SMB Digest January 14, 2014 Volume 14 Issue 3
ISSN 1086-6566
Editor: Wandi Ding wding1(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,
Access the Bulletin of Mathematical Biology, the official journal
Inquiries about membership or BMB fulfillment should be sent to
membership(at)smb(dot)org .
Issue's Topics:
Workshop on CBIBM: Deadline January 15th
AAI Short Course-Advanced Data Analytics-Jan 29
Conference&Bard Ermentrout's 60th Birthday:March 10-12
VISIONAIR Open Forum in Poznan February 5-6
Computational Neuroscience online course
SSTiC 2014: January 18, 2nd registration deadline
STEP program towards Molecular & Integrative Physiology
BioInformatics Analyst-Trainer position at Oregon State University
Postdoc in Computational Biology at APCTP
Postdoc in Mathematical Demography and Ecology, U Amsterdam
Postdoc in disease modeling at the University of Minnesota
Postdoc position-Oregon State University
Selected NIH Intramural Research Positions-January Update
Program Directors Position: NSF-DMS
3 Principal Investigators in Computational Biology
SMBnet Reminders
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Date: Thu, Jan 9, 2014 at 12:50 PM
Subject: Workshop on CBIBM: Deadline January 15th
*Call for Presentations and Papers on Cell Based and Individual Based Modelling
*Part of the 2014 ICCS: 10th to the 12th of June in Cairns Australia
*Deadline for abstract or paper submission: 15th of January 2014
The workshop on Cell Based and Individual Based Modelling (CBIBM),
is now accepting abstracts for oral presentations and also 10 page paper
submissions. The workshop will be taking place as part of the 2014
International Conference on Computational Science in Cairns, Australia
from the 10th to the 12th of June and covers all aspects of cell based
and individual based modelling and simulation, from methodological
or tool developments through to applications of cell based models.
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Date: Sun, Jan 12, 2014 at 6:39 PM
Subject: AAI Short Course-Advanced Data Analytics-Jan 29
AAI Short Course-Advanced Data Analytics-an Introduction
Wednesday 29 January 2014
The AAI short course "Advanced Data Analytics-an Introduction"
may well be of interest to you and your organisation and key personnel.
This Data Analytics introductory short course will provide an early
and rewarding understanding of the level of analytics which your
organisation and your people should be seeking.
Course outcomes Upon completion of this course students will:
-Understand why advanced data analytics is essential to your business
success
-Understand the key terms and concepts used in advanced data analytics
-Understand relations of big data, clouding computing and analytics
-Be familiar with basic skills of statistics in data analytics,
including descriptive analysis, regression, multivariate data analysis
-Learning basic data mining and data warehousing, visualization and
reporting, such as supervised vs unsupervised methods, clustering,
association rule and frequent mining and so on
-Knowing key techniques in machine learning, such as Parametric
and non-parametric models, learning and inference, Maximum-likelihood
estimation, and Bayesian approaches and so on
-Be given the introduction of social media analytics, multimedia
analytics, and the real projects or case studies conducted in AAI
Future short courses on Data Analytics and Big Data may be viewed at
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Date: Tue, 7 Jan 2014 8:22 PM
Subject: Conference & Bard Ermentrout's 60th Birthday:March 10-12
Nonlinear dynamics and stochastic methods: from neuroscience to other
biological applications March 10-12, 2014 Pittsburgh, PA
This conference on nonlinear dynamics and stochastic methods will
bring together a mix of senior and junior scientists to report on
theoretical methods that proved successful in mathematical neuroscience,
and to encourage their dissemination and application to modeling in
computational medicine and other biological fields. This conference
will coincide with a celebration of G. Bard Ermentrout's sixtieth
birthday. The invited speakers will present on mathematical topics
such as dynamical systems, multi-scale modeling, phase resetting
curves, pattern formation and statistical methods. The mathematical
tools will be demonstrated in the context of the following main
topics: i) Rhythms in biological systems; ii) The geometry of systems
with multiple time scales; iii) Pattern formation in biological
systems; iv) Stochastic models: statistical methods and mean
field approximations.
The conference runs from March 10-12, 2014 at the University of
Pittsburgh, Pittsburgh, PA. Travel support may become available
for young investigators. Currently, this conference is partial
funded by the Mathematical Biosciences Institute and the University
of Pittsburgh.
REGISTRATION APPLICATION, ABSTRACT SUBMISSION, AND SCHEDULE:
Important Dates: Travel award application and abstract submission
deadline Passed.
Registration application deadline January 14th 11:59 pm (EST):
Researchers interested in attending the conference should submit
a registration application. The attendees will be selected among
these based on research interest overlapping with the conference
theme, and to ensure diversity and breadth of participation by
individuals and institutions.
Decisions regarding Registration and Abstracts: January 17th
SPONSORS:
Department of Mathematics, University of Pittsburgh
Mathematical Biosciences Institute
National Science Foundation (pending)
Confirmed Speakers:
Paul Bressloff (University of Utah)
Carson Chow (National Institutes of Health)
Sharon Crook (Arizona State University)
Jack Cowan (University of Chicago)
Jonathan Drover (Cornell Medical College, NYC)
Leah Edelstein-Keshet (University of British Columbia,
Vancouver - Canada)
Roberto Fernandez Galan (Case Western Reserve University)
Pranay Goel (Indian Institute of Science, Education and Research,
Pune - India)
Boris Gutkin (Ecole Normale Superieure/ ENS, Paris - France)
Zachary Kilpatrick (University of Houston)
Nancy Kopell (Boston University)
Cheng Ly (Virginia Commonwealth University)
Remus Osan (Georgia State University)
George Oster (University of California, Berkeley)
John Rinzel (New York University)
Jonathan Rubin (University of Pittsburgh)
Daniel Simons (University of Pittsburgh)
David Terman (Ohio State University)
If you have questions now please contact one of the organizers,
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Date: Thu, Jan 9, 2014 at 4:03 AM
Subject: VISIONAIR Open Forum in Poznan February 5-6
Invite you to the VISIONAIR Open Forum in Poznan 5-6 February 2014 :
To remind you that you are welcome to apply for a project using high
level visualisation and interaction facilities (see details below)
Are you interested in:
Using visualization and interaction facilities, to which you do not
have access? Better understanding your data/information by visualizing
them in 3D, in full or partial immersive modes in more than High
Definition (up to 4K 3D and 8K)? Exploring new ways to define new
processes or practices in order to navigate and interact intuitively
through your information with new interaction mode (tracking,
haptic perception, etc.)? Participating in a European infrastructure
that offers a range of unique, world-class visualization capabilities?
If the answer is ?yes? to any of these questions the VISIONAIR
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Date: Fri, Jan 10, 2014 at 6:44 PM
Subject: Computational Neuroscience "massively open" online course
After a successful first offering last Spring (about 50K registered
students), we are pleased to announce the second offering of our
Computational Neuroscience MOOC ("massively open" online course)
Registration is free, requires only an email address, and is open to all.
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Date: Sun, Jan 12, 2014 at 4:54 AM
Subject: SSTiC 2014: January 18, 2nd registration deadline
2014 TARRAGONA INTERNATIONAL SUMMER SCHOOL ON TRENDS IN COMPUTING
SSTiC 2014, Tarragona, Spain, July 7-11, 2014. Organized by
January 18, 2nd registration deadline.
REGISTRATION: It has to be done at
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Date: Fri, Jan 10, 2014 at 5:22 PM
Subject: STEP program towards Molecular & Integrative Physiology
The Department of Molecular & Integrative Physiology at the
University of Michigan is pleased to offer Summer Fellows under
the Short Term Education Program towards Digestive and Metabolic
Physiology to support undergraduate students from mathematics,
engineering, computational sciences, or other quantitative
backgrounds to apply their expertise to research relevant to
digestive and metabolic physiology and associated diseases.
Student currently enrolled at any degree granting university or
college are eligible to apply, with preference give to those
students interested in a career in research. Each student will
be matched, based on their interests, to a laboratory led by a
faculty member of the Department of Molecular & Integrative
Physiology. This collection of laboratories is involved in
nationally recognized research, in topics such as obesity and
diabetes, endocrine and metabolic diseases, kidney and urologic
diseases, nutrition and weight control.
The stipend for 2014 will be $4200 for twelve weeks of full-time
work from May 27 to August 15. The start and end date of the
fellowship may be change to accommodate overlap with academic year
at home institution, if necessary. The laboratory hands-on research
is completed with a weekly seminar series with presentations on
responsible conduct of research, career advice and couching, and
how loss of physiological regulation leads to digestive and metabolic
diseases. There will be a research forum at the end of the summer in
which fellows will present their work, as well as opportunities to
attend research seminars throughout the summer.
Further details and application materials are available from the
fellowship website:
The deadline for applications is February 15, 2014.
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Date: Fri, Jan 10, 2014 at 6:22 PM
Subject: BioInformatics Analyst-Trainer position at Oregon State University
BIOINFORMATICS ANALYST-TRAINER Position
Bioinformatics Analyst-Trainer (Faculty Research Assistant),
Oregon State University's (OSU) Center for Genome Research and
Biocomputing (CGRB). Full time + benefits. Responsibilities and
duties include participating in bioinformatics research, designing
and presenting bioinformatics training courses and supporting
peer-to-peer training networks in bioinformatics.
Closing Date: 02/14/14 at 11:59 pm. OSU is an AA/EOE.
More information and application procedures can be found at
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Date: Tue, 7 Jan 2014 10:31 PM
Subject: Postdoc in Computational Biology at APCTP
Postdoc in Computational Biology
The Design Principles of Cellular Networks group at APCTP seeks for
one postdoc who has strong interest in computational biology.
The postdoctoral position is initially for two years with possible
extensions. Applicants should send (1) a curriculum vitae,
(2) description of research interests, and (3) list of two
Screening of applications begins immediately and will continue
until the position is filled. If you have any questions about
the group or the position, please feel free to contact us.
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Date: Wed, Jan 8, 2014 at 4:42 AM
Subject: Postdoc in Mathematical Demography and Ecology, U Amsterdam
A Post-Doctoral position is available with Prof. Hal Caswell, in
the Theoretical Ecology Research Group within the Institute for
Biodiversity and Ecosystem Dynamics at the University of Amsterdam.
This position is part of a research program Individual Stochasticity
and Population Heterogeneity in Plant and Animal Populations, which
is funded by an ERC Advanced Grant. The overall goal of this research
program is to develop a comprehensive theory for incorporating
individual stochasticity and heterogeneity into demographic models,
and for analyzing the consequences of these sources of demographic
variation for population growth, structure, and persistence.
Applications of the theory will include populations of conservation
and management concern, evolutionary questions related to senescence
and resource allocation, and the measures of health status and
health expectancy in human populations.
This postdoctoral project will focus on mathematical and theoretical
developments of Markov chain models for variation in lifetime
reproduction and other measures of lifetime success, variation in
longevity, and the incorporation of heterogeneity into branching
process and diffusion models. Analyses will be developed at the
level of cohorts (survival, longevity, lifetime reproduction,
lifetime health status) and the level of populations (population
growth, structure, persistence, and extinction) using matrix
population models. Sensitivity analysis using methods from matrix
calculus will be an integral part of the research. The development
of new theory for multistate models, for stochastic environments,
and for coupled populations will be an important component. The
Theoretical Ecology group currently comprises 2 professors, 3
assistant professors, 1 post-doc, and 4 PhD students, and
currently hosts two ERC Advanced Grants. It has active research
programs in structured population modelling, resource-consumer
interactions, epidemiology, demography, and evolutionary and
eco-evolutionary theory.
Requirements
·PhD in mathematical/theoretical ecology, mathematical biology,
or demography, or in applied mathematics or statistics with
experience in population biology, or similar background.
·Experience with development and analysis of population models;
·Programming skills; the project will use Matlab and possibly
other languages;
·Fluent in English
·Good scientific writing skills
·Ability to work in a multidisciplinary research team.
For additional information, please contact Hal Caswell at
To apply, please visit the University of Amsterdam website at:
Applications should include a detailed CV with a list of publications,
a description of research experience and interests, and the names and
contact addresses of two academic references from whom information
about the candidate can be obtained. Combine all these items into
a single PDF file.
Applications should be sent by e-mail only before January 28, 2014
Please quote the vacancy number in the subject field. Interviews,
possibly via Skype, will be held in after 28 January, 2014.
The positions will start in early 2014. The full-time appointment
will be on a temporary basis for initially one year, with an
extension to a maximum period of 3 years after a positive evaluation.
The full-time gross monthly salary will range from ? 2427 to ? 3831.
The Collective Labour Agreement Dutch Universities is applicable.
The annual salary will be increased by 8 % holiday allowance and
8.3 % end-of-year bonus.
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Date: Fri, Jan 10, 2014 at 8:43 AM
Subject: Postdoc in disease modeling at the University of Minnesota
POSTDOCTORAL POSITION IN DISEASE MODELING
POSITION: The Veterinary Population Medicine Department of the
College of Veterinary Medicine has an opening for a 100% Post-doctoral
Associate position funded by USDA. The position will focus on network
modeling and analytic epidemiology.
QUALIFICATIONS: The candidate must have a Ph.D. or equivalent degree
by start date. Candidates with a background in disease ecology,
statistics, infectious disease modeling, engineering, applied
mathematics or a related field will be given preference. Strong
organizational, programming, and quantitative analysis skills are
necessary. Desired qualifications include excellent oral/written
communication; leadership and interpersonal skills; previous
experience with network models; and demonstrated ability to
work in teams. Veterinary experience is desired but not required.
DUTIES: Research activities will focus on identification of
cost-effective risk-based surveillance strategies for bovine
tuberculosis, including development of a simulation model of the
spread of disease within and between cattle herds, identification
of risk factors for a targeted surveillance strategy, and assessment
of the cost-effectiveness of targeted surveillance strategies for early
detection of infections based on identified risk factors. Duties will
include statistical data analysis using network models, development of
infectious disease models, working in diverse collaborative groups, and
publishing findings.
APPLICATION:
To apply go to the University of Minnesota employment website:
Completed applications will be reviewed immediately and continue until
the position is filled. Applicants must apply online and submit a CV,
letter of intent, and three letters of reference to: Anna Jones,
Veterinary Population Medicine Department, 225 VMC, 1365 Gortner
Avenue. Questions regarding the position may be directed to Dr. Scott
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Date: Fri, Jan 10, 2014 at 5:10 PM
Subject: Postdoc position-Oregon State University
Aquatic disease modeling - Post-doctoral scholar position
Location Oregon State University, Corvallis, Oregon
Available February 2014, Closing Until filled
Position: The candidate will work with a team of researchers on myxozoan
pathogens Qualifications Applicant should have analytical skills that
include multivariate analysis, spatial and (Ceratomyxa shasta,
Parvicapsula minibicornis) of salmon in the Pacific NW. A long-term
disease monitoring program on the Klamath River measures inter-annual
variation in disease effects and severity. This position will
collaborate on models being developed for predicting invertebrate
host distribution and salmon disease mortality under projected future
river conditions. The researcher will be responsible for integrating
data from a variety of long-term datasets, for identifying information
gaps and designing targeted studies to address these. Time series
analysis, knowledge of river hydrology and geomorphology, climate
change, fisheries biology and disease ecology. The position will
primarily involve data analysis and scientific publication writing,
but some field work and laboratory experimentation will be required.
Field duties may include exposures of salmonid fish and sampling
habitats for annelid hosts. The candidate will be expected to be
available for travel to remote field sites, to work well in a team
and to assume an active role in the maintenance and leadership of
the lab. Diving experience useful. Applicants should have a proven
publication record and the ability to write efficiently. Applicants
must have completed all requirements for their doctoral program
in a biological science, with expertise in the fields of aquatic
ecology, disease ecology, statistics or fisheries biology.
Appointment 1.0 FTE; 1 year with the possibility for renewal based
on a satisfactory. To Apply Send the following materials:
performance review and the annual nature of federal funding.
Stipend and benefits are commensurate Postdoctoral Standards at OSU;
-letter of interest, describing how your experience, qualifications,
interests have prepared you for this position,
-a resume including the names, addresses, and telephone numbers of
three professional references, to:
Dr. Jerri Bartholomew
Director, John L. Fryer Salmon Disease Laboratory
Department of Microbiology
220 Nash Hall, Corvallis, OR 97331
Phone: 541-737-1856
dr-jerri-bartholomew
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Date: Tue, 7 Jan 2014 6:17 PM
Subject: Selected NIH Intramural Research Positions-January Update
Tenure-Track Position
Early Independent Scientist Program, NIH-wide
(deadline: January 31)
The National Institutes of Health, the nation's premier agency for
biomedical and behavioral research, is recruiting for Early Independent
Scientists in 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 1,000
tenured and tenure-track investigators and 5,000 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 Common Fund's "NIH Director's Early Independence Award" program,
program to support recent doctoral graduates in independent positions
without the need to perform a postdoctoral career fellowship.
Thus, the graduate can immediately start an independent career after
graduation. 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. At the time of application,
candidates must be within 12 months of completing their Ph.D., M.D.,
or D.D.S. degree; or for clinician-scientists, within twelve months
of completing their core clinical residency program. Complete
applications must be received by December 13, 2013. Candidates should
submit electronically a cover letter, curriculum vitae, and a 2- to 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;
thereafter, and work with the candidates to submit an application to the
NIH Common Fund program by January 31, 2014.
Candidates must meet eligibility requirements of the Common Fund 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.
Tenure-Track Position
Computational biophysics or computational neuroscience, NIDA
(deadline: February 1)
The Intramural Research Program (IRP), National Institute of Drug Abuse
(NIDA), a research component of the National Institutes of Health (NIH),
Department of Health and Human Services (DHHS), is seeking an outstanding
tenure-track scientist to develop a computational biophysics or
computational neuroscience research program to complement and expand
existing research programs at the NIDA IRP.
The successful candidate must possess a Ph.D. in pharmacology,
neuroscience, or biophysics with additional training and emphasis on
developing computational models. Expertise in state of the art
computational hardware and software and a strong publication record
highlighting his/her contributions to elucidating the molecular
mechanisms underlying drug addiction and identifying therapeutic
targets is highly desirable. In view of the required integrative
approach, the successful candidate will be expected to collaborate
with other research groups within NIDA - a proven ability to establish
and sustain collaborative work is required. Candidates
must submit a CV, a statement of proposed research objectives and goals
(3 pages or less), 3 letters of recommendation to: Joshua Kysiak,
Intramural Program Specialist, NIDA IRP, 251 Bayview Boulevard,
Suite 200, Room 04A524, Baltimore, Maryland 21224. Telephone 443-740-2465,
will begin on or about February 1, 2014, but applications will
be accepted until the position is filled. The DHHS and NIH are
equal opportunity employers.
Tenure-Track, Tenure-Eligible Positions
Biostatistics, bioinformatics, and computational biology, NIEHS
(deadline: February 10)
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 multiple full-time
appointments at either the tenure-track or tenure-eligible level
(Assistant, Associate, and Full Professor equivalents) in the areas of
biostatistics, bioinformatics, and computational biology. The NIEHS
is located in the Research Triangle Park (RTP), a world renowned
research center which is near to major universities and institutes
including the University of North Carolina, NC State University, Duke
University, and SAMSI. The positions are within the Biostatistics
which enjoys ties to nearby departments of statistics and biostatistics.
The successful candidate will develop and direct a high-quality,
independent research program on analytic methods applicable to
understanding the effects of the environment on human health.
Investigators in the NIH intramural program have no formal teaching
duties and are funded internally, with the potential for generous
long-term, continuous support. They are expected to engage directly
in research and methods development with postdoctoral fellows,
students, and support staff and to collaborate with colleagues in
solving important scientific problems related to the Institute's
mission. Applicants should have a Ph.D. or equivalent doctoral degree
and a proven record in the development of analytic methods with
biomedical application. Experience working with epidemiologic or
high dimensional genetic, epigenetic, and genomic datasets is highly
desirable, but not required. Applicants at the tenure-eligible level
should have a proven record of innovation in the field and possess
skills and experience well-suited to a leadership position in the
Branch. Excellent start-up funds, salary and benefits packages will
be provided to the selected applicants. Applications from women and
underrepresented minorities are strongly encouraged. Appointees may be
U.S. citizens, resident aliens, or non-resident aliens with, or
eligible to obtain, a valid employment-authorization visa.
Interested persons should send their curriculum vitae, a two page
statement of research interests and goals, and arrange for 3 letters
of recommendation to be sent to Ms. Emily Starnes at
applications will not be accepted. We will begin evaluating
applications on or about Feb 10, 2014. Applications will continue
to be accepted until vacancies are filled.
The NIH Intramural Research Program
Link to Fellowships and Positions of Interest to fellows
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Date: Tue, Jan 7, 2014 at 3:27 PM
Subject: Program Directors Position: NSF-DMS
Program Director in DMS in the area of Mathematical Biology.
The Dear Colleague Letter related to this can be found at
Anyone interested may also contact Mary Ann Horn directly at
mhorn@nsf.gov.
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Date: Tue, Jan 7, 2014 at 10:03 AM
Subject: 3 Principal Investigators in Computational Biology
The Institut de recherches cliniques de Montréal (IRCM) is in the
process of developing a center in computational biology. In order
to pursue this development, the IRCM seeks outstanding candidates
to fill three (3) positions of Research Unit Director (Principal
Investigator) in the field of Computational Biology at the junior
and/or senior level. The IRCM is an independent biomedical research
institute affiliated with the Université de Montréal and associated
to McGill University with a mission to bridge basic biomedical and
clinical research and to provide excellent training for young
scientists. The IRCM brings together 35 basic and clinical research
units that are supported by state-of-the-art Core facilities
including proteomics, genomics, cellular imaging and transgenic services.
Position of Senior Principal Investigator: Candidates must have an
established research program and a track record of outstanding
accomplishments.
Position of Junior Principal Investigator: Candidates must have
a Ph.D. and/or M.D. degree, significant postdoctoral experience
and must develop a vigorous independent and competitive research
program.
Three (3) Research Unit Director positions are available and the
IRCM is committed to build critical mass in Computational Biology.
Candidates with expertise in Epigenomics, Transcriptomics, Systems
and Network Biology, Metabolomics, Mathematical Modeling of
Biological Systems and related areas are encouraged to apply.
Research at the IRCM is multi-disciplinary and includes Systems
Biology, Cancer, Genetic Diseases, Cardiovascular and Metabolic
Diseases, Immunity and Viral Infections, Neurobiology and
Developmental Biology. Having research interests complementary
to those themes will be considered as a significant asset.
The position of Research Unit Director at the IRCM is equivalent
to a university faculty position. The candidate will direct
his/her own research unit at the IRCM along with a faculty
appointment at the Université de Montréal and potential for
professor positions at McGill University.
Interested applicants should submit a full CV, a publication list,
a summary of their most significant research contributions, a
short description of present and future research program and
Review of applications will continue until appropriate candidates
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Subject: SMBnet Reminders
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