----------------------------------------------------
Subject: SMB Digest v14i26
SMB Digest June 26, 2014 Volume 14 Issue 26
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:
Mentoring at 2014 JSMB/SMB Annual Meeting, Jul 28-Aug 1, Osaka
Conference: Undergraduate Capstone, Aug 11-15, MBI, Ohio State
Symposium: Eco^2 = Ecology x Economics, Sep 8-10, London
Workshop: Boot Camp: How to Simulate..., Sep 29-Oct 1, MBI
International School: ADdressing..., Nov 16-21, Lisbon
Conference: BICT 2014, Bio-inspired..., Dec 1-3, Boston
Conference: SIAM Applications of..., May 17-21, Snowbird, USA
CfP: MBMB, Computational Structural Biology, Special Issue
CfP: Neurocomputing, Dimensionality Reduction..., Special Issue
Online Lectures: Nonlinear Dynamics and Chaos, Steven Strogatz
New Release: Stoch SS: Stochastic Simulation Service, V 1.3
PhD Position: Saliva Secretion Multiscale Modeller, U Auckland
PhD Position/Post-docs: Infectious/Foodborne Diseases, Cornell
Post-doc: Infectious Disease Modeller, U Oxford
Post-docs: BAMBOO team, INRIA-UCBL, Lyon, France
Research Assistant/Associate/Fellow: Imperial College London
University Assistants with Doctor: U Graz, Austria
SMBnet Reminders
----------------------------------------------------
From: Caroline Bampfylde <caroline.bampfylde@gov.ab.ca>
Date: June 18, 2014 2:07:44 PM
Subject: Mentoring at 2014 JSMB/SMB Annual Meeting, Jul 28-Aug 1, Osaka
Applications are being accepted for mentors and mentees to participate
in the mentoring programme for junior scientists attending the 2014
Annual SMB / Joint JSMB conference in Osaka (28 Jul - 1 Aug).
Following the successful mentoring program at previous annual meetings,
we are again offering a mentoring program for the benefit of junior
scientists attending the 2014 Annual Meeting. The goal of this program
is two-fold:
-to optimize the educational and professional experience of mentees
attending the conference;
-to assist the mentees' socialization into the field of mathematical
biology.
Participants may register as a mentor or mentee or both. The deadline
for applications is July 9th, 2014. To register email:
mentoring@biomath.co.uk with the following information in the main text
of your email message:
-Name, career stage, and affiliation (department and institution);
-A brief description of your research interests (one paragraph will
suffice);
-Mentees: What are your personal goals for participation in the
mentoring program?
Which keywords does your research falls under (may be more than one):
Agriculture, Behavior, Bioengineering, Biofluid dynamics, Bioimaging,
Bioinformatics, Biophysics, Cancer, Cancer therapy, Cardiac physiology,
Cell biology, Computational biology, Developmental biology, Ecology,
Ecosystems, Education, Epidemiology, Evolutionary biology, Genetics,
Genomics, Immunology, Molecular biology, Morphology, Neurobiology,
Physiology, Population biology, Population genetics, Regulatory
networks, Spatial ecology, Systems biology, Tumor modeling
-Mentees: Do you have any special requests? For example, perhaps you
would like a mentor who speaks a certain language, lives in a certain
geographical region, has a dual-career family, etc. Or perhaps you know
of a senior scientist coming to the conference whom you would like to
have as a mentor (if that person were available).
-Mentors: Do you have any special expertise that may be of benefit to
mentees? Please include with your information whether you are willing to
interact with mentees in a language other than English, whether you can
advise on dual-career issues, etc.
Caroline Bampfylde & Carrie A. Manore
SMB Mentoring Committee
----------------------------------------------------
From: Shelton, April J. <shelton.221@mbi.osu.edu>
Date: June 26, 2014 1:49:23 PM
Subject: Conference: Undergraduate Capstone, Aug 11-15, MBI, Ohio State
2014 Undergraduate Capstone Conference
August 11 - 15, 2014, MBI, Ohio State University, Columbus, OH
NOW ACCEPTING APPLICATIONS!
MBI Undergraduate Capstone Conference, August 11-15
The MBI Capstone conference offers undergraduate student researchers in
the mathematical biosciences an opportunity to present their work on the
national stage.
This student centered conference features:
-Recruitment fair for graduate studies
-Panels on jobs and graduate opportunities
-Keynotes from prominent Math Biologist
-Social event at the Columbus Zoo/Aquarium
-Talks and posters by student researchers
Deadline for applications: July 12, 2014
To apply visit http://www.mbi.osu.edu/event?id=874
----------------------------------------------------
From: Matthew Smith <Matthew.Smith@microsoft.com>
Date: June 23, 2014 12:44:32 AM
Subject: Symposium: Eco^2 = Ecology x Economics, Sep 8-10, London
Some of you are likely to be interested in the large BES symposium that
we have found ourselves running this year, in London, Sept 8-10,
entitled 'Eco^2: Exploring the fundamental links between the sciences of
ecology and economics'. We expect around 300 attendees, half ecologists
half economists. Compared to the few other meetings that aim to explore
the links between economics and ecology, this one will focus much more
on the fundamental, conceptual links, which also means that it is likely
to feature quite a lot of theory and modelling. We are organizing it in
collaboration with LSE, and adopting an unusual, highly interactive
format, including panel sessions and problem solving sessions.
For more info see http://www.aka.ms/ecosquared
----------------------------------------------------
From: Shelton, April J. <shelton.221@mbi.osu.edu>
Date: June 23, 2014 10:56:40 AM
Subject: Workshop: Boot Camp: How to Simulate..., Sep 29-Oct 1, MBI
MBI Boot Camp: How to Simulate and Analyze Your Cancer Models with
COPASI
September 29 - October 1, 2014, MBI, Ohio State University, Columbus, OH
NOW ACCEPTING APPLICATIONS!
The Mathematical Biosciences Institute is now accepting applications for
the MBI Boot Camp: How to Simulate and Analyze Your Cancer Models with
COPASI
September 29 - October 1, 2014
COPASI is a simulation software that allows one to translate the
biochemical interactions between species into dynamical systems
represented by the sets of either stochastic or deterministic equations.
COPASI developers, who will also lead this boot camp, have created a
user-friendly graphical interface, which can help researchers to apply
sophisticated analytical tools to their models.
This workshop provides an introduction to the ease and power of the
software.
To learn more or to apply visit http://mbi.osu.edu/event?id=757.
----------------------------------------------------
From: Marie-France Sagot <Marie-France.Sagot@inria.fr>
Date: June 18, 2014 4:14:42 AM
Subject: International School: ADdressing..., Nov 16-21, Lisbon
ADDICTION
International School on ADdressing DIfficult problems in a
Computationally Tractable fashION
with a special interest in computational biology
Lisbon (Portugal), 16-21 November 2014
http://team.inria.fr/bamboo/en/events/school-addiction/
CALL FOR PARTICIPATION
GENERAL INFORMATION ABOUT ADDICTION
ADDICTION is the second international event organised by the Inria AMICI
International Partnership (http://team.inria.fr/bamboo/amici/).
Its focus is on:
- smart data structures;
- algorithm engineering and experimental algorithms;
- probabilistic algorithms;
- (M)ILP approaches simple and enumerative.
On the application side there will be a special interest in
computational biology. The School is addressed to young researchers at
the PhD student or postdoc level, but may, depending on space, greet
other interested participants. The scope of ADDICTION is international.
COURSES AND LECTURERS
The school features the following four lecturers:
Friedrich Eisenbrandt (EPFL, Switzerland)
Giuseppe Italiano (University of Rome "Tor Vergata", Italy)
Kurt Melhorn (Max-Planck-Institute für Informatik at Saarbrücken,
Germany)
Eli Upfal (Brown University, USA)
A title for their lectures will be provided soon on the school?s website.
LOCATION
ADDICTION will be held at the Olissippo Marquês de Sá hotel, in Lisbon,
Portugal. The hotel is a 2-minutes walk away from the Calouste
Gulbenkian Museum and its beautiful park. It is located just between two
of the main Metro lines of Lisbon.
Situated on the west coast of the country, where the Tagus river meets
the Atlantic Ocean, Lisbon is the western-most capital in mainland
Europe. It is known as the white city, thanks to its unique luminosity.
The light, the atmosphere and the climate offer marvelous walks all over
the city. Lisbon is extremely lively, with a wealth of cultural events
happening every day, and a vibrant nightlife. A huge selection of
restaurants is available, featuring Portuguese and international
cuisine.
Lisbon can be easily reached by daily direct flights from major
international cities.
ORGANISATION
Scientific directors:
Pierluigi Crescenzi (University of Florence, Italy)
Alberto Marchetti-Spaccamela (University of Rome I, Italy)
Marie-France Sagot (Inria and University of Lyon 1, France)
Leen Stougie (Free University Amsterdam and CWI, Netherlands)
Organisation:
Florence Bouheddi and Marie-France Sagot (Inria), with the help of
Susana Vinga (IDMEC-IST, Lisbon)
REGISTER EARLY TO SAVE!
Prospective participants should register by September 20, 2014. The form
will be soon available on the school web site.
The early registration fee is 250 euros for PhD students and 300 euros
for postdocs or other researchers. These fees cover access to the
school, mid-day meals, coffee breaks and gala dinner.
Accommodation can be provided by the hotel at a preferential rate until
a date that will be indicated on the school website.
After September 20, 2014, depending on space, registration will remain
possible but the fees will be at the higher rate of 300 euros for PhD
students and 350 euros for postdocs or other researchers.
----------------------------------------------------
From: Jun Suzuki <jxs@cs.umb.edu>
Date: June 26, 2014 6:43:16 PM
Subject: Conference: BICT 2014, Bio-inspired..., Dec 1-3, Boston
CFP: 8th International Conference on Bio-inspired Information and
Communications Technologies (BICT 2014, formerly BIONETICS)
http://www.bionetics.org/
December 1 (Mon) - December 3, 2014 (Wed)
Boston, MA, USA
In-corporation with ACM
BICT 2014 aims to provide a world-leading and multidisciplinary venue
for researchers and practitioners in diverse disciplines that seek the
understanding of key principles, processes and mechanisms in biological
systems and leverage those understandings to develop novel information
and communications technologies (ICT). BICT 2014 targets two thrusts:
THRUST 1: Indirect/Weak Bioinspiration (ICT designed after biological
principles, processes and mechanisms). Examples include evolutionary
computation, artificial gene regulatory networks, neural computation,
swarm intelligence, cellular automata, artificial immune systems,
artificial life, artificial chemistry, reaction-diffusion computing,
simulated annealing, self-organization and network science.
THRUST 2: Direct/Strong Bioinspiration (ICT utilizing biological
materials and systems). Examples include cellular computing, molecular
computing/communication, membrane computing, DNA computing and
memory, bacterial computing, Physarum computing and quantum computing.
Expected, but not exclusive, topics are:
-Signal/information processing and communication for bio-inspired ICT
-Algorithms and their applications for bio-inspired ICT
-Formal models and methods for bio-inspired ICT
-Bio-inspired software and hardware systems
-Modeling, simulations and empirical experiments of bio-inspired ICT
-Self-* and stability properties in bio-inspired ICT
-Security, robustness and resilience in bio-inspired ICT
-Design, configuration and management issues in bio-inspired ICT
-Software engineering and performance engineering in bio-inspired ICT
-Tools, testbeds and deployment aspects in bio-inspired ICT
-Applications, experiences and standardization of bio-inspired ICT
-Socially-aware, game theoretic and other metaphor-assisted
interdisciplinary research
Application domains include, but not limited to, autonomic computing,
bioinformatics, biomedical engineering, computer networks, computer
vision, data mining, e-health, green computing and networking,
grid/cloud computing, intelligent agents, mechanical engineering,
molecular communication, nano-scale computing and networking,
optimization, pervasive computing, robotics, security, social networks,
software engineering and systems engineering.
IMPORTANT DATES:
Regular paper submission due: August 4
Short and poster/demo paper submission due: September 22
Notification for regular papers: September 15
Notification for short and poster/demo papers: October 6
Camera ready due: October 13
SPECIAL TRACKS:
In addition to the regular track that covers general/mainstream topics,
BICT 2014 features the following special tracks that focus on specific,
emerging or underrepresented topics.
-Artificial, Biological and Bio-Inspired Intelligence (ABBII)
-Artificial Intelligence and Software Engineering (AISE)
-Body Area Soft Computing (BASC)
-Biologically-Inspired Process Calculi (BIPC)
-Bio-Inspired Machine Vision (BIMV)
-Bio-inspired/Biomimetic Microsystems & Microdevices (BMM)
-Bio-inspired Wireless Network Security (BWNS)
-Complex Adaptive Systems (CAS)
-Engineering Applications from Molecular and Gene Regulatory Networks
(EMNET)
-Molecular Communication and Networking (MCN)
-Morphogenetic Collective Systems (MCS)
-Modularization for Practical Software Engineering (MPSE)
-Resilient Networks (RN)
-Swarm and Modular Robotics (SAMR)
-Smart Body Area Networks (SBAN)
-Security and Privacy in Bio-inspired Networks (SPBN)
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's paper template. 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 through ACM Digital Library 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
-Elsevier Nano Communication Networks Journal
-Int'l Journal of Software Engineering and Knowledge Engineering
-Cloud-integrated Cyber-Physical Systems (Springer book)
KEYNOTE SPEAKERS:
-Andrew Adamatzky, University of the West of England, Bristol, UK
-Gabriel Ciobanu, Romanian Academy, ICS, Iasi, Romania
-Andrew Eckford, York University, Canada
-Valeriy Perminov, BioTeckFarm, Ltd., Russia
-Hiroki Sayama, SUNY Binghamton, USA
-Theresa Schubert, Bauhaus-Universität Weimar, Germany
-Jon Timmis, University of York, UK
-Honggang Wang, University of Massachusetts, Dartmouth, USA
-Justin Werfel, Harvard University, USA
GENERAL CHAIR:
Jun Suzuki, University of Massachusetts, Boston, USA
PC CHAIR:
Tadashi Nakano, Osaka University, Japan
PC VICE CHAIRS:
Andrew Adamatzky, University of the West of England, UK
Gabriel Ciobanu, Romanian Academy, Institute of Computer Science,
Romania
Douglas Dow, Wentworth Institute of Technology, USA
Hiroaki Fukuda, Shibaura Institute of Technology, Japan
Tyler Garaas, Mitsubishi Electric Research Laboratories, USA
Preetam Ghosh, Virginia Commonwealth University, USA
Isao Hayashi, Kansai University, Japan
Yu-Hsiang Hsu, National Taiwan University, Taiwan
Saori Iwanaga, Japan Coast Guard Academy, Japan
Masao Kubo, National Defense Academy, Japan
Paul Leger, Universidad Católica del Norte, Chile
Shih-Hsi "Alex" Liu, California State University, Fresno, USA
Michael L. Mayo, US Army Engineer Research and Development Center, USA
Parisa Memarmoshrefi, University of Goettingen, Germany
Marjan Mernik, University of Maribor, Slovenia
Alan Millard, University of York, UK
Michael Moore,
Marc Pomplun, University of Massachusetts Boston, USA
Florian Raudies, Boston University, USA
Hiroshi Sato, National Defense Academy, Japan
Hiroki Sayama, SUNY Binghamton, USA
Tomohiro Shirakawa, National Defense Academy of Japan, Japan
Jon Timmis, University of York, UK
Athanasios Vasilakos, University of Western Macedonia, Greece
Honggang Wang, University of Massachusetts Dartmouth, USA
Jun Zhou, Shanghai Jiao Tong University, China
----------------------------------------------------
From: Kirsten Wilden <Wilden@siam.org>
Date: June 19, 2014 9:47:12 AM
Subject: Conference: SIAM Applications of..., May 17-21, Snowbird, USA
Conference Name:
SIAM Conference on Applications of Dynamical Systems (DS15)
Location:
Snowbird Ski and Summer Resort, Snowbird, Utah, USA
Dates:
May 17-21, 2015
Organizing Committee Co-chairs:
Lora Billings, Montclair State University, USA
Panayotis Kevrekidis, University of Massachusetts Amherst, USA
Organizing Committee:
Chiara Daraio, ETH Zürich, Switzerland
Michelle Girvan, University of Maryland, USA
Jan Medlock, Oregon State University, USA
Igor Mezic, University of California, Santa Barbara, USA
Louis M. Pecora, US Naval Research Laboratory, USA
Anthony Roberts, University of Adelaide, Australia
Björn Sandstede, Brown University, USA
Mary Silber, Northwestern University, USA
Michael J. Ward, University of British Columbia, Canada
Invited Speakers:
Andrea Bertozzi, University of California, Los Angeles, USA
Bard Ermentrout, University of Pittsburgh, USA
Jeff Gore, Massachusetts Institute of Technology, USA
Hod Lipson, Cornell University, USA
Jeff Moehlis, University of California, Santa Barbara, USA
Adilson E. Motter, Northwestern University, USA
Alan Perelson, Los Alamos National Laboratory, USA
Andrew Stuart, University of Warwick, United Kingdom
The Call for Presentations for this conference is available at:
http://www.siam.org/meetings/ds15/
Twitter hashtag: #SIAMDS15
SUBMISSION DEADLINES
October 20, 2014: Minisymposium proposals
November 17, 2014: Abstracts for minisymposia, contributed lectures and
poster submissions
TRAVEL FUND APPLICATION DEADLINE
November 3, 2014: SIAM Student Travel Award and Post-doc/Early Career
Travel Award Applications
For additional information, contact the SIAM Conference Department
(meetings@siam.org).
----------------------------------------------------
From: Geng, Weihua <wgeng@mail.smu.edu>
Date: June 20, 2014 5:14:54 PM
Subject: CfP: MBMB, Computational Structural Biology, Special Issue
The journal Molecular Based Mathematical Biology (MBMB) will publish a
special issue entitled "Computational structural biology: 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 to the
structures study of macromolecules, such as DNA, RNA, and proteins.
MBMB (http://www.degruyter.com/view/j/mlbmb) is a recently established
journal, whose aim is to promote the mathematical study and findings of
biological structure, functions and dynamics at the molecular scale.
Original papers and high-quality review articles on the aforementioned
topics are solicited for this special issue.
Potential topics include, but are not limited to:
- Geometric and topological modeling of macromolecules
- Biomolecular solvation, explicit and implicit solvation models
- Protein folding, protein-protein interactions
- Brownian dynamics, molecular dynamics, and Monte Carlo modeling of
biomolecular systems
- Modeling and simulation of Ion-channels and membrane
- Electrostatics computing and applications, N-body problems
- Biomolecular simulations and software developments
- Multiscale modeling
- Mathematical methods for molecular imaging and visualization
Before submission authors should carefully read over the author
guidelines, which are located at http://www.degruyter.com/view/j/mlbmb.
All manuscripts are subject to the standard peer review process before
publication. Please note the publisher has waived the Article Processing
Charges for this special issue, but articles will be open-access in
accordance with the overall goals of the journal. Prospective authors
should submit an electronic copy of their manuscript via email to
mlbmb.editorial@degruyteropen.com.
We are looking forward to your submission. If you have any questions,
please contact Dr. Weihua Geng at wgeng@smu.edu.
Important Dates: Manuscript Due: September 1, 2014;
First Round of Reviews: October 15, 2014;
Anticipated Publication Date: December 31, 2014.
Guest editors: Dr. Weihua Geng (lead), Southern Methodist University;
Dr. Jaydeep Bardhan, Northeastern University; Dr. Duan Chen, University
of North Carolina at Charlotte; Dr. Jin Yu, Beijing Computational
Science Research Center.
----------------------------------------------------
From: ??? <pyw@tju.edu.cn>
Date: June 26, 2014 3:37:25 AM
Subject: CfP: Neurocomputing, Dimensionality Reduction..., Special Issue
Call For Papers
Neurocomputing
Special Issue on Dimensionality Reduction for Visual Big Data
Website:
http://www.journals.elsevier.com/neurocomputing/call-for-papers/dimensionality-reduction-for-visual-big-data
Aims and Scope:
The emergence of "big data" has brought about a paradigm shift
throughout computer science, such as the fields of computer vision,
machine learning and multimedia analysis. Visual big data, which is
specifically on visual information such as images and videos, accounts
for a large and important part in big data. Lots of theories and
algorithms have been developed for visual big data in recent years.
Dimensionality reduction techniques, which aim at finding and exploiting
low-dimensional structures in high-dimensional data, are playing an
increasingly important role in the analytics of visual big data, not
only in overcoming the curse of dimensionality, but also in saving the
computation and storage burden. Indeed, as the volume of such visual big
data increases, scientists are interested in addressing increasingly
complex problems ? particularly how to account for spatio-temporal data
analysis, how to make reduction algorithms efficient and scalable and
how to adapt them to new applications. Unfortunately, conventional
statistical and computational tools are often severely inadequate for
processing and analyzing this kind of large-scale, multi-source and
high-dimensional visual big data. Fueled by the availability of abundant
contextual and social information, metadata, and geo-tagging, recent
years have seen progress in advanced dimensionality reduction methods
for visual big data.
This special issue targets a mixed audience of researchers from several
communities, including machine learning, computer vision, multimedia
analysis, data mining, social networks, etc. The marriage between
"dimensionality reduction" and "visual big data" will bring huge
opportunities as well as challenges to these communities. We believe
this special issue will offer a timely collection of novel research
results to benefit the researchers and practitioners working in these
communities.
Topics of Interest:
This special issue is devoted to the publications of high quality papers
on technical developments and practical applications around advanced
dimensionality reduction techniques for visual big data. It will serve
as a forum for recent advances in the fields of multimedia analysis,
computer vision, machine learning, etc. We invite original and high
quality submissions addressing all aspects of these fields. Relevant
topics include, but are not limited to, the following:
-Supervised /unsupervised /semi-supervised dimensionality reduction for
visual big data
-Subspace learning for visual big data
-Manifold learning for visual big data
-Tensor analysis for visual big data
-Deep learning for visual big data
-Non-negative matrix factorization for visual big data
-Kernel-based dimensionality reduction for visual big data
-Sparse Representation for visual big data
-Transfer learning for visual big data
-Incremental learning for visual big data
-Efficient learning algorithms for visual big data
-Binary coding and hashing for visual big data
-Applications of dimensionality reduction for visual big data
Submission Details:
Authors should prepare their manuscripts in the Neurocomputing
publishing format according to the Guide for Authors available from the
online submission page of Neurocomputing at
http://ees.elsevier.com/neucom/. Please select "SI: Visual Big Data" as
their Article Type during submission. All submitted papers will be
peer-reviewed following the Neurocomputing reviewing procedures.
Important Dates:
-Paper Submission: Jul. 1, 2014
-First Round Notification: Aug. 1, 2014
-Revision: Sep. 1, 2014
-Final Decision: Oct. 1, 2014
-Publication Date: Dec. 1, 2014
Guest Editors:
Yanwei Pang
Professor
School of Electronic Information Engineering
Tianjin University, Tianjin 300072, China,
pyw@tju.edu.cn
Ling Shao
Associate Professor
Department of Electronic & Electrical Engineering
University of Sheffield, United Kingdom
ling.shao@sheffield.ac.uk
----------------------------------------------------
From: Steven Strogatz <shs7@cornell.edu>
Date: June 16, 2014 6:27:01 PM
Subject: Online Lectures: Nonlinear Dynamics and Chaos, Steven Strogatz
Here's the link and the announcement:
https://www.youtube.com/playlist?list=PLbN57C5Zdl6j_qJA-pARJnKsmROzPnO9V
Nonlinear Dynamics and Chaos - Steven Strogatz, Cornell University
This course of 25 lectures, filmed at Cornell University in Spring 2014,
is intended for newcomers to nonlinear dynamics and chaos. It closely
follows Prof. Strogatz's book, "Nonlinear Dynamics and Chaos: With
Applications to Physics, Biology, Chemistry, and Engineering." The
mathematical treatment is friendly and informal, but still careful.
Analytical methods, concrete examples, and geometric intuition are
stressed. The theory is developed systematically, starting with
first-order differential equations and their bifurcations, followed by
phase plane analysis, limit cycles and their bifurcations, and
culminating with the Lorenz equations, chaos, iterated maps, period
doubling, renormalization, fractals, and strange attractors. A unique
feature of the course is its emphasis on applications. These include
airplane wing vibrations, biological rhythms, insect outbreaks, chemical
oscillators, chaotic waterwheels, and even a technique for using chaos
to send secret messages. In each case, the scientific background is
explained at an elementary level and closely integrated with the
mathematical theory. The theoretical work is enlivened by frequent use
of computer graphics, simulations, and videotaped demonstrations of
nonlinear phenomena. The essential prerequisite is single-variable
calculus, including curve sketching, Taylor series, and separable
differential equations. In a few places, multivariable calculus (partial
derivatives, Jacobian matrix, divergence theorem) and linear algebra
(eigenvalues and eigenvectors) are used. Fourier analysis is not
assumed, and is developed where needed. Introductory physics is used
throughout. Other scientific prerequisites would depend on the
applications considered, but in all cases, a first course should be
adequate preparation.
----------------------------------------------------
From: Giovanni Bellesia <giovanni.bellesia@gmail.com>
Date: June 26, 2014 12:31:10 PM
Subject: New Release: Stoch SS: Stochastic Simulation Service, V 1.3
We are excited to announce the release of StochSS: Stochastic Simulation
Service, Version 1.3.
StochSS is an integrated development environment featuring state of the
art algorithms for discrete stochastic biochemical simulation. StochSS
is designed to enable you to easily scale up your simulations in
complexity, deploying compute resources as needed. The current version
includes algorithms for stochastic simulation of well-mixed systems with
parameter estimation via the Monte Carlo expectation-maximization with
modified cross-entropy method, simulation of ODE models with sensitivity
analysis, tools for converting ODE models into stochastic models,
support for Windows systems, and enhanced management of cloud computing
resources.
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: James Sneyd <j.sneyd@auckland.ac.nz>
Date: June 23, 2014 4:17:57 PM
Subject: PhD Position: Saliva Secretion Multiscale Modeller, U Auckland
A PhD scholarship is available, to work in the group of James Sneyd,
University of Auckland, New Zealand. This scholarship is funded by a
grant from the NIH (NIDCR) and pays stipend and fees, at rates
commensurate with other PhD students in New Zealand.
The project is the construction and analysis of a multiscale model of
saliva secretion, including the calcium dynamics of exocrine epithelial
cells, water transport in parotid acinar and duct cells, and the use of
Markov Chain Monte Carlo methods for data fitting. The research is in
collaboration with the laboratory of David Yule (U. Rochester, New
York).
The successful applicant will have a high-quality degree in applied
mathematics, engineering, bioengineering, physics, chemistry, or
physiology, or some equivalent experience. Experience with computational
methods is essential.
For more information about Auckland, visit http://www.aucklandnz.com.
To apply, email your cv and transcript, and a brief statement about your
research interests and experience, to James Sneyd
(j.sneyd@auckland.ac.nz).
----------------------------------------------------
From: Ivanek-Miojevic, Renata <RIvanek@cvm.tamu.edu>
Date: June 24, 2014 11:02:00 AM
Reply-To: Yrjo Grohn <ytg1@cornell.edu>
Subject: PhD Position/Post-docs: Infectious/Foodborne Diseases, Cornell
Two Post-doctoral and one PhD student positions available at Cornell
University:
Two of my post docs are moving to faculty positions and one to the
Pharmaceutical industry; thus I am seeking two post docs and one PhD
student to join my research group.
My research focuses on mathematical, statistical and economic modeling
of infectious and foodborne diseases. The goal of my research is to
optimize intervention strategies (health and management) in food supply
systems.
Depending on the applicant?s background and interest the postdoc/PhD
student could focus on any particular area or combinations of the
following: 1) mathematical modeling of infectious diseases (e.g.,
Mycobacterium avium subsp. paratuberculosis (MAP) and M. bovis (bovine
tuberculosis or bTB) transmission in agricultural systems); 2) system
dynamic modeling of antimicrobial resistance in food animal systems; and
3) optimizing milk quality in dairy farms. Please see the most recent
references to each of these projects:
http://www.vet.cornell.edu/popmed/bios/grohn.cfm
I would like to encourage individuals with a background in mathematical
modeling of infectious diseases and/or population biology/analytical
epidemiology/economics to apply. Knowledge of Bayesian methods would be
a plus. Computer and mathematical expertise and a strong interest in
infectious diseases are required.
Interested candidates should submit their curriculum vitae, a statement
of interest, and the names and contact information of two referees to
Yrjo Grohn ytg1@cornell.edu
Review of applications will begin immediately and the positions are
available starting September 1st 2014.
----------------------------------------------------
From: Julie Robotham <Julie.Robotham@phe.gov.uk>
Date: June 18, 2014 6:57:46 AM
Subject: Post-doc: Infectious Disease Modeller, U Oxford
Job: Infectious Disease Modeller, Oxford NIHR Health Protection Research
Unit (HPRU) in Healthcare Associated Infections and Antimicrobial
Resistance - University of Oxford and Public Health England
University of Oxford and Public Health England are accepting
applications for an Infectious Disease Modeller, as part of the newly
formed Oxford NIHR Health Protection Research Unit (HPRU) in Healthcare
Associated Infections and Antimicrobial Resistance.
The HPRU is working at the forefront of research into translating next
generation pathogen sequencing into routine clinical and public health
practice, and developing informatics infrastructures to deliver local,
regional and national surveillance to better understand pathogens and
recognise infection threats.
The Modeller will develop mathematical models of the dynamics of spread
of healthcare associated infections and antimicrobial resistant bacteria
in hospitals and the community, and will work in close collaboration
with modellers in PHE, Colindale and the established vigorous
multi-disciplinary Oxford group.
The successful applicant will have strong modelling skills, together
with a keen interest in clinical medicine, an enquiring and flexible
attitude and will be highly motivated and enthusiastic about working
collaboratively with researchers from different disciplines.
The role will be based at either the John Radcliffe Hospital, Oxford or
Public Health England, Colindale (candidates choice).
Only applications received before 12.00 midday on 9 July 2014 can be
considered.
For more information and application, please visit:
http://www.jobs.ac.uk/job/AIY844/infectious-diseases-modeller/
----------------------------------------------------
From: Marie-France Sagot <Marie-France.Sagot@inria.fr>
Date: June 22, 2014 7:50:47 AM
Subject: Post-docs: BAMBOO team, INRIA-UCBL, Lyon, France
Two postdoc opportunities at Inria in Lyon, France
In the context of a FP7 KBBE European Project, BacHBerry (?BACterial
Hosts for production of Bioactive phenolics from bERRY fruits"), we are
seeking two postdoc candidates, each for one year, renewable for up to
two years.
The candidates will work in the BAMBOO team at the Inria-UCBL in Lyon,
France (http://team.inria.fr/bamboo/), in interaction with the partners
of BacHBerry, in particular the CSI team at the IDMEC-IST in Lisbon,
Portugal (http://www.idmec.ist.utl.pt/).
Both BAMBOO and CSI are methodological teams with an expertise in
computational and systems biology.
This project aims at tapping the potential of living organisms or
systems to develop or make natural chemical compounds that are believed
to be useful for medicine, agriculture, bioremediation, biodegradation,
or etc. Most often, the compound is already produced by the organism but
in small quantity, and one needs then to manipulate it in order for the
production to be increased. Other situations require transplanting part
of the chemical factory of an organism into another, in general a
bacterium, for better efficiency. In some cases, the transplant might
better be split among a community of different bacteria in interaction.
BacHBerry is more specifically interested in the generation of bacterial
platforms for sustainable bio-based production of phenolic compounds
found in berry fruits. Phenolics are recognised for their antioxydant
health-promoting and functional properties, and applied across
applications as diverse as aromas, colours, nutraceuticals, and medicines.
More specifically, we are looking for candidates with a PhD in one of
the following areas: computer science, mathematics, statistics,
computational biology, metabolic engineering, regulation, or related,
with a strong taste for inter-disciplinary research, and with very good
interpersonal skills.
Ideally, the person will have a long experience with graph algorithms,
discrete combinatorics and/or optimisation techniques.
Unsual CVs are welcome. Knowledge of the portuguese language would
also be a plus :-)
Applications should include a motivation letter, a CV, and the address
of three references.
The applications should be sent to:
Marie-France Sagot, marie-france.sagot@inria.fr
putting also in copy the partner in Lisbon:
Susana Vinga, susanavinga@gmail.com
ideally before July 31, 2014.
----------------------------------------------------
From: Head of Ops <head.ops@imperial.ac.uk>
Date: June 17, 2014 8:27:03 AM
Subject: Research Assistant/Associate/Fellow: Imperial College London
Research Assistant, Associate or Fellow in Organisation Change,
Sustainability and Evaluation
NIHR Health Protection Research Unit in Healthcare Associated Infection
and Antimicrobial Resistance, at Imperial College London
Fixed term for up to 3 years.
Salary range:
Research Assistant: £28,770 - £31,880 per annum
Research Associate: £32,750 - £41,540 per annum
Research Fellow: £38,330 - £43,820 per annum
closing date is 7th July.
See link below for more details and to apply
https://www4.ad.ic.ac.uk/OA_HTML/OA.jsp?page=/oracle/apps/irc/candidateSelfService/webui/VisVacDispPG&akRegionApplicationId=821&transactionid=96728708&retainAM=Y&addBreadCrumb=S&p_svid=43748&p_spid=1668144&oapc=7&oas=Q6FGZxpPTcXlOUu_Af312A
----------------------------------------------------
From: Weiss, Tanja <tanja.weiss@uni-graz.at>
Date: June 18, 2014 6:56:35 AM
Subject: University Assistants with Doctor: U Graz, Austria
Institute of Mathematics and Scientific Computing is filling a
University Assistant with doctorate
(40 hours a week; fixed-term employment for the period of 6 years;
Envisaged Job Starting Date 01 October 2014)
For more information follow the link:
http://jobs.uni-graz.at/en/MB/105/99
Institute of Mathematics and Scientific Computing is filling a
University Assistant with doctorate
(40 hours a week; fixed-term employment for the period of 6 years;
Envisaged Job Starting Date 01 October 2014)
For more information follow the link:
http://jobs.uni-graz.at/en/MB/98/99
----------------------------------------------------
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