Subject: Society for Mathematical Biology Digest
SMB Digest October 7, 2014 Volume 14 Issue 41
ISSN 1086-6566
Editor: Ray Mejía ray(at)smb(dot)org
Note:
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Issue's Topics:
IMO Workshop 4, Viruses in Cancer, Nov 17-21, Tampa
New Springer Books
Keystone Symposia 2015 Sirtuin Biology Conference
ToC: MBE Volume 11 Number 6, December 2014
PhD Position, Tumour Spheroid Modelling, Auckland Bioeng Institute
Postdoctoral Opportunity, Harvard Medical School
Tenure-Track Position, Mathematics, Temple University
Assistant Professor, Department of Biology, University of West Georgia
Announcing NSF-NCS: Integrative Strategies; Industry/University Coop...
Upcoming Deadlines: Biomedical Computing, Informatics, Big Data ...
New NIH Funding Opportunities to Investigate the 4D Nucleome
SMBnet Reminders
----------------------------------------------------
From: Anderson, Alexander (Sandy) <
Alexander.Anderson@moffitt.org>
Date: Tue, Sep 30, 2014 at 5:31 PM
Subject: IMO Workshop 4, Viruses in Cancer, Nov 17-21, Tampa
Dear Colleague,
We are currently organizing the 4th Integrated Mathematical Oncology
(IMO) workshop that will run from November 17-21st at Moffitt (see link
for flyer below). This workshop is designed to motivate and facilitate a
hands-on modeling experience focused on Viruses in Cancer. Comprising of
both an educational event and competition and for the 1st time, run in
conjunction with Moffitt's, Center for Infection Research in Cancer. The
workshop will divide into four teams (or maybe 5) integrating clinical,
experimental and theoretical members that will focus their energies on
developing and implementing a mathematical model focused on understanding
the role of viruses in cancer. Both infection, progression and treatment
are all possible focuses - provided viruses are central to the research
question. Each team consists of around 10-12 participants from mixed
disciplines and career stages, chosen to provide complimentary skills to
help the 3 team co-leaders achieve success. The teams are expected to come up
with a question, build a model, solve it and give a presentation all within
4 intense days. The morning of the 18th and the morning of the final day,
the 21st, are dedicated to presentations and judging.
A new addition to this years workshop will be an opportunity for participants
to showcase their own research during a poster session on the 17th,
this will be preceded by a "speed dating for scientists" to break the ice
among diverse groups of scientists. To facilitate integration and motivate
participation we are offering an Amazon gift voucher to active participants
of the winning team and to the runner up team. I am also pleased to say that
the leaders of the winning team will be awarded a $50K pilot grant, that
will be administered primarily by the IMO but most likely will facilitate
experimental and clinical validation.
For the 2nd year running we are offering travel awards, these are extremely
limited and competitive - not a first come first served basis. Each award
will cover flight + accommodation + per diem for up to 5 nights and allow
for both national and international scientists to participate in this unique
hands on educational event. If you are a Postdoc, PhD student or junior
faculty interested in participating in the workshop as a team player, please
register asap at
http://imo4.eventbrite.com and follow instructions. Time
is very tight, so please don't wait to register for this exciting opportunity.
Download the workshop flyer here:
http://labpages.moffitt.org/andersona/images/workshop/IMO_IV.pdf
Register for the workshop here:
http://imo4.eventbrite.com
----------------------------------------------------
From: <
SpringerAlerts@springeronline.com>
Date: Tue, Sep 30, 2014 at 8:21 PM
Subject: New Springer Books
NEW PRINT & EBOOKS
------------------
Mathematics
Mathematical and Computational Biology
Mathematical Modeling of Biological Processes
Book Series: Lecture Notes on Mathematical Modelling in the Life Sciences
Friedman, Avner; Kao, Chiu-Yen
http://www.springer.com/-/0/koX7aghXSICr-Xl6Rxqiig
Mathematics as a Laboratory Tool
Milton, John; Ohira, Toru
http://www.springer.com/-/3/koX7aghXSICr-Xl6Rxqiig
New Frontiers of Multidisciplinary Research in STEAM-H (Science, Technology,
Engineering, Agriculture, Mathematics, and Health)
Book Series: Springer Proceedings in Mathematics & Statistics, Vol. 90
Editor/s: Toni, Bourama
http://www.springer.com/-/1/koX7aghXSICr-Xl6Rxqiig
----------------------------------------------------
From: <
keystonesymposia@keystonesymposia.org>
Date: Tue, Sep 30, 2014 at 7:43 PM
Subject: Keystone Symposia 2015 Sirtuin Biology Conference
See
http://www.keystonesymposia.org/views/web/marketing/emails/2015_C3_Email.html#utm_source=2015C3email&utm_medium=emaillink&utm_campaign=2015C3email
----------------------------------------------------
From: Liwei Ning <
editorial@aimsciences.org>
Date: Thu, Oct 2, 2014 at 12:16 PM
Subject: ToC: MBE Volume 11 Number 6, December 2014
Mathematical Biosciences and Engineering (MBE)
Volume: 11, Number: 6 December 2014
http://aimsciences.org/journals/contentsListnew.jsp?pubID=711
1. Spatiotemporal complexity in a predator--prey model with weak Allee
effects
Pages : 1247 - 1274
Yongli Cai, Malay Banerjee, Yun Kang and Weiming Wang
2. Modeling colony collapse disorder in honeybees as a contagion
Pages : 1275 - 1294
Christopher M. Kribs-Zaleta and Christopher Mitchell
3. Epidemic models for complex networks with demographics
Pages : 1295 - 1317
Zhen Jin, Guiquan Sun and Huaiping Zhu
4. Dynamics of two phytoplankton populations under predation
Pages : 1319 - 1336
Jean-Jacques Kengwoung-Keumo
5. Modeling the impact of twitter on influenza epidemics
Pages : 1337 - 1356
Kasia A. Pawelek, Anne Oeldorf-Hirsch and Libin Rong
6. A model for the nonlinear mechanism responsible for cochlear amplification
Pages : 1357 - 1373
Kimberly Fessel and Mark H. Holmes
7. Threshold dynamics of an SIR epidemic model with hybrid of multigroup
and patch structures
Pages : 1375 - 1393
Toshikazu Kuniya, Yoshiaki Muroya and Yoichi Enatsu
8. A new model with delay for mosquito population dynamics
Pages : 1395 - 1410
Hui Wan and Huaiping Zhu
9. A stochastic simulation model for Anelosimus studiosus during prey capture:
A case study for determination of optimal spacing
Pages : 1411 - 1429
Michele L. Joyner, Chelsea R. Ross, Colton Watts and Thomas C. Jones
10. Effects of elongation delay in transcription dynamics
Pages : 1431 - 1448
Xuan Zhang, Huiqin Jin, Zhuoqin Yang and Jinzhi Lei
11. A mathematical model for antibiotic control of bacteria in peritoneal
dialysis associated peritonitis
Pages : 1449 - 1464
Colette Calmelet, John Hotchkiss and Philip Crooke
----------------------------------------------------
From: Gib Bogle <
g.bogle@auckland.ac.nz>
Date: Mon, Sep 29, 2014 at 8:07 PM
Subject: PhD Position, Tumour Spheroid Modelling, Auckland Bioeng Institute
PhD Project: Tumour Spheroid Modelling
A stipend for this project will be paid under Marsden Grant funding:
Tuition fees will be covered and the successful applicant will receive
$25,000 p.a.
Background
The tumour spheroid, which is grown in vitro from human tumour cells, is
a very powerful cell culture model in cancer research. All tumours are
initially avascular, and as the cells multiply the tumour core becomes
hypoxic. Bill Wilson's team at the Auckland Cancer Society Research Centre
(ACSRC) develops hypoxia-activated prodrugs (HAPs), compounds that have
cytotoxic activity switched on when taken up by a hypoxic cell. Spheroids
provide an important way to test these drugs, and to explore the influence
of the factors that determine their effectiveness.
Agent-based spheroid model
In the agent-based approach each cell in the aggregation is simulated as
a separate entity that responds to its microenvironment. A preliminary
agent-based model (ABM) for tumour spheroids has been developed, simulating
cell growth, division and death taking into account the diffusion and
consumption of oxygen and nutrients.
Project aims
The first goal is to calibrate and validate the ABM on the basis of data from
tumour spheroid growth experiments with a range of medium conditions. Once
the model has been shown to be capable of reliably predicting the results of
these growth experiments, it will be extended to incorporate drug effects,
again validating against experiments. Since radiotherapy is ineffective
against hypoxic cancer cells, we are very interested in exploring therapeutic
protocols that combine radiation and HAPs, and killing by radiation will
also be implemented in the model. At this point we will be able to design
(and test through experiment) optimal combined treatment protocols.
Importance
This project will break new ground in cancer modelling - there are
currently no published studies on the 3D agent-based simulation of
drug-induced killing of tumours. Those models of drug therapy that have
been published are continuum-based, incapable, we believe, of achieving
the level of detail and realism that the agent-based approach provides. Our
opinion seems to be shared by the Marsden reviewers, one of whom wrote: "This
proposal is original and has significant merit: Developing a pre-clinical
'in vitro-in silico' drug/RT testing platform would have obvious benefit for
integrative oncology research as well as, potentially, for the development
of new treatment paradigms; this would be an accomplishment beyond Auckland
or NZ, rather it would have an impact on the cancer modeling field itself."
Requirements
We are looking for a very good student, someone with strong mathematical,
computational modelling, and programming skills. Interest in and willingness
to learn basic cell biology is also important - this project is highly
interdisciplinary, and will involve working closely with Dr Kevin Hicks,
Professor Bill Wilson and the experimental team at the ACSRC.
Contact:
Gib Bogle
Auckland Bioengineering Institute
g.bogle@auckland.ac.nz
09-837-7186
----------------------------------------------------
From: Doe, Aimee <
Aimee_Doe@hms.harvard.edu>
Date: Mon, Oct 6, 2014 at 3:19 PM
Subject: Postdoctoral Opportunity, Harvard Medical School
Job Title: Personalized Medicine Research Fellowship
Summary: The Center for Biomedical Informatics (CBMI) at Harvard Medical
School has one research fellowship available for immediate appointment. The
position is part of the Laboratory for Personalized Medicine (LPM,
lpm.hms.harvard.edu), whose focus is to reengineer translational science and
accelerate the migration of biomedical informatics methodology, analysis and
applications into the clinical enterprise in support of personalized medicine.
LPM's objective is to identify clinically impactful devices, procedures,
and biomedical informatics resources; test the clinical validity of those
items with likely impact in the personal medicine clinical enterprise;
and to execute high priority projects that translate key technologies
into the clinical IT enterprise in support of personalized, preventive
health care. The long-term goal is to create a translational science
method and environment that supports the continuous and systematic testing
and translation of highest priority technologies and discoveries into the
clinical enterprise. This objective is at the heart of translational science
and will support the joint HMS and Harvard Affiliate CTSC efforts. Current
projects include large-scale genomic analysis, using network medicine to
discover novel drug targets and the development of optimized treatment
plans for segmented patient populations.
Role and Duties: As a member of LPM, the Fellow is expected to assume
important roles in prioritized LPM projects including: work with LPM project
leadership to identify and describe key pilot projects, participate in
multidisciplinary project team projects to achieve research milestones,
provide teaching assistance to the Bioinformatics Track in the Master
of Medical Sciences in Biomedical Informatics program at Harvard Medical
School, and support basic science, clinical researchers, and LPM's healthcare
collaborations.
Qualifications: The ideal candidate has received their PhD in the biomedical
informatics, biomedical science or clinical informatics fields and/or has
received a MD, RN, or related advance clinical degree within the last three
years. Candidate must excel at modern bioinformatics skills such as python,
perl, R, cluster computing or similar. Preference will be given to applicants
with demonstrated research aptitude and a driving interest in improving the
healthcare system. The diversity of subject matter will require a creative
mind and a candidate capable of deploying imaginative strategies and who is
dedicated to solving complex and challenging problems. Applicants should
be highly motivated and flexible, with excellent communication skills,
and work well within an interdisciplinary environment.
How to apply: Email applications including curriculum vitae, summary statement
of personal objective and research interests, PDFs of no more than three
papers, and the names and email addresses of three references to: Peter J.
Tonellato, Ph.D.,
peter_tonellato@hms.harvard.edu,
617-432-7185
For general interest in working at the LPM send CV, statement of objective
and interests.
----------------------------------------------------
From: Isaac Klapper <
tue87237@temple.edu>
Date: Thu, Oct 2, 2014 at 11:33 AM
Subject: Tenure-Track Position, Mathematics, Temple University
The Department of Mathematics, Temple University is inviting applications for
positions at the rank of tenure-track Assistant Professor. (In exceptional
cases, more advanced ranks may be considered.) Candidates should have
outstanding potential. Postdoctoral experience is expected.
Our targeted research area for this year is Applied and Computational
Mathematics.
Temple's College of Science and Technology is in the process of sustained
growth in computational science. Candidates engaged in interdisciplinary
research are particularly encouraged to apply. We offer highly competitive
salaries, teaching loads, and start-up packages.
Applications should include the standard AMS Cover Sheet for Academic
Employment, a cover letter, a curriculum vitae (including publication list),
a statement about current and future research, and a statement on teaching
experience. A complete application will also include at least three letters
of recommendation addressing research and one letter addressing teaching. All
application materials should be submitted via
mathjobs.org.
Inquiries may be directed to
mathematics@temple.edu.
Review of applications will begin November 1, 2014.
Temple University is an Affirmative Action/Equal Opportunity Employer,
and is committed to increasing the diversity of its faculty. We especially
encourage applications from women, minorities, and other under-represented
groups in the mathematical sciences.
----------------------------------------------------
From: Andrew Edelman <
aedelman@westga.edu>
Date: Mon, Oct 6, 2014 at 9:14 AM
Subject: Assistant Professor, Department of Biology, University of West Georgia
The Department of Biology at the University of West Georgia invites
applications for a full-time, tenure-track assistant professor position
beginning in August 2015. We are particularly interested in candidates with
experience in population biology, ecology or evolutionary biology utilizing
field-based and/or bioinformatics/computational techniques. Teaching
responsibilities will include general biology courses as well as
development of undergraduate and graduate courses in the candidate's area
of expertise. The successful candidate will also be expected to establish
a productive research program involving both undergraduate and graduate
students.
The University of West Georgia (
http://www.westga.edu/) is a comprehensive
university of approximately 12,000 students located on a 644-acre wooded
campus in Carrollton, Georgia with a satellite campus in Newnan, Georgia. The
Department of Biology is a growing program that consists of 16 tenure-track
faculty with over 500 undergraduate majors and a M.S. program. Applicants
must have a Ph.D. degree in biology or a related field and postdoctoral
experience is preferred. To apply, please email a PDF consisting of a cover
letter, teaching philosophy, research statement and copies of transcripts
to
biosearch@westga.edu. Also arrange for three letters of recommendation
to be emailed to the same address from the writers' institutional email
address. Review of applications will begin November 15 and continue until
position is filled. The University of West Georgia is an Affirmative
Action/Equal Opportunity Institution.
----------------------------------------------------
From: Whang, Kenneth C. <
kwhang@nsf.gov>
Date: Tue, Sep 30, 2014 at 2:55 PM
Subject: Announcing NSF-NCS: Integrative Strategies; Industry/University Coop...
Dear Colleagues,
NSF has three new announcements today related to the BRAIN initiative
(
http://www.whitehouse.gov/brain) and NSF's Understanding the Brain
(
http://www.nsf.gov/brain) activities:
NSF 14-611 Integrative Strategies for Understanding Neural and Cognitive
Systems (NSF-NCS)
http://www.nsf.gov/ncs
NSF 14-125 Industry/University Cooperation in Areas Related to Understanding
the Brain's Structure and Function
http://www.nsf.gov/pubs/2014/nsf14125/nsf14125.jsp;
http://www.nsf.gov/eng/iip/iucrc/
NSF 14-126 Intent to support an Ideas Lab on multiscale integration of
brain activity and structure with brain function
http://www.nsf.gov/pubs/2014/nsf14126/nsf14126.jsp
----------------------------------------------------
From: Whang, Kenneth C. <
kwhang@nsf.gov>
Date: Wed, Oct 1, 2014 at 8:32 AM
Subject: Upcoming Deadlines: Biomedical Computing, Informatics, Big Data ...
http://bd2k.nih.gov/funding_opportunities.html#sthash.CsPkYLb8.dpbs
· Analysis Methods and Software Title Number Opening Date Closing Date
Early Stage Development of Technologies in Biomedical Computing, Informatics,
and Big Data Science (R01) PA-14-155 05/02/2014 05/08/2017
· Extended Development, Hardening and Dissemination of Technologies in
Biomedical Computing, Informatics and Big Data Science (R01 PA-14-156
05/05/2014 05/08/2017
· Early Stage Development of Technologies in Biomedical Computing,
Informatics, and Big Data Science (R43/R44) PA-14-154 07/05/2014 05/08/2017
· Early Stage Development of Technologies in Biomedical Computing,
Informatics, and Big Data Science (R41/R42) PA-14-157 07/05/2014 05/08/2017
· Development of Software and Analysis Methods for Biomedical Big Data
in Targeted Areas of High Need (U01) RFA-HG-14-020 5/19/14 06/20/14
Deadlines:
http://grants.nih.gov/grants/funding/submissionschedule.htm
American Epilepsy Society Seizure Prediction Challenge
http://www.kaggle.com/c/seizure-prediction
$20,000 Prize
Contest closes Nov 17
----------------------------------------------------
From: "Murcia, Ellie (NIH/OD) [E]" <
murciae@OD.NIH.GOV>
Date: Mon, 29 Sep 2014 15:29:18 +0000
Resent-from: Raymond Mejía <
mejiar@helix.nih.gov>
Subject: New NIH Funding Opportunities to Investigate the 4D Nucleome
New Funding Opportunities to Investigate the 4D Nucleome!
The Common Fund's 4D Nucleome program
(
http://commonfund.nih.gov/4Dnucleome/index) aims to understand the
principles underlying nuclear organization in space and time, the role
nuclear organization plays in gene expression and cellular function, and
how changes in nuclear organization affect normal development as well as
various diseases. This program will develop technologies, resources and
data to enable the study of the 4D Nucleome, including novel tools to
explore the dynamic nuclear architecture and its role in gene expression
programs, models to examine the relationship between nuclear organization
and function in both normal development and disease, and reference maps of
nuclear architecture in a variety of cells and tissues.
The 4D Nucleome program has released six new Funding Opportunity
Announcements:
* Nuclear Organization and Function Interdisciplinary Consortium
(NOFIC)(U54) <
http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-14-006.html>
(RFA-RM-14-006)
NOFIC will be composed of multidisciplinary teams that will develop and
validate novel approaches and genome-wide mapping technologies that will
lead to a deeper understanding of nuclear organization in time and space,
and the role of this organization in regulating gene expression programs.
* Nucleomics Tools (U01)
<
http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-14-007.html>
(RFA-RM-14-007)
This initiative will stimulate the development and validation of chemical
and biochemical technologies for measuring three dimensional interactions
between specific places in the genome (genomic loci), or between genomic
loci and regulators of genome organization and function, in mammalian cells.
* Study of Nuclear Bodies and Compartments (U01)
<
http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-14-008.html>
(RFA-RM-14-008)
This initiative will support the development of tools and strategies to
study the three dimensional architecture of the nucleus in relationship to
the spatial arrangement of nuclear bodies and molecular machinery regulating
gene expression, the structure and function of poorly characterized nuclear
structures and compartments, and the role of specialized proteins and RNAs
in nuclear organization and function.
* 4D Nucleome Imaging Tools (U01)
<
http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-14-009.html>
(RFA-RM-14-009)
This initiative will stimulate the development of higher throughput, higher
resolution, and higher content imaging approaches that can measure changes
in nuclear organization in live single cells.
* 4D Nucleome Network Organizational Hub (U01)
<
http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-14-010.html>
(RFA-RM-14-010)
The 4DN-OH will develop a community website to facilitate sharing of data,
reagents, standards, and protocols; help foster collaborations between 4D
Nucleome investigators; organize yearly scientific meetings; and oversee
administrative aspects of the program. 4DN-OH will also administer the
Opportunity Pool, a fund to support new projects and initiatives that
address identified needs arising throughout the lifetime of the program.
* 4D Nucleome Network Data Coordination and Integration Center (U01)
<
http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-14-011.html>
(RFA-RM-14-011)
4DN-DCIC will track, store, and display all data generated by 4D Nucleome
investigators; provide a Data Analysis Center to assist with integrated
analyses; develop metrics and standards to be adopted by the community at
large; and provide visualization tools to facilitate access and understanding
of complex datasets.
The NIH Common Fund supports goal-driven, research networks in which
investigators generate data, solve technological problems, and/or otherwise
pilot resources and tools that will be stimulatory to the broader research
community. Common Fund programs are designed to achieve their goals within a
maximum of 10 years. More information about the programs currently supported
by the Common Fund can be found at <
http://www.commonfund.nih.gov>.
----------------------------------------------------
Subject: SMBnet Reminders
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End of SMB Digest
****************************************************
----------------------------------------------------