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Subject: SMB Digest v14i27
SMB Digest July 3, 2014 Volume 14 Issue 27
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,
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Access the Bulletin of Mathematical Biology, the official journal of
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Issue's Topics:
Workshop: Information and Entropy, Apr 8-10, NIMBioS
Book Announcement: Stochastic Processes in Cell..., Bressloff
Book Announcement: Chemical Kinetics, Stochastic..., Santillan
PhD Position: Computational Systems Biology, Uppsala U, Sweden
Post-doc: Theoretical Evolutionary Biology, Western U, Canada
Post-doc: Biophysics/Computational Systems Biology, Rice U
Selected NIH Intramural Research & Other Positions-July Update
SMBnet Reminders
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From: Catherine Crawley <ccrawley@nimbios.org>
Date: July 1, 2014 10:16:46 AM
Subject: Workshop: Information and Entropy, Apr 8-10, NIMBioS
The National Institute for Mathematical and Biological Synthesis
(NIMBioS) is now accepting applications for its Investigative Workshop,
"Information and Entropy," to be held April 8-10, 2015, at NIMBioS.
Objectives: Information theory and entropy methods are becoming powerful
tools in biology, from the level of individual cells, to whole
ecosystems, to experimental design, model-building, and the measurement
of biodiversity. The aim of this investigative workshop is to synthesize
different ways of applying these concepts to help systematize and unify
work in biological systems. Early attempts at "grand syntheses" often
misfired, but applications of information theory and entropy to specific
highly focused topics in biology have been increasingly successful. In
ecology, entropy maximization methods have proven successful in
predicting the distribution and abundance of species. Entropy is also
widely used as a measure of biodiversity. Work on the role of
information in game theory has shed new light on evolution. As a
population evolves, it can be seen as gaining information about its
environment. The principle of maximum entropy production has emerged as
a fascinating yet controversial approach to predicting the behavior of
biological systems, from individual organisms to whole ecosystems. This
investigative workshop will bring together top researchers from these
diverse fields to share insights and methods and address some
long-standing conceptual problems.
Goals of the workshop:
1. To study the validity of the principle of Maximum Entropy Production
(MEP), which states that biological systems - and indeed all open,
non-equilibrium systems - act to produce entropy at the maximum rate.
2. To familiarize all the participants with applications to ecology of
the MaxEnt method: choosing the probabilistic hypothesis with the
highest entropy subject to the constraints of our data. We will compare
MaxEnt with competing approaches and examine whether MaxEnt provides a
sufficient justification for the principle of MEP.
3. To clarify relations between known characterizations of entropy, the
use of entropy as a measure of biodiversity, and the use of MaxEnt
methods in ecology.
4. To develop the concept of evolutionary games as "learning" processes
in which information is gained over time.
5. To study the interplay between information theory and the
thermodynamics of individual cells and organelles.
Location: NIMBioS at the University of Tennessee, Knoxville
Co-Organizers: John Baez, Mathematics, Univ. of California, Riverside;
Marc Harper, Educational and Biotechnology Consultant;
John Harte, Environmental Science, Policy and Management, Univ. of
California, Berkeley
For more information about the workshop and a link to the online
application form, go to http://www.nimbios.org/workshops/WS_entropy
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: November 12, 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: Walker, Danielle, Springer US <Danielle.Walker@springer.com>
Date: July 1, 2014 9:57:39 AM
Subject: Book Announcement: Stochastic Processes in Cell..., Bressloff
Forthcoming from Springer
Paul Bressloff, Stochastic Processes in Cell Biology, Interdisciplinary
Applied Mathematics Series
This book develops the theory of continuous and discrete stochastic
processes within the context of cell biology. A wide range of biological
topics are covered including normal and anomalous diffusion in complex
cellular environments, stochastic ion channels and excitable systems,
stochastic calcium signaling, molecular motors, intracellular transport,
signal transduction, bacterial chemotaxis, robustness in gene networks,
genetic switches and oscillators, cell polarization, polymerization,
cellular length control, and branching processes. The book also provides
a pedagogical introduction to the theory of stochastic process ? Fokker
Planck equations, stochastic differential equations, master equations
and jump Markov processes, diffusion approximations and the system size
expansion, first passage time problems, stochastic hybrid systems,
reaction-diffusion equations, exclusion processes, WKB methods,
martingales and branching processes, stochastic calculus, and numerical
methods.
This text is primarily aimed at graduate students and researchers
working in mathematical biology and applied mathematicians interested in
stochastic modeling. Applied probabilists and theoretical physicists
should also find it of interest. It assumes no prior background in
statistical physics and introduces concepts in stochastic processes via
motivating biological applications.
The book is highly illustrated and contains a large number of examples
and exercises that further develop the models and ideas in the body of
the text. It is based on a course that the author has taught at the
University of Utah for many years.
Due Fall 2014 -
http://www.springer.com/new+%26+forthcoming+titles+%28default%29/book/978-3-319-08487-9
----------------------------------------------------
From: Walker, Danielle, Springer US <Danielle.Walker@springer.com>
Date: July 1, 2014 11:35:55 AM
Subject: Book Announcement: Chemical Kinetics, Stochastic..., Santillan
Forthcoming from Springer
Moises Santillan, Chemical Kinetics, Stochastic Processes, and
Irreversible Thermodynamics, Lecture notes on Mathematical Modelling in
the Life Sciences series
This book brings theories in nonlinear dynamics, stochastic processes,
irreversible thermodynamics, physical chemistry, and biochemistry
together in an introductory but formal and comprehensive manner. Coupled
with examples, the theories are developed stepwise, starting with the
simplest concepts and building upon them into a more general framework.
Furthermore, each new mathematical derivation is immediately applied to
one or more biological systems. The last chapters focus on applying
mathematical and physical techniques to study systems such as: gene
regulatory networks and ion channels.
The target audience of this book are mainly final year undergraduate and
graduate students with a solid mathematical background (physicists,
mathematicians, and engineers), as well as with basic notions of
biochemistry and cellular biology. This book can also be useful to
students with a biological background who are interested in mathematical
modeling, and have a working knowledge of calculus, differential
equations, and a basic understanding of probability theory.
Due Summer 2014 -
http://www.springer.com/new+%26+forthcoming+titles+%28default%29/book/978-3-319-06688-2
----------------------------------------------------
From: Andreas Hellander <andreas.hellander@it.uu.se>
Date: June 30, 2014 1:47:02 PM
Subject: PhD Position: Computational Systems Biology, Uppsala U, Sweden
One PhD student position is available, to work in the group of Andreas
Hellander, Division of Scientific Computing, Department of Information
Technology, Uppsala University, Uppsala, Sweden.
Description of the subject area:
The overall objective of the project is to develop methods for efficient
and flexible simulation of (spatial) stochastic models of biochemical
reactions. The application area is molecular systems biology and the aim
of the research is to develop methods to understand how e.g. gene
regulation is controlled on a molecular level. The group
(www.andreashellander.se) participates in national and international
software projects (www.urdme.org, www.pyurdme.org, www.stochss.org) and
in the computational systems biology project at the Division of
Scientific Computing. (http://www.it.uu.se/research/project/csbio).
Job assignment:
To develop computational methods for simulation of molecular control
systems, in particular methods that account for the multiscale
properties of such models. To participate in the development of
computational software based on the developed methods.
For more information and for instructions for how to apply, see
http://www.uu.se/en/join-us/jobs-detail-page/?positionId=40073
The salary is approximately 24000 SEK/month.
Application deadline: Aug 31, 2014.
For more information, contact Andreas Hellander,
andreas.hellander@it.uu.se
----------------------------------------------------
From: Lindi Wahl <lwahl@uwo.ca>
Date: June 24, 2014 4:12:59 PM
Subject: Post-doc: Theoretical Evolutionary Biology, Western U, Canada
POST-DOCTORAL FELLOW IN THEORETICAL EVOLUTIONARY BIOLOGY
Department of Applied Mathematics
Western University, London, Ontario, Canada
Start date: September 2014 (flexible/negotiable)
Term: 2 years (subject to satisfactory progress)
Salary: 45,000 to 50,000 CDN$ p.a.
DESCRIPTION
Research in theoretical evolutionary biology at Western tackles problems
in both experimental evolution and sociobiology (see
www.apmaths.uwo.ca/~lwahl and www.apmaths.uwo.ca/~gwild for greater
detail). We are hiring a post-doctoral fellow interested in modeling
evolution as it occurs in both laboratory experiments, and field
settings.
The successful candidate will be expected to carry out both independent
and collaborative research, and will mentor graduate students in the
group. The successful candidate may also apply for sessional teaching
positions (one term per year) in order to supplement his/her income and
gain teaching experience, if so desired (subject to departmental
approval).
----------------------------------------------------
From: Oleg Igoshin <igoshin@rice.edu>
Date: July 1, 2014 10:56:33 AM
Subject: Post-doc: Biophysics/Computational Systems Biology, Rice U
A Postdoctoral Positions in Computational Systems Biology are available
in the laboratory of Prof. Igoshin in the Dept of Bioengineering at Rice
University. We are looking for motivated postdoctoral fellows to work on
several projects in the group. Our group specializes in computational
systems biology with emphasis in evolutionary design principles and the
characterization of biochemical networks, pattern formation in bacterial
biofilms, and genetic networks in bacterial and stem cell development.
Current funding comes from both NIH and NSF. Two current projects
available in the group are briefly described below however motivated
postdoctoral fellows may be able to pick their own direction as long as
its aligns with groups research interests. Please visit
http://igoshin.rice.edu/ or contact Prof. Igoshin for more information.
PROJECTS:
1) A key property of living cells is their ability to react to internal
or external stimuli with specific biochemical responses. Bacteria have
evolved to sense and rapidly adapt to environmental stimuli by changes
in gene expression. Many molecular details of stress response networks
regulating these responses have been uncovered for many model bacteria.
However, we still lack network-level knowledge of these responses across
species, which is necessary to obtain a deeper understanding of cellular
functions and to best apply results obtained with model bacteria to
bacterial species that are poorly characterized or cannot be cultured in
a laboratory. In this project we are focusing on two of the common basic
building blocks of bacterial stress-response network to explore how
network organization affects the physiologically relevant dynamical
properties.
2) In recent years the ubiquity of microbial communities in nature has
become apparent: for instance, most bacteria related to human diseases
are associated with biofilms. However, it is still not clear how
individual cells self-organize in these communities and how community as
a whole responds to environmental cues. This project aims to discover
the mechanisms of self-organization in dynamic single-species biofilms
(swarms). In these swarms, bacteria display collective surface motility,
cooperatively sense the environment, execute collective developmental
programs and often differentiate into distinct cell types performing
specialized functions. This research focuses on developmental
aggregation in biofilms formed by Myxococcus xanthus - an important
model organism for studying microbial cooperation, development, and
collective motility. Research will involve statistical image
analysis/quantification, data analysis and agent-based modeling based on
available biological data of our collaborators.
QUALIFICATIONS AND RESPONSIBILITIES:
PhD in science or engineering and research experience in computational
biology is required for this position. Candidates with publications in
the field of mathematical/computational biology related to systems
biology modeling are strongly preferred. Previous experience in image
analysis, bioinformatics and/or modeling bacterial networks is a plus.
Strong interest in interdisciplinary collaboration and English
proficiency are also expected. Some of the research will be conducted in
tight collaboration with experimental colleagues and the main results
are at least partially expected to be published in biological journals.
ABOUT RICE AND HOUSTON:
Rice is consistently ranked as one of the nation?s best teaching and
research universities.
It is a member institution of the world largest Medical Center (TMC).
Rice is committed to cutting edge interdisciplinary biological research.
It is a home to Center of Theoretical Biological Physics (ctbp.rice.edu)
and PhD Program in Systems, Synthetic and physical Biology
(sspb.rice.edu).
The Department of Bioengineering is consistently ranked among the
nation's top 10 bioengineering graduate programs. Rice is situated in
the Museum district of Houston, TX ? the fourth largest city in the US.
CONDITIONS:
Rice University is committed to affirmative action and equal opportunity
employer and offers competitive postdoctoral salary and benefits. The
position is open from August 1, 2014 until filled. The initial
appointment is for 1 year with possible continuation upon satisfactory
performance.
APPLICATION PROCEDURE:
Applicants should submit their CV and research statement letter
justifying their interests in the group to igoshin@rice.edu.
----------------------------------------------------
From: Owens, Roland (NIH/OD) [E] <owensrol@mail.nih.gov>
Date: July 1, 2014 10:28:55 AM
Resent-From: Raymond Mejía <mejiar@helix.nih.gov>
Subject: Selected NIH Intramural Research & Other Positions-July Update
The NIH Intramural Research Program
http://irp.nih.gov/
http://irp.nih.gov/careers/tenured-and-tenure-track-scientific-careers
Link to Fellowships and Positions of Interest to fellows
https://www.training.nih.gov/
https://www.training.nih.gov/career_services/jobs
Link to NIH Jobs
http://www.jobs.nih.gov/
----------------------------------------------------
Subject: SMBnet Reminders
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