Subject: Society for Mathematical Biology Digest
SMB Digest January 21, 2015 Volume 15 Issue 3
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:
Correction: Call for Minisymposium Proposals for SMB'15
Summer Undergraduate Research Programs:U of Michigan Medical School
Course: Intro to Infectious..., London School..., June 22-July 3
ToC: Journal of Mathematical Neuroscience
PhD Positions: Colorado School of Mines
PhD Studentship: Cardiac Modelling, Gent U, Belgium
Postdoc Position: Bioengineering, U of Padua, Italy
Postdoc Position: Machine learning..., iSSB, France
Position: Data scientist-emerging infectious diseases, U of Georgia
Software Developer, Center for Biomedical... Harvard Medical School
SMBnet Reminders
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From: Yi Jiang <
yijianglanl@gmail.com>
Date: Tue, Jan 6, 2015 at 12:18 PM
Subject: Correction: Call for Minisymposium Proposals for SMB'15
You are cordially invited to submit a minisymposium proposal for the 2015
Annual Meetings of SMB, to be held in Atlanta, June 30 - July 3, 2015.
The deadline for minisymposium proposal is January 31, 2015.
Call for Proposals:
http://math.gsu.edu/~smb/call_for_papers.htmlConference page:
http://math.gsu.edu/~smb/---------------------------------------------------------------
From: Santiago Schnell <
schnells@umich.edu>
Date: Wed, Jan 14, 2015 at 11:40 AM
Subject: Summer Undergraduate Research Programs:U of Michigan Medical School
The Department of Molecular & Integrative Physiology at the University of
Michigan is pleased to offer summer fellowship programs to support
undergraduate students that are interested in research in physiology and/or
biomedical sciences. Any student who is currently enrolled at any
degree-granting University or College is invited to apply, with preference
given to those students interested in a career in research.
The department offers three programs:
1) Students from quantitative science majors (e.g. engineering, math,
computer science) will join our Short Term Educational Program (STEP) towards
Digestive and Metabolic Physiology:
https://sites.google.com/a/umich.edu/step/home2) Biological science students will join our traditional Summer
Undergraduate Research Fellowship (SURF):
https://sites.google.com/a/umich.edu/surf/home3) Underrepresented groups and those from economically disadvantaged
backgrounds will join out Summer Undergraduate Research In Physiology
(SURP) program:
https://sites.google.com/a/umich.edu/surp/homeEach student will be matched, based on his or her interests, to a laboratory
that is led by a faculty member of the Department of Molecular & Integrative
Physiology or of the University of Michigan Medical School. The selected
laboratories are involved in nationally recognized research, in topics such
as hormones and signal transduction, obesity and diabetes, reproduction and
circadian rhythms including sleep, gastrointestinal physiology including
digestive diseases, and many aspects of cardiovascular disease.
There will be a lecture series, a research forum at the end of the summer
in which fellows will present their work, and opportunities to attend
research seminars throughout the summer.
Further details and application materials are available from the fellowship
website:
http://medicine.umich.edu/dept/molecular-integrative-physiology/education/undergraduate-opportunities The deadline for applications is February 15, 2015.
Please help us advertise this opportunity and encourage undergraduate
students at your institution to apply.
--------------------------------------------------------------
From: Emilia Vynnycky <
Emilia.Vynnycky@phe.gov.uk>
Date: Fri, Jan 16, 2015 at 1:25 PM
Subject: Course: Intro to Infectious..., London School..., June 22-July 3
2 week intensive course on:
"INTRODUCTION TO INFECTIOUS DISEASE MODELLING AND ITS APPLICATIONS"
organized jointly between the London School of Hygiene & Tropical Medicine
and Public Health England
Venue: London School of Hygiene & Tropical Medicine
Course dates: 22nd June ? 3rd July 2015
Cost: £2,205
Summary:
Mathematical modelling is increasingly applied to predict the future
incidence and control of infectious diseases. Applications include
predicting the impact of control strategies, such as vaccination or
treatment, against pandemic influenza, Ebola, measles, HIV, vector-borne
diseases and veterinary problems. Modelling was used extensively in the
UK during the swine flu pandemic to monitor the extent of ongoing
transmission and the potential impact of interventions such as school
closures and vaccination.
This two week intensive course introduces professionals working on
infectious diseases in human or animal populations to this exciting and
expanding area. The emphasis of the course is on developing a conceptual
understanding of the basic methods and on their practical application,
rather than the manipulation of mathematical equations. The course provides
numerous practical examples, including real-time modelling of outbreaks,
pandemic influenza, sexually transmitted infections, HIV, Ebola,
vector-borne and animal diseases, as well as tuberculosis, measles and
rubella, and health economics.
By the end of the course, participants will have deepened their current
understanding of infectious disease epidemiology and have gained an
understanding and practical experience of the basics of infectious disease
modelling, which will be important in their future work.
Who should attend:
The course is designed for individuals interested in expanding their
knowledge of the techniques for analysing and interpreting epidemiological
data on infectious diseases and for predicting the impact of control
programmes, including medical and health professionals, policy makers,
veterinary scientists, health economists, medical statisticians and
infectious disease researchers.
Specialist mathematical training is not a prerequisite. However,
individuals with degrees in mathematical disciplines working on some
aspect of infectious disease dynamics and/or control, who wish to learn
about the potential of infectious disease modelling will also benefit.
Further details about the course content and an application form are
available at:
http://www.lshtm.ac.uk/study/cpd/siidma.html or contact one
of the course organizers:Emilia Vynnycky or Richard White (e-mail:
emilia.vynnycky@lshtm.ac.uk or
emilia.vynnycky@phe.gov.uk or
richard.white@lshtm.ac.uk) or the LSHTM Registry
(email:
shortcourses@lshtm.ac.uk)
Other shortcourses at LSHTM:
The website
http://www.lshtm.ac.uk/study/cpd/shortcourses.html provides
details about other shortcourses at LSHTM.
For details about the advanced course on modelling fitting, see
http://www.lshtm.ac.uk/study/cpd/infectious_disease_modelling.html ------------------------------------------------------------------
From: Stephen Coombes <
stephen.coombes@nottingham.ac.uk>
Date: Sat, Jan 17, 2015 at 8:31 AM
Subject: ToC: Journal of Mathematical Neuroscience
The Journal of Mathematical Neuroscience publishes research articles on the
mathematical modeling and analysis of all areas of neuroscience. The
current list of journal articles is available at
http://www.mathematical-neuroscience.com/Uncertainty Propagation in Nerve Impulses Through the Action Potential
Mechanism, Torres Valderrama A, Witteveen J, Navarro M and Blom J
http://www.mathematical-neuroscience.com/content/5/1/3Coarse-Grained Clustering Dynamics of Heterogeneously Coupled Neurons
Moon SJ, Cook KA, Rajendran K, Kevrekidis IG, Cisternas J and Laing CR
http://www.mathematical-neuroscience.com/content/5/1/2Shifting Spike Times or Adding and Deleting Spikes?How Different Types of
Noise Shape Signal Transmission in Neural Populations
Voronenko SO, Stannat W and Lindner B
http://www.mathematical-neuroscience.com/content/5/1/1Numerical Bifurcation Theory for High-Dimensional Neural Models
Laing CR
http://www.mathematical-neuroscience.com/content/4/1/13Adaptation and Fatigue Model for Neuron Networks and Large Time Asymptotics
in a Nonlinear Fragmentation Equation
Pakdaman K, Perthame B and Salort D
http://www.mathematical-neuroscience.com/content/4/1/14and see also the recent Special Issue on Uncertainty and the Brain
http://www.mathematical-neuroscience.com/series/UBAll articles are Open Access.
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From: Cecilia Diniz Behn <
cdinizbe@mines.edu>
Date: Fri, Jan 16, 2015 at 4:21 PM
Subject: PhD Positions: Colorado School of Mines
The Applied Mathematics and Statistics (AMS) Department at Colorado School
of Mines invites applications from exceptional students with interests in
mathematics, statistics, and biology to join our newly formed Mathematical
and Statistical Biology research group. Research interests of affiliated
faculty include computational neuroscience, physiologically-based modeling
of sleep and circadian rhythms, glucose/insulin dynamics, in-host viral
dynamics and viral structure, survival analysis, epidemiological sampling
design, infectious disease data and disease mapping, and the application
of high performance computational tools to simulate biological processes.
The graduate program at Mines prides itself on being highly interdisciplinary
with ties to research hospitals, national laboratories, and other
universities throughout the region. Graduate students will have the
opportunity to develop and apply new mathematical and statistical methods
to real-world problems while working closely with AMS faculty and their
experimentalist and clinician collaborators. Additional application
information is available on our website:
http://ams.mines.edu/ams.php/graduate/Admissions------------------------------------------------------------
From: Sasha Panfilov <
alexander.panfilov@ugent.be>
Date: Tue, Jan 20, 2015 at 6:01 AM
Subject: PhD Studentship: Cardiac Modelling, Gent U, Belgium
PhD Studentship in Cardiac Modelling
A four year PhD studentship is available at Department of Physics and
Astronomy, Gent University, Belgium.The aim of this PhD project is study
of effects of opening of hemichannels on onset of cardiac arrhythmias.
Hemichannels are large conducting non-selective channels which opening has
a significant effect on ionic fluxes through cardiac membrane. The work
will be performed in a close collaboration with a group which performs
experimental measurements of properties of hemichannels in various
conditions. On basis of these data a model of a hemichannel should be
developed and integrated into an existing multiscale anatomical model of
the human heart. This anatomical model will be used to study how opening
of hemichannels affects the onset of cardiac arrhythmias and their dynamics.
We seek a motivated candidate with broad interest in biophysics,
integrative computational and mathematical biology, biomedical engineering.
Prior experience in cardiac modelling is an advantage, but not necessary.
Although most of the programs are already available at our group, a
working knowledge of C/C++ is desirable.
Salary: approx. 1850 euro/month (net).
Length: 4 years.
Starting date: between March and August 1st 2015.
For further information about this position, please contact
Prof. A.V.Panfilov (Alexander.Panfilov@UGent.be). Application letters
including a CV, a short statement of research interests, and contact details
of three referees should be sent by email to the above-mentioned address.
----------------------------------------------------------
From: Morten Gram Pedersen <
pedersen@dei.unipd.it>
Date: Sat, Jan 17, 2015 at 5:29 AM
Subject: Postdoc Position: Bioengineering, U of Padua, Italy
A postdoc position in the Bioengineering group at the University of Padua
is available.
The postdoctoral fellow will work on modeling of glucose-sensing endocrine
cells (e.g. insulin-secreting pancreatic beta-cells, glucagon-secreting
pancreatic alpha-cells, GLP-1 secreting intestinal L-cells). Depending on
the experience and interest of the fellow, the research project can focus
on electrical activity, calcium dynamics and exocytosis, G-protein activated
signalling cascades, multi-scale modeling, etc., by using computational and
theoretical analysis of existing and new models.
For further information and to express interest please contact Dr. Morten
Gram Pedersen (
pedersen@dei.unipd.it ?
http://www.dei.unipd.it/~pedersen/)
------------------------------------------------------------
From: Mohamed Elati <
mohamed.elati@issb.genopole.fr>
Date: Tue, Jan 20, 2015 at 3:07 PM
Subject: Postdoc Position: Machine learning..., iSSB, France
The institute of Systems and Synthetic Biology (iSSB) has an immediate
opening for a postdoctoral position in the field of machine learning for
systems biology.
We invite applications from researchers who hold (or are very close to
completion) a PhD in machine learning, active learning, computational
system biology or a related field.
The successful candidate will join an interdisciplinary team of computational
and molecular biologists (
http://www.issb.genopole.fr/Research/teams/mega),
working on an exciting ICST European project: AdaLab (Adaptive Automated
Scientific Laboratory:
http://www.chistera.eu/projects/adalab ) funded by
CHIST-ERA. She/He will be responsible for developing machine-learning
algorithms for network inference and experimental design, and for building
a knowledge base about the yeast diauxic shift to be used in the Robot
Scientist platform (Prof. Ross King).
The successful candidate will be offered an initial contract for 24 months
with possible extension for an additional 12 months depending on
performance.
The iSSB is part of Genopole, the premier French BioPark of leading
research academic and private laboratories in biotechnology, genomics,
post-genomics and related sciences. It is located in Evry (Paris region).
Applicants should send a full CV, the contact details of three referees,
and a cover letter to Dr. Mohamed Elati
(
http://www.issb.genopole.fr/~elati/) at
mohamed.elati@issb.genopole.fr----------------------------------------------------------------------
From: John M. Drake <
jdrake@uga.edu>
Date: Thu, Jan 15, 2015 at 1:51 PM
Subject: Position: Data scientist-emerging infectious diseases, U of Georgia
We are seeking a data scientist (scientific programmer, analyst, and graphic
designer/data visualization specialist) to join Project AERO:
http://daphnia.ecology.uga.edu/midas/ at the University of Georgia in Athens.
Project AERO is an NIH-funded study to develop model-free statistical
learning algorithms for detecting the approach to criticality in emerging
and re-emerging childhood infections. Research includes both theoretical
and empirical components. For more details and to apply, visit the UGA Job
Site:
https://www.ugajobsearch.com/applicants/jsp/shared/Welcome_css.jspand search for posting number 20142111. This position will be open until
filled.
-------------------------------------------------------------------
From: Vale, Jennifer A. <
Jennifer_Vale@hms.harvard.edu>
Date: Fri, Jan 16, 2015 at 8:10 AM
Subject: Software Developer, Center for Biomedical... Harvard Medical School
Business Title Software Developer for the Refinery Team
School/Unit Harvard Medical School
Location USA - MA - Boston
Time Status Full-time
Department Center for Biomedical Informatics at Countway
Salary Grade 057
Union 00 - Non Union, Exempt or Temporary
Duties & Responsibilities:
The Park Lab in the Center for Biomedical Informatics at Harvard Medical
School is leading the development of the Refinery Platform
(
http://www.refinery-platform.org), an innovative open-source, web-based
software environment for the management, analysis, and visualization of
epigenomic and genomic data.
As part of an initiative with the Harvard Stem Cell Institute, the Park Lab
is looking for an experienced and enthusiastic software developer to
participate in extending Refinery Platform for the Harvard Stem Cell Commons
(
http://stemcellcommons.org). A major goal of the system is to provide a
shared environment to enable users to compare stem cell data across
different laboratories, experimental platforms, organisms, and cell types.
This position is funded for one year from date of hire, with the
expectation of renewal.
The software developer should be comfortable with and be experienced in
working on both server-side components (including compute clusters and/or
clouds) and client-side (web UI) components, as well as modern software
engineering practices such as automated testing and continuous integration/
deployment.
Furthermore, the developer must be proficient in Django or other Python web
frameworks and have working knowledge of either SQL or NoSQL databases.
Expertise in HTML5, JavaScript, and modern UI frameworks such as AngularJS
or Bootstrap is expected and experience in REST API design and
implementation is desired.
Basic Qualifications:
BSc in Bioinformatics, Computer Science, or a related field and 3-5 years
related experience. At least two years of experience in web application
development with tools such as Python web frameworks (e.g., Django) and
JavaScript frameworks (e.g., AngularJS).
Additional Qualifications:
MSc in Bioinformatics, Computer Science or a related field and 5 years
work experience, Bioinformatics, Galaxy; AWS/Cloud, Docker, Vagrant,
Apache; SQL (e.g., PostgreSQL), South, Solr/Elasticsearch; Celery;
REST; D3.js, CSS, LESS/SASS, Bootstrap; Git, Automated testing,
continuous integration/deployment. Self-motivated, self-starter, able
to manage own time and learn.
Additional Information:
Applicants should include a link to some of their code in GitHub or another
repository hosting service, as well as a cover letter describing why this
position interests them and how it fits their experience and interests.
Appointment End Date: 31-Aug-2015
Interested applicants please apply directly online at,
www.employment.?harvard.?edu. Please search requisition number (Auto Req. ID)
34675BR
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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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