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Subject: SMB Digest v12i48
SMB Digest November 26, 2012 Volume 12 Issue 48
ISSN 1086-6566
Editor: Ray Mejía ray(at)smb(dot)org
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:
Research Program: Mathematical Biology, March 4 - June 14, Lyon
Conference: Computational Cell Biology, Aug 14-16, Blacksburg
International Conference: Computational Science, June 5-7, Barcelona
Earl Stadtman Tenure-Track Investigator Search Symposium Website, NIH
Query: PhD Proposal "Noise as a Computational Resource in Brains ..."
PhD Studentship: Modelling in Mosquito Populations, CEH, Wallingford
Postdoc: Biological Oceanography, Tulane University
Postdocs: Microfluidic Single-cell Analysis & Cell Signaling, ETH
NIH Research & Other Selected Positions, November Update
SMBnet Reminders
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From: "Hugues Berry" <hugues.berry@inria.fr>
Date: Fri, 16 Nov 2012 22:13:41 +1300 (NZDT)
Subject: Research Program: Mathematical Biology, March 4 - June 14, Lyon
Dear colleagues,
we organize a research program on "Mathematical Biology", in Lyon (France)
from March 4th to June 14th, 2013.
http://mathbio2013.sciencesconf.org/
These activities are funded in part by the labex MILYON
(http://milyon.universite-lyon.fr/).
The highlights of the program are:
1- Conference « Biological invasions and evolutionary biology, stochastic
and deterministic model », March 11-15, 2013
Organizing committee : Jean Bérard (Univ. Lyon 1), Vincent Calvez (ENS de
Lyon) et Gaël Raoul (CEFE, Montpellier)
2- Conference « Cell biology », March 25-29, 2013
Organizing committee : Hugues Berry (INRIA) et Vincent Calvez (ENS de Lyon)
3- Conference « Systems Biology Approach to Infectious Processes »,
May 13-15, 2013
Organizing committee : Hubert Charles (BioSyL)- François Loïc Cosset
(Ecofect)- Fabien Crauste (Milyon)- Eric Fleury (BioSyL)- Olivier Gandrillon
(BioSyL)- Daniel Kahn (BioSyL)- Jacqueline Marvel (BioSyL)- Dominique Pontier
(Ecofect) and Sylvie Ricard-Blum (BioSyL)
4- Spring school « Multiscale modeling in the life sciences », May 27-31, 2013
Organizing committee : Vincent Calvez (ENS de Lyon), Thomas Lepoutre (INRIA),
Vitaly Volpert (Univ. Lyon 1)
5- Conference in honour of Michael Mackey's 70th birthday, June 3-7, 2013
Organizing committee : Samuel Bernard (Univ. Lyon 1), Fabien Crauste (Univ.
Lyon 1), Moises Santillan (IPN, Mexico), Laurent Pujo-Menjouet (Univ. Lyon 1)
If you wish to participate in one of these activities, please visit the
website, http://mathbio2013.sciencesconf.org/
Grants will be available for PhD students, especially to participate in the
spring school from May 27th to May 31st. You are very welcome to contact
the organizing committee.
We are looking forward to seeing you in Lyon next year.
The organizing committee,
M. Adimy (INRIA), J. Bérard (Univ. Lyon 1), S. Bernard (Univ. Lyon 1) H. Berry
(INRIA), V. Calvez (ENS de Lyon), F. Crauste (Univ. Lyon 1), O. Gandrillon
(Univ. Lyon 1), E. Grenier (ENS de Lyon), Th. Lepoutre (INRIA), L. Pujo-
Menjouet (Univ. Lyon 1), G. Raoul (CNRS, CEFE), B. Ribba (INRIA), V. Volpert
(Univ. Lyon 1).
----------------------------------------------------
From: Jianhua Xing <jxing@vt.edu>
Date: Wed, Nov 21, 2012 at 6:24 PM
Subject: Conference: Computational Cell Biology, Aug 14-16, Blacksburg
Please join us for the International Conference on Computational Cell
Biology: From the past to the future, which we will hold August 14-16, 2013
on Virginia Tech's campus in Blacksburg, Virginia. This conference has been
designed to highlight the interplay between cutting-edge biomathematical
approaches and experimental techniques to complex biological problems,
identify future directions in the field of computational cell biology,
and provide a rare opportunity for young researchers to interact with
some leading scientists. The conference will be held on the occasion of our
colleague Dr John Tyson's 65th birthday. During the formal conference banquet
we will celebrate John's life-time contributions in research and education.
The conference includes invited and contributed talks, poster presentations,
and interactive session on education. Selected students may get the
registration fee reduced or waived. Our confirmed invited speakers include:
Uri Alon (Weizmann Institute of Science)
Daniela Cimini (Virginia Tech)
James Ferrell (Stanford University)
Albert Goldbeter (Universite Libre de Bruxelles)
James Keener (University of Utah)
Arthur Lander (UC Irvine)
Rong Li (Stowers Institute)
Bela Novak (University of Oxford)
Thomas Pollard (Yale University)
Please visit:
http://www.cpe.vt.edu/ccb/index.html
Looking forward to seeing you in Blacksburg,
Jianhua Xing
on behalf of the Organizing Committee
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From: ShifletAB <shifletab@wofford.edu>
Date: Sun, Nov 25, 2012 at 3:35 PM
Subject: International Conference: Computational Science, June 5-7, Barcelona
This year the International Conference on Computational Science
(ICCS 2013) will be held in beautiful Barcelona, Spain, June 5 - June 7
(http://www.iccs-meeting.org/iccs2013/ <http://www.iccs-meeting.org/> ), and
two workshops will focus on education: "The Workshop on Teaching Computational
Science" (WTCS 2013; http://webs.wofford.edu/shifletab/iccs) and "The Workshop
on Educational Approaches for Integrating Bioinformatics into Computer
and Life Science" (WEAIB 2013; http://ccli.ist.unomaha.edu/iccs2013). We
hope you will consider submitting a paper for one of these or another
conference workshop. The paper submission deadlines are December 15, 2012
(WTCS 2013) and January 15, 2013 (WEAIB 2013). Please let us know if you
have any questions.
Hope to see you at ICCS,
Co-Chairs of "The Workshop on Teaching Computational Science":
Angela B. Shiflet, Ph. D. (shifletab@wofford.edu), Wofford College Dr. Alfredo
Tirado-Ramos, Ph. D. (atirado@emory.edu), Emory U.
Co-Chairs of "The Workshop on Educational Approaches for Integrating
Bioinformatics into Computer and Life Science":
Mark A. Pauley, Ph.D. (mpauley@unomaha.edu), University of Nebraska at Omaha
William E. Tapprich, Ph.D. (wtapprich@unomaha.edu), University of Nebraska
at Omaha.
----------------------------------------------------
From: "Owens, Roland (NIH/OD) [E]" <owensrol@mail.nih.gov>
Sent: Wednesday, November 21, 2012 7:53 PM
Resent-From: Raymond Mejía <mejiar@helix.nih.gov>
Subject: Earl Stadtman Tenure-Track Investigator Search Symposium Website, NIH
Dear Colleagues:
The website for the schedule of the first-round seminars for the NIH-Wide
Earl Stadtman Tenure-Track Investigator Search is now available at:
https://ccrod.cancer.gov/confluence/x/VwQSBQ
The first of these seminars will be next Monday, Nov. 26 and the last is
scheduled for Dec. 21, 2012. The schedule is not yet complete, but this
site will be continuously updated. These seminars are public. Feel free to
distribute this link. This is a great opportunity to see a diverse group
of outstanding early-career scientists.
Earl Stadtman Investigator Search Steering Committee
Kathryn Carbone-NIDCR
Michael Krause-NIDDK
Karyl Barron-NIAID
Roland Owens-OD
[Editor - See http://www.nih.gov/about/visitorsecurity.htm prior to visiting
the NIH.]
----------------------------------------------------
From: Olivier Hagnes <olivierhagnes@yahoo.com>
Date: Mon, Nov 19, 2012 at 10:29 AM
Subject: Query: PhD Proposal "Noise as a Computational Resource in Brains ..."
Dear all,
Below might be of interest. I am planning for my PhD proposal and comments
would greatly be appreciated.
Best,
Olivier
Noise as a Computational Resource in Brains and Neuromorphic Hardware (NOICOR)
Its working hypothesis is, that brains employ their inherent stochasticity,
apparent in all brain systems in the form of trial-to-trail variability,
as a computational resource. NOICOR can analyze computational capabilities
and learning capabilities of stochastic dynamic systems in general and of
highly structured brain circuits in particular. It can explore through
theoretical analysis and computer simulations the hypothesis that the
knowledge encoded in the brain to some extent in the form of "embodied"
probability distributions over network states and trajectories of network
states, from which networks of neurons sample through their stochastic
dynamics. Previous computational brain models had focused instead on the
elimination of noise in order to support deterministic computing paradigms.
Objectives of NOICOR:
1. to answer several fundamental theoretical questions as follows,
-- Does a data-based (rather than constructed) model for a stochastic network
of spiking neurons in the brain also have a stationary distribution p,
for which it can therefore carry out probabilistic inference?
-- Does this hold in particular also for detailed (and diverse) data-based
models for neurons and synapses, as they are for example reported in the
experimental literature?
--How do biological details of neurons, synapses, and connectivity patterns
affect the convergence time of these stochastic systems?
-- How can the overall network activity support a fast generation and
readout of network states y with high probability?
-- How do changes in network connectivity, synaptic weights, and other
network parameters affect the stationary distribution p that is embodied
by the network?
2. to provide a systematic understand which constraint satisfaction problems
(CSPs) can be solved efficiently by stochastic networks of spiking neurons,
and which dynamical and connectivity properties optimize their convergence
speed.
3. to provide a theoretical framework for understanding temporal aspects of
computations in stochastic networks of spiking neurons. This can provide a
theoretical framework for understanding temporal aspects of computations in
stochastic networks of spiking neurons.
4. to analyze network learning from the perspective of stochastic
computations.
5. to develop on the basis of theoretical insight gained from work on the
preceding objectives new methods for analyzing simultaneous recording from
many neurons in the cortex, and to develop in collaboration with experimental
neuroscientists- methods for testing predictions of competing models for
the organization of computations in cortical networks of neurons. This can
provide new methods for analyzing the high dimensional data streams which
result from fast 2-photon imaging of dynamics of Ca in hundreds of neurons,
or in dendritic branches of pyramidal cells, especially in combination with
ontogenetic controls.
6. to develop principled methods for using noise as a computational resource
in neuromorphic and other novel computing hardware, and to significantly
advance the state of the art with regard to complexity of computational
problems that can be solved by neuromorphic computers. In fact, NOICOR
develops principle methods for using noise as a computational resource in
future computing hardware.
This research can provide a first theoretical foundation for computations
in neuromorphic hardware that uses noise as a computational resource
and can design a new paradigm for solving NP-complete problem through
stochastic hardware approximations, based on insight from work on the
second objective. The sixth objective can mark a drastic departure from
the direction of previous research on the design of future computing hardware.
----------------------------------------------------
From: White, Steven M. <smwhit@ceh.ac.uk>
Date: Fri, Nov 23, 2012 at 10:36 AM
Subject: PhD Studentship: Modelling in Mosquito Populations, CEH, Wallingford
Modelling the phenological effects of multiple environmental drivers on
mosquito populations. What is needed for the mosquito perfect storm?
Project Outline:
Understanding how environmental drivers alter mosquito temporal abundance in
a way that is likely to cause outbreaks of mosquito-borne zoonotic disease
(MBZD - e.g. West Nile virus) is central to predicting and managing
such diseases. Environmental drivers (such as rainfall, temperature,
evaporation, competition and predation) alter development, fecundity,
survival and therefore abundance of mosquitoes. This has direct effects
on pathogen transmission rates but perhaps the most subtle and profound
effects derive from species phenology. Since it is the temporal pattern
of female-blood feeding mosquito abundance in relation to the availability
of susceptible hosts that governs whether a MBZD exhibits high-prevalence
sustained transmission in wildlife, and therefore potential for disease
spill-over to man and domestic animals. Furthermore, the timing and magnitude
of multiple environmental drivers could combine to provide the perfect storm,
causing mosquito dynamic abundance capable of sustaining MBZD.
The aim of this project is to investigate the role of environmental drivers
in mosquito populations. The student will develop and analyse a system
of state-dependent delayed differential equations in which environmental
drivers affect life-history parameters and development lags focusing on
the mosquito species Culex pipiens the key maintenance vector of many
MBZDs including West Nile virus. The model will be analysed by extensive
numerical simulation techniques using a suitable programming language. In
addition, the student will collect and maintain field caught populations
of Culex pipiens mosquitoes in the UK and undertake empirical studies to
parameterise the models. Finally, the student will spatially extend the
model using remotely sensed and large scale datasets to produce realistic,
spatially explicit risk maps of UK mosquito outbreaks.
The successful candidate will have a strong background in mathematics,
statistics, theoretical physics or theoretical ecology. In addition,
the candidate will have demonstrated substantial knowledge of numerical
analysis techniques for solving differential equations in a suitable
scientific programming language (e.g. Fortran, Matlab etc). Training will
be given in mosquito laboratory and field work. A demonstrated interest
in population ecology, population modelling and/or vector-borne disease
ecology is desirable.
This project will be based at the Centre for Ecology & Hydrology (CEH)
Wallingford in Oxfordshire, UK under the supervision of Dr Steven White
and will be co-supervised by Dr Christina Cobbold (School of Mathematics
and Statistics, University of Glasgow), Dr Miles Nunn (CEH Wallingford)
and Dr Beth Purse (CEH Edinburgh).
Funding Notes:
To apply for this project please send a CV and covering letter with details
of two referees to the contact supervisor. The deadline for applications
is 31st January 2013.
CEH are committed to a high quality graduate training programme to ensure
that the successful candidate has access to opportunities to develop
their career skills and experience. For eligible students a stipend and
fees will be provided at the RCUK rate. Please refer to the CEH website
at www.ceh.ac.uk for details of our scientific research and to the NERC
website at http://www.nerc.ac.uk/funding/available/postgrad/ for details
of funding eligibility.
References:
1. Gurney, W. S. C., et al. "The systematic formulation of tractable
single-species population models incorporating age structure." J. Anim.
Ecol. (1983): 479-495.
2. White, S. M., et al. "Modelling pulsed releases for sterile insect
techniques: fitness costs of sterile and transgenic males and the effects
on mosquito dynamics." J. Appl. Ecol. 47.6 (2010): 1329-1339.
3. Searle, K. R., et al. "Identifying environmental drivers of insect
phenology across space and time: Culicoides in Scotland as a case study."
Bull. Entomol. Res. 1.1 (2012): 1-16.
4. Golding, N., et al. "West Nile virus vector Culex modestus established in
southern England." Parasit Vectors 5 (2012): 32.
5. Purse, B. V., et al. "Impacts of climate, host and landscape factors on
Culicoides species in Scotland." Med. Vet. Entomol. (2012).
Contact Supervisor: Dr Steven White (steven.white@ceh.ac.uk)
----------------------------------------------------
From: Caz Taylor <caz@tulane.edu>
Date: Mon, Nov 19, 2012 at 10:20 AM
Subject: Postdoc: Biological Oceanography, Tulane University
POSTDOCTORAL POSITION IN BIOLOGICAL OCEANOGRAPHY
TULANE UNIVERSITY
A postdoctoral position in computational biological oceanography is available
under the mentorship of Dr. Caz Taylor (Department of Ecology and Evolutionary
Biology and Center for Computational Science, Tulane University, New Orleans).
The successful candidate will further develop existing computational
particle tracking models that use underlying oceanographic data to simulate
pelagic larval movement in the Gulf of Mexico. The models will be applied
to research on the movements and population connectivity of blue crabs in
the Northern Gulf of Mexico and the effects of the Deepwater Horizon oil
spill on this economically and ecologically important species. This research
is part of a larger project that includes investigations into population
genetics, evolutionary dynamics, population dynamics, fisheries management
and ecotoxicology. The postdoctoral researcher will develop his/her own
research questions and will be expected to present results at scientific
conferences and publish in peer-reviewed journals.
The preferred start date is January 1 2013 but some flexibility is
possible. The initial appointment will be for two years with an extension
of one additional year depending on performance. Starting salary is $40,000
per year plus standard benefits.
Requirements include: (1) Strong computational and programming skills,
prefer experience in C++ and Matlab; (2) Demonstrated research excellence;
(3) Strong oral and written communication skills. Preference will be given
to applicants whose research interests and expertise complement the research
project but outstanding applicants looking to broaden their field of interest
will also be seriously considered.
Tulane University is an equal employment opportunity/affirmative action
employer committed to excellence through diversity. All eligible candidates
are invited to apply for position vacancies as appropriate.
To apply, send a cover letter and CV electronically to:
Dr. Caz Taylor caz@tulane.edu
http://caz.tulane.edu/?page_id=87
Applications will be reviewed on a continuing basis until the position
is filled.
----------------------------------------------------
From: Savas Tay <savas.tay@gmail.com>
Date: Fri, Nov 23, 2012 at 10:02 AM
Subject: Postdocs: Microfluidic Single-cell Analysis & Cell Signaling, ETH
Postdoctoral position at ETH Zurich on microfluidic single-cell
analysis and cell (NFkB) signaling
Tay Lab (www.bsse.ethz.ch/microfluidics) at the Department of Biosystems
Science and Engineering is looking for postdocs who fit the following
profiles:
1) A biologist/computational biologist who has experience with cell signaling
or the systems biological approach. This postdoc will have access to the
state-of-the-art high-throughput microfluidic cell culture systems and
gene expression systems (high-throughout qPCR, digital PCR) at Tay Lab to
investigate NF-kappaB dynamics in single cells. These systems was recently
used in this paper: "Single-cell NF-kappaB dynamics reveal digital activation
and analogue information processing", Tay et al. Nature 466, 267-271
2) An engineer or physicist who has experience with microfluidics and its
biological applications. The focus of this position will be developing
microfluidic/optofluidic systems for single-cell analysis for systems
biology and biomedical applications.
Excellence in scientific research evidenced by a strong publication record is
expected. ETH Zurich (in Switzerland) provides an international environment
and excellent benefits. The salary for this position is 82,000 CHF (~85,000
USD) a year. The language of education and research is English.
Highly motivated candidates should send research interests, full CV including
details of experimental and computational skills, publications, and contact
information for 3 references to savas.tay@gmail.com
----------------------------------------------------
From: "Owens, Roland (NIH/OD) [E]" <owensrol@mail.nih.gov>
Date: Tue, 20 Nov 2012 17:09:23 -0500
Resent-From: Raymond Mejía <mejiar@helix.nih.gov>
Subject: NIH Research & Other Selected Positions, November Update
Early Independent Scientist Program
Trans-NIH Recruitment
(deadline: December 14)
The National Institutes of Health, the nation's premier agency for biomedical
and behavioral research, is recruiting early independent scientists to
the NIH Intramural Research Program (IRP). We are looking for new Ph.D.,
M.D., D.D.S., or equivalent doctoral researchers who have the creativity,
intellect, and maturity to flourish in an independent research position.
The IRP is home to more than 1,100 tenured and tenure-track principal
investigators and 7,000 trainees. We provide an environment that
encourages and supports innovative, high-impact research. To enhance the
development and early-stage careers of exceptional investigators, the IRP
is participating in the NIH Director's Early Independence Award Program
http://commonfund.nih.gov/earlyindependence/. The NIH has developed this
program to support recent doctoral graduates in independent positions without
the need to train further in a post-doctoral fellowship. Successful Early
Independence Award candidates will be provided the resources to establish
an independent research program, including salary and benefits, support
for lab personnel, lab space, supplies, and start-up equipment.
Complete applications must be received by December 14, 2012. Candidates should
submit electronically a cover letter, curriculum vitae, and a 3-page statement
of research interests and future plans, and arrange to have 3 letters of
reference sent to: Charles Dearolf, Ph.D.; Assistant Director for Intramural
Research; National Institutes of Health; dearolfc@od.nih.gov. The NIH will
notify selected candidates shortly thereafter, and work with the candidates
to submit an application to the NIH Common Fund program by January 20, 2013.
Candidates must meet eligibility requirements of the Common Fund program, as
described in http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-12-018.html.
At the time of this application, candidates must be within 12 months
(before or after) of completing their Ph.D., M.D., or D.D.S. degree; and
for clinician-scientists, within twelve months of completing their core
clinical residency program.
The NIH recognizes a unique and compelling need to promote diversity in the
biomedical, behavioral, clinical, and social sciences research workforce. The
NIH expects its efforts to diversify the workforce to lead to the recruitment
of the most talented researchers from all groups. We encourage applications
from talented researchers from diverse backgrounds underrepresented in
biomedical research, including underrepresented racial and ethnic groups,
persons with disabilities, and women for participation in all NIH-funded
research opportunities.
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/
Searchable database of all NIH intramural research projects
http://intramural.nih.gov/search/index.tml
Clinical Training at NIH
http://www.cc.nih.gov/training/index.html
http://www.cc.nih.gov/training/gme.html
I also wish to make you aware of two national resources available on the web.
The NIH Clinical Center Grand Rounds and Wednesday Afternoon Lecture Series
(WALS) are videocast live and archived for later access.
NIH Clinical Center Grand Rounds
Schedule:
http://clinicalcenter.nih.gov/about/news/grcurrent.html
Archives:
http://videocast.nih.gov/PastEvents.asp?c=27
NIH Wednesday Afternoon Lecture Series
Schedule:
http://wals.od.nih.gov/
Archives:
http://videocast.nih.gov/PastEvents.asp?c=3
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Subject: SMBnet Reminders
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The contents of this publication may be reproduced in whole or in part with
attribution.
End of SMB Digest
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