SMB Digest February 4, 2015 Volume 15 Issue 5
ISSN 1086-6566
Editor: Wandi Ding ding.smb.digest(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:
The Institute of Mathematical Sciences (ICMAT) Newsletter
New book: Mathematical Modelling of Zombies
NIMBioS-XSEDE Tutorial: Introduction to Using R for HPC, Feb. 27
aSSB'15 Thematic Research School, Strasbourg, March 23-27
Conf: modelling biological..., U of Leicester, UK, April 28-May 1
Workshop: Mathematical Trends in..., U of Copenhagen, July 1-3
CfA: q-bio Summer School 2015, July 6-21, 13-28
Postdoc Position: Computational Physiology and..., Switzerland
Selected NIH Intramural Research plus other Openings, Feb. 2015
Faculty Position: Applied Mathematics, Wageningen U
SMBnet Reminders
---------------------------------------------------------
From: Antonio Gómez-Corral <
antonio.gomez@icmat.es>
Date: Wed, Jan 28, 2015 at 3:55 AM
Subject: The Institute of Mathematical Sciences (ICMAT) Newsletter
The Institute of Mathematical Sciences (ICMAT) is bringing out a bulletin
with the aim of providing the scientific community, and all those
interested in the advances in the mathematical discipline, with information
about the research activity of excellence conducted at the center.
The eight number of the ICMAT Newsletter is devoted largely to Mathematical
Biology. Along with the news, agenda and editorial sections, it includes
two reports (on "The strange relation between numbers and neurons";
and "Differential equations against HIV"), three interviews
(Philip K. Maini, Professor of Mathematical Biology at Oxford University;
Ingrid Daubechies, former chair of the International Mathematical Union;
and Mats Gyllenberg, researcher in biomathematics at the University of
Helsinki), and the sections "Scientific reports" and "Personalities".
PDF English/Spanish versions of this issue are available at
http://www.icmat.es/outreach/newsletter/num8 ------------------------------------------------------------------
From: Robert Smith? <
smithr@math.mcmaster.ca>
Date: Wed, Jan 28, 2015 at 1:25 PM
Subject: New book: Mathematical Modelling of Zombies
New book: Mathematical Modelling of Zombies
In 2009, Professor Robert Smith? became famous for an academic paper that
used mathematical modelling to examine a hypothetical zombie outbreak. Now
he's taking it to the next level and has developed an entire mathematical
textbook to prepare you for the undead apocalypse!
Well, okay, it also teaches you useful skills about how to mathematically
model infectious diseases. But in this book, there's only one disease that
counts: zombies.
The zombie apocalypse could occur at any time! And the best weapon against
them is: braaaiiinnnsss! Your apocalypse survival kit will include such
essentials as:
-mathematical models
-differential equations
-individual-based modelling
-zombie swarming
-statistical estimation
-fuzzy decision-making
-network theory
-discrete-time models
-spatial diffusion of the undead
-adaptive strategies for zombie attacks.
Chapters also look at how modelling can advise government policy, how
theoretical results can be communicated to a non-mathematical audience
and how models can be formulated with only limited information. Robert
Smith? also develops a mathematical model to track the viral spread of the
story of his original math paper through the media.
The aim of this collection is to illustrate the power of mathematical
modelling using the fun hook of zombies.
http://www.press.uottawa.ca/mathematical-modelling-of-zombies --------------------------------------------------------------
From: Catherine Crawley <
ccrawley@nimbios.org>
Date: Mon, Feb 2, 2015 at 11:08 AM
Subject: NIMBioS-XSEDE Tutorial: Introduction to Using R for HPC, Feb. 27
The National Institute for Mathematical and Biological Synthesis (NIMBioS)
will host a half-day tutorial, "An In-depth Introduction to Using R for
HPC," from 1-5 p.m. Friday, Feb. 27 at NIMBioS. The tutorial will be
live streamed.
For more information about the tutorial and a link to register,
go to
http://www.nimbios.org/tutorials/TT_RforHPCCo-Organizers: Drew Schmidt, Extreme Science and Engineering Discovery
Environment (XSEDE) and Eric Carr, NIMBioS. This is a joint training
between the University of Tennessee, NIMBioS, XSEDE (
https://www.xsede.org/)
and NICS (
https://www.nics.tennessee.edu/).
Who Should Attend: The tutorial is ideally suited for those already
working with R, as well as service providers who are serving R customers.
The content is appropriate for any students, researchers, or staff who
are working with R and interested in performance.
No travel support will be provided for this tutorial. Please register to
receive materials and system requirements for the tutorial. There will
be limited space for local attendance so be sure to indicate on the
registration form if you will be attending in person or via the live
stream.
Registration deadline: February 25, 2015
-------------------------------------------------------------------
From: Dominique Zeliszewski <
dominique.zeliszewski@issb.genopole.fr>
Date: Fri, Jan 30, 2015 at 8:26 AM
Subject: aSSB'15 Thematic Research School, Strasbourg, March 23-27
We are pleased to announce the aSSB'15 Thematic Research School on
"advances in Systems and Synthetic Biology-Modelling complex biological
systems in the context of genomics". The upcoming session will take place
in Strasbourg on 23-27 March 2015. The program includes conferences
(listed below), many hands-on tutorials, selected talks by students and
postdocs, and poster sessions. This cross-disciplinary Thematic School on
Systems and Synthetic Biology is the fourteenth edition of a series started
in 2002. Early bird registration deadline: February 9th, 2015, on the
dedicated website (
http://epigenomique.free.fr/en/index.php).
aSSB'15 speakers and sessions:
Jacques DEMONGEOT (AGIM, UJF, Grenoble, FR), special guest
1. Cell modeling
Albert GOLDBETER (ULB, Bruxelles, BE), keynote speaker
Laurence CALZONE (Inst. Curie, Paris, FR)
2. Modeling biological networks
Nicolas LE NOVÈRE (Babraham Inst., Cambridge, UK)
François FAGES (INRIA, Rocquencourt, FR)
2. Plant systems and synthetic biology
Anne OSBOURN (John Innes Centre, Norwich, UK)
Oliver EBENHOEH (U. Aberdeen, UK)
3. Yeast systems and synthetic biology
Joel BADER (Johns Hopkins U., Baltimore, US)
Damien COUDREUSE (U. Rennes, FR)
4. Enzyme and metabolic modeling
Magali REMAUD (Toulouse White Biotech, FR)
Jürgen ZANGHELLINI (ACIB, Graz, AT)
Art and Biology
Jens HAUSER (Synth-ethic, Vienna, AT & Paris, FR)
aSSB SCIENTIFIC BOARD:
Patrick Amar (U. Paris-Sud, FR)
Gilles Bernot (U. Nice-Sophia, FR)
Marie Beurton-Aimar (U. Bordeaux, FR)
Attila Csikasz-Nagy (Edmund Mach Fundation, S. Michele all'Adige, IT)
Jürgen Jost (MPI-MIS Leipzig, DE)
Ivan Junier (CRG, Barcelona, ES)
Marcelline Kaufman (U. Libre de Bruxelles, BE)
François Képès (CNRS Evry, FR), Chair
Pascale Le Gall (Ecole Centrale Paris, FR)
Sheref Mansy (U. Trento, IT)
Jean-Pierre Mazat (U. Bordeaux, FR)
Victor Norris (U. Rouen, FR)
William Saurin (Sobios, Sophia-Antipolis, FR)
El Houssine Snoussi (U. Mohammed 5-Souissi, Rabat, MA)
Ines Thiele (U. Luxembourg, LU)
Birgit Wiltschi (Austrian Centre of Industrial Biotechnology, Graz, AT)
------------------------------------------------------------------
From: Morozov, Andrey (Dr.) <
am379@leicester.ac.uk>
Date: Thu, Jan 29, 2015 at 7:06 AM
Subject: Conf: modelling biological..., U of Leicester, UK, April 28-May 1
Modelling Biological Evolution 2015: Linking Mathematical Theories with
Empirical Realities.
Combined with the London Mathematical Society workshop
"Mathematical and Computational Models in Evolutionary Biology: Shifting
the Existing Paradigms".
A conference combined with a LMS workshop on mathematical modelling in
evolutionary biology will take place in the Department of Mathematics in
University of Leicester from April 28th to May 1st 2015. The joint meeting
will focus on various aspects of modelling evolution in different biological
systems ranging from macromolecules and cells to processes in sociobiology,
including the evolution of human culture and behaviour. Various methods
and modelling techniques will be represented including general aspects of
game theory, adaptive dynamics, optimization, reinforcement learning,
model reduction, individual based models as well as their combinations.
An important part of the meeting will be comparison of the results obtained
based on different mathematical techniques to stimulate further advances in
modelling biological evolution. The event is also expected to be an open
forum for communication between empirical biologists and mathematicians
with the main goal of enhancing interdisciplinary approaches and stimulating
further advances in understanding biological evolution.
The list of keynote speakers includes:
Samuel Alizon (Montpellier, France)
Nick Britton (University of Bath, UK)
Sergey Gavrilets (University of Tennessee, Knoxville, USA)
Alexander Gorban (University of Leicester, UK)
Ivana Gudelj (University of Exeter, UK)
Rebecca Hoyle (University of Southampton, UK)
Yoh Iwasa (Kyushu University, Japan)
John McNamara (University of Bristol, UK)
Katerina Stankova (Maastricht University, the Netherlands)
Arne Traulsen (Max-Planck-Institute, Ploen, Germany)
The further information including the Keynote Speakers, the Advisory
Scientific Committee, conference fees as well as the deadlines can be
found on the conference webpage:
http://www.math.le.ac.uk/people/ag153/homepage/MBE15/MBE15.htm To register your interest in this email:
am379@leicester.ac.uk. For
further information visit the website at
http://www.math.le.ac.uk/people/ag153/homepage/MBE15/MBE15.htm.
There will be a limited support for young researchers (UK based research
students). The main organizer is Dr. Andrew Morozov. The meeting is
supported by an LMS Conference grant and by the University of Leicester.
-------------------------------------------------------------------
From: Elisenda Feliu <
efeliu@math.ku.dk>
Date: Tue, Jan 27, 2015 at 3:32 PM
Subject: Workshop: Mathematical Trends in..., U of Copenhagen, July 1-3
Workshop on Mathematical Trends in Reaction Network Theory
July 1-3, 2015, Copenhagen, Denmark
http://www.math.ku.dk/~efeliu/trendsrnt/Submission for contributed talks and poster presentation are now accepted.
Deadline for submission: March 15, 2015.
The workshop focusses on current and new trends in mathematical reaction
network theory, which we consider broadly to be the theory describing the
behaviour of systems of (bio)chemical reactions. In recent years, new
interesting approaches using theory from dynamical systems, stochastics,
algebra and beyond, have appeared. We aim to provide a forum for
discussion of these new approaches and to bring together researchers from
different communities.
-Confirmed invited speakers:
Gheorghe Craciun (University of Wisconsin, Madison, US)
David Doty (California Institute of Technology, US)
Manoj Gopalkrishnan (Tata Institute of Fundamental Research, India)
Michal Komorowski (Institute of Fundamental Technological Research,
Polish Academy of Sciences, Poland)
Nikki Meskhat (North Carolina State University, US)
Alan D. Rendall (Johannes Gutenberg Universität Mainz, Germany)
János Tóth (Budapest University of Technology and Economics, Hungary)
Sebastian Walcher (RWTH Aachen, Germany)
The workshop is organised by the group Mathematics of Reaction Networks
at the Department of Mathematical Sciences at the University of Copenhagen.
---------------------------------------------------------------------
From: Bridget S Wilson <
BWilson@salud.unm.edu>
Date: Wed, Jan 28, 2015 at 8:35 AM
Subject: CfA: q-bio Summer School 2015, July 6-21, 13-28
Applications are now being accepted for the Ninth Annual q-bio Summer School.
The application requires a CV and a 1-page statement of interest in the
summer school (combined into a single .pdf). Scholarships are available.
Applications will be due on Monday, February 16 at 11:59pm (MST).
Submitted applications may be revised until that time.
To apply now, please visit our website:
http://q-bio.org/wiki/The_Ninth_q-bio_Summer_SchoolThe q-bio Summer School will cover nine different general topic areas and
be held at three different campuses. The specific dates and campus
locations are:
1. July 6-21, 2015 at the Colorado State University in Fort Collins, CO
2. July 13-28, 2015 at the University of New Mexico in Albuquerque, NM
3. July 13-28, 2015 at the University of California in San Diego, CA.
The main topics of the 2015 summer school are:
Biomolecular Simulations (Albuquerque, NM)
Cell Signaling (Albuquerque, NM)
Membrane Biology (Albuquerque, NM)
Viral Dynamics (Albuquerque, NM)
Cancer Dynamics (Fort Collins, CO)
Complex Biological Dynamics (Fort Collins, CO)
Stochastic Gene Regulation (Fort Collins, CO)
Computational Synthetic Biology (San Diego, CA)
Experimental Synthetic Biology (San Diego, CA)
Please see the school wiki (
http://q-bio.org/wiki/The_Ninth_q-bio_Summer_School)
for more information about each specific topic.
For inquiries about the scientific content at the summer school, please
contact:
Brian Munsky (Fort Collins Campus):
munsky@engr.colostate.eduBill Hlavacek (Albuquerque Campus):
wshlavacek@gmail.comLev Tsimring (San Diego Campus):
ltsimring@ucsd.eduPoint of Contact: Shannan Yeager, q-bio Program Manager,
syeager@newmexicoconsortium.orgFor more information, please visit the school wiki at:
http://q-bio.org/wiki/The_Ninth_q-bio_Summer_SchoolPlease visit and join the q-bio group on LinkedIn:
http://www.linkedin.com/groups/qbio-5075101Online Application website:
https://www.openconf.org/qbioss2015/openconf.php---------------------------------------------------------------------
From: Edgar Delgado-Eckert <
edgar.delgado-eckert@unibas.ch>
Date: Mon, Feb 2, 2015 at 7:28 AM
Subject: Postdoc Position: Computational Physiology and..., Switzerland
Post Doc in Computational Physiology and Biostatistics: 60-80% negotiable
The Clinical Morphology and Biomedical Engineering section of the Medical
Faculty at the University of Basel, together with the University Children's
Hospital of Basel, are offering a Post Doc position within the
Computational Physiology and Biostatistics Group, led by Dr. Edgar
Delgado-Eckert.
One of the main current research activities of this group is the analysis
of time series of physiological signals, such as cardiac activity, body
temperature, movement patterns, and several lung function parameters.
The mathematical and statistical analysis of these time series is aimed
at developing new quantitative approaches of clinical, diagnostic, and/or
prognostic value, as well as conducting epidemiological studies within
different cohorts.
The mathematical and computational methodology used for the analysis of
these time series comprises techniques borrowed from nonlinear dynamics,
such as the largest Lyapunov exponent, and from statistics and information
theory, including sample entropy, and long range correlations revealed
by detrended fluctuation analysis.
Job Description
The candidate is expected to actively participate in some of the ongoing
projects, by contributing their own ideas, applying their expertise,
mentoring master and PhD students involved in the projects, and
implementing algorithms on the computational platforms we use
(mainly Matlab and R). In addition, the candidate will have the opportunity
to develop their own projects in coordination with the rest of the group.
Profile requirements
- PhD degree in Mathematics, Physics, Statistics, Computer Science,
Bioinformatics, Bioengineering, Computational Systems Biology or a closely
related field.
- Evidence of the ability to independently conduct scientific research in
the areas of Computational Physiology or Biology, Biomathematics,
Biostatistics, Bioinformatics or a closely related field is expected, in
the form of peer-reviewed scientific publications in which the candidate
appears as the first author. Submitted but not yet accepted manuscripts
do count.
- Good programming skills and some experience with the environments Matlab
and R
- Of advantage is basic knowledge in human physiology, particularly cardiac
and respiratory function.
Applications should include a curriculum vitae and three letters of
reference. The applicant should be aware that referees may be contacted.
Please send application documents by email (with "computational physiology"
in the subject line) to
edgar.delgado-eckert@ukbb.ch or via
postal services to:
Dr. Edgar Delgado-Eckert
Studienzentrum Pneumologie
Universitätskinderspital beider Basel (UKBB)
Spitalstrasse 33
Postfach
4031 Basel
Switzerland.
Dr. Edgar Delgado-Eckert's research group website:
http://www.ukbb.ch/en/research/research-groups/pneumology/computational-physiology-and-biostatistics.html-------------------------------------------------------------------
From: Raymond Mejía <
mejiar@helix.nih.gov>
Date: Mon, Feb 2, 2015 at 11:14 AM
Subject: Selected NIH Intramural Research plus other Openings, Feb. 2015
Tenure-Track Epidemiologists, NIEHS (deadline: March 9)
The National Institute of Environmental Health Sciences (NIEHS),
part of the National Institutes of Health (NIH), located in Research
Triangle Park, North Carolina, is recruiting for one or more tenure-track
epidemiologists. Successful candidate(s) will be expected to develop an
outstanding, investigator-initiated research program in any of the
following areas: reproduction, pregnancy outcomes, pediatrics, early
origins of disease, life-course epidemiology, adult health/chronic
disease, or other areas of environmental epidemiology. Biologically-based
epidemiological research (including genetics, epigenetics, metabolomics,
microbiomics, and biomarkers) and primary data collection are encouraged.
Successful candidates should plan to work both independently and as part
of multi-disciplinary or collaborative teams. The Branch provides an
academic atmosphere with excellent support. Funds are available for
research and support staff, including fellows, programmers, and field
workers. The Branch has several large, ongoing cohort studies with
biological samples that can serve as platforms for additional research.
There are opportunities for adjunct appointments at nearby universities
and for mentoring pre- and post-doctoral fellows. Position(s) will be
filled at the tenure-track level. Time to tenure will vary depending
upon research accomplishments; an accelerated timetable is possible for
more established exceptional candidates. Salary is "hard money" and will
be commensurate with experience and qualifications of the candidate.
Federal benefits apply. Information on the NIEHS Epidemiology Branch
can be found at
http://www.niehs.nih.gov/epi.
Candidates should have a doctoral degree and a record of accomplishment in
epidemiology, including a strong publication record and research experience.
Applications from women and under-represented minorities are strongly
encouraged. Interested persons should submit one combined PDF of their
curriculum vitae and a two-page statement of research interests and goals,
and also arrange for 3 letters of recommendation to be sent to Ms. Katherine
Fine
atdir-appls@niehs.nih.gov citing your name and Vacancy Announcement
DIR 15-1 in the subject line. We will begin evaluating complete applications
on March 9, 2015. Applications will continue to be accepted until vacancies
are filled.
The NIH is dedicated to building a diverse community in its training and
employment programs. HHS and NIH are equal opportunity employers.
Applications from women, minorities and persons with disabilities are
strongly encouraged.
Deputy Director
Division of Cancer Epidemiology and Genetics, NCI
(deadline: March 20)
The Division of Cancer Epidemiology and Genetics (DCEG), National Cancer
Institute (NCI), National Institutes of Health (NIH) is recruiting an
accomplished, senior scientist to serve as Deputy Director in the Office of
the Director, DCEG. DCEG's epidemiologists, geneticists, and
biostatisticians conduct population and multidisciplinary research to
discover the genetic and environmental determinants of cancer and new
approaches to cancer prevention. The Division's research has an impact
on public health policy in the United States and around the world.
The Deputy Director will be a senior investigator with resources to lead an
internationally recognized scientific research program. The Deputy Director
will also play a key role in identifying new research opportunities and
directions for the Division, provide technical/scientific advice, and
assist the Division Director in making decisions concerning the initiation,
expansion, integration, or termination of programs based on research
goals, available resources, program evaluations, and emerging scientific
opportunities. The Deputy Director will serve as liaison to NCI and NIH
standing committees, and represent the Division to other agencies and
outside organizations in order to coordinate activities, enhance
communication, and develop new initiatives and infrastructure.
The successful candidate must be a senior scientist who holds either a
medical degree or a doctoral degree in epidemiology, genetics, genomics,
or related fields, and who has had substantial relevant experience and
responsibility for managing and directing a broad scientific program in
cancer epidemiology and/or genetics and is a successful mentor. He or
she must demonstrate relevant management experience as a senior level
scientific administrator who has led investigators involved in conducting
interdisciplinary studies of cancer epidemiology and/or genetics and whose
work has been extensively published in peer-reviewed scientific or medical
journals and presented at scientific meetings.
The Deputy Director will be eligible for a tenured appointment at a salary
commensurate with his/her qualifications and experience. Full Federal
benefits including leave, health and life insurance, long-term care
insurance, retirement, and savings plan (401k equivalent) will be provided.
Qualified candidates may be considered for the NIH Senior Biomedical
Research Service. Interested individuals should send a cover letter,
curriculum vitae and bibliography, a brief summary of research interests
and accomplishments, scientific administrative experience, copies of up
to five publications or preprints, and the names and addresses of three
references to: Ms. Catherine McClave, Division of Cancer Epidemiology and
Genetics, National Cancer Institute, 9609 Medical Center Drive, Rm.
7E-440, Bethesda, MD 20892-9774. Or e-mail
mcclavec@mail.nih.gov.
Applications received by March 20, 2015 will be considered for a first
round of interviews, but applications will be accepted until the position
is filled. The DHHS and NIH are equal opportunity employers.
Also see:
The NIH Intramural Research Program
http://irp.nih.gov/http://irp.nih.gov/careers/tenured-and-tenure-track-scientific-careersLink to Fellowships and Positions of Interest to fellows
https://www.training.nih.gov/https://www.training.nih.gov/career_services/jobsLink to NIH Jobs
http://www.jobs.nih.gov/---------------------------------------------------------------
From: Molenaar, Jaap <
jaap.molenaar@wur.nl>
Date: Tue, Feb 3, 2015 at 3:08 AM
Subject: Faculty Position: Applied Mathematics, Wageningen U
Assistant Professor Applied Mathematics, Tenure Track at Wageningen
University
Function description
Within the Chair Mathematical Methods of Wageningen University we have a
vacancy (tenure track) for an assistant professor in Applied Mathematics.
His area of research is intended to be Systems Biology. This relatively
new field of research connects the fields of mathematical modelling and
biology. Especially at the lower levels of aggregation in biology (cell,
tissue, organs) a tremendous progress in experimental possibilities has
taken place. Consequently, the role of mathematical modelling is becoming
more and more important, since modelling is the natural way to deduce
insight in the mechanisms underlying the many processes driving living
systems. Not only the lower levels of aggregations are studied within our
chair group, we also develop models for the ecological levels and study
how to connect the different levels.
As a candidate, you are expected to develop a research profile in Systems
Biology that strengthens the ongoing research in the group and forms or
develops into an own line of research. You are capable of attracting PhDs
and external funding, are a stimulating teacher in courses for
non-mathematicians, and contribute in a significant way to the
international profile of the group.
Requirements:
You are a good researcher and teacher. Preferably, your background is
mathematics with a strong emphasis on mathematical modelling. Candidates
with a background in physics, chemistry, informatics, or biology may also
apply, provided that they have a very strong inclination to the mathematical
aspects of these fields. You are experienced in applying your modelling
skills in the Life Sciences, or strongly intending to obtain this
experience. See also
http://www.biometris.wur.nl under "vacancies".
For applications, see:
https://www.academictransfer.com/employer/WUR/vacancy/26443/lang/en/For additional information: prof. dr. J. Molenaar, 0317-486042 or via
Jaap.Molenaar@wur.nl You may apply between 2 and 21 February 2015.
---------------------------------------------------------------
Subject: SMBnet Reminders
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End of SMB Digest
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