytic tools and statistical algorithms; advanced simulations
of material properties; advances in predictive modeling that leverage
machine learning, data mining, and sparse approximation; and software
and data infrastructure that is accessible, extensible, reliable,
interoperable, and reusable.
----------------------------------------------------
Subject: SMBnet Reminders
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