----------------------------------------------------
Subject: SMB Digest v12i32
SMB Digest August 6, 2012 Volume 12 Issue 32
ISSN 1086-6566
Editor: Richard Schugart richard(dot)schugart(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:
Workshop: Development & Cancer: CompuCell3D..., Oct 8-13, Leden
New Book: A First Course in Systems Biology
ToC: BMB, Volume 74, Issue 9
Math Survey
Support Activities, Deadline Sep 1, NIMBioS, UT, Knoxville
Post-docs: NIMBioS, UT, Knoxville
Post-doc: Design Principles of Biological Control, Imperial Col
Post-docs/PhDs: Computat. Biology, Pohang U Sci & Tech, Korea
NIH Research and Scientific/Clinical Positions - August Update
SMBnet Reminders
----------------------------------------------------
From: Blaisse, R.G. <blaisse@lorentzcenter.nl>
Date: August 6, 2012 9:45:00 AM
Subject: Workshop: Development & Cancer: CompuCell3D..., Oct 8-13, Leden
Announcement Lorentz Center workshop @Snellius
Application opens at 7 August and closes at 21 August 2012 (17.00hrs)
Modeling of Multicellular Development and Cancer: European
CompuCell3DSBW Hands-on Workshop, which will be held from 8-13 October
2012 at the Lorentz Center @Snellius in Leiden (NL)
Scientific Topic: Computational modeling of tissues and organs with
cellular and subcellular resolution is becoming an integral part of
contemporary bioscience. The Glazier-Graner-Hogeweg (GGH) or Cellular
Potts Model (CPM) as implemented in the modeling environment CompuCell3D
allows researchers to rapidly build complex models of multi-cell
processes in development and disease of tissues with user-selectable
resolution, from sub-cellular compartmental models to continuum models
of tissues. To efficiently link dynamics at the subcellular scale to the
multicellular scale, users build biochemical reaction models using
Systems Biology Workbench (SBW) to control properties of simulated cells
in CompuCell3D. CompuCell3D and SBW are simulation environments that
target complementary areas of biological modeling. By combining the
capabilities of both frameworks users can build truly multi-scale models
of tissues, organs or organisms with minimal amount of hardcoded,
heuristic rules. CompuCell3D and SBW are open source, allowing users to
extend, improve, validate, modify and share the core software. For more
information please visit: http://www.compucell3d.org/ (CompuCell3D and
GGH/CPM) and http://www.sys-bio.org/ (SBW).
Meeting Format: Lorentz Center organizes scientific meetings for small
groups of up to 25 participants, including both senior and junior
scientists. Lorentz Center meetings dedicate a considerable amount of
time to discussion sessions, thus stimulating an interactive atmosphere
and encouraging collaborations between participants. This format
typically generates extensive debates and enables significant progress
to be made within the research topic of the meeting.
Lorentz Center Facilities: The meeting is held at the Lorentz Center
@Snellius, located at the Faculty of Science campus of Leiden
University, the Netherlands. The Lorentz Center provides each
participant with office space and wireless internet access. Lorentz
Center also provides various practical services for the participants,
such as arranging accommodations at the nearby hotel "Van der Valk Hotel
Leiden", visa assistance and bike rental. For further information,
please refer to our website: http://www.lorentzcenter.nl
Costs and Refunds: Lorentz Center does not charge registration fees. In
addition, Lorentz Center hosts a welcome reception and two meeting
dinners (on Wednesday and Friday), all free of charge.
Thanks to the generosity of European Science Foundation (ESF) and the
Lorentz Center, participants are provided with accommodation at the
hotel "Van der Valk Hotel Leiden". Lorentz Center and ESF will also
reimburse your travel expenses up to a maximum of 300 euros (within
Europe) or 800 euros (outside Europe).
Please note that it is our responsibility to mention that the
information of the participants of the workshop (title, full name,
gender and affiliation) will be entered into the ESF database.
Application and important deadlines: Application opens on Tuesday 7
August 2012 and closes at Tuesday 21 August 2012 at 17.00hrs. You can
apply via
http://www.lorentzcenter.nl/lc/web/2012/534/info.php3?wsid=534&venue=Snellius
Please note that your admittance to the workshop is at the discretion of
the scientific organizers (James Glazier, Roeland Merks, Herbert Sauro
and Maciej Swat) on the basis of a short motivation and biography (to be
submitted through the application form). You will be informed on your
admission by 13 September 2012 at the latest. Note that there are only a
limited amount of spaces available.
It is required to participate for the whole workshop week.
For further information about the workshop program, venue, and
scientific topics, please check our webpage. As the coordinator of all
practical matters involved in this Lorentz Center workshop, I will be
happy to answer your questions.
Kind regards,
On behalf of the organizers,
Renee Blaisse
Workshop Coordination
email: blaisse@lorentzcenter.nl
telephone: +31 71 527 8523
----------------------------------------------------
From: Eberhard Voit <eberhard.voit@bme.gatech.edu>
Date: August 3, 2012 9:42:23 AM
Subject: New Book: A First Course in Systems Biology
New Book: A First Course in Systems Biology
Book Summary
A First Course in Systems Biology is a textbook designed for advanced
undergraduate and graduate students. Its main focus is the development
of computational models and their applications to diverse biological
systems.
Because the biological sciences have become so complex that no
individual can acquire complete knowledge in any given area of
specialization, the education of future systems biologists must instead
develop a student's ability to retrieve, reformat, merge, and interpret
complex biological information.
This book provides the reader with the background and mastery of methods
to execute standard systems biology tasks, understand the modern
literature, and launch into specialized courses or projects that address
biological questions using theoretical and computational means. The
format is a combination of instructional text and references to primary
literature, complemented by sets of small-scale exercises that enable
hands-on experience, and larger-scale, often open-ended questions for
further reflection.
Additional information can be found at:
http://www.garlandscience.com/product/isbn/9780815344674
----------------------------------------------------
From: Springer <springeralerts@springer.delivery.net>
Date: August 3, 2012 7:11:42 AM
Subject: ToC: BMB, Volume 74, Issue 9
Volume 74 Number 9 is now available on SpringerLink
http://www.springerlink.com/content/0092-8240/74/9/
IN THIS ISSUE:
Permanence in an Intraguild Predation Model with Prey Switching
Joaquin Zabalo
Impact of Latently Infected Cells on Strain Archiving Within HIV Hosts
Zoë Ward & Jane White
Revising the Role of Species Mobility in Maintaining Biodiversity in
Communities with Cyclic Competition
M. W. Adamson & A. Y. Morozov
From the Cell Membrane to the Nucleus: Unearthing Transport Mechanisms
for Dynein
Laurie Crossley, Caroline A. Garrett, Majid Hafezparast &
Anotida Madzvamuse
Coupling Fluid and Solute Dynamics Within the Ocular Surface Tear Film:
A Modelling Study of Black Line Osmolarity
V. S. Zubkov, C. J. W. Breward & E. A. Gaffney
Investigating Alcohol Consumption as a Risk Factor for HIV Transmission
in Heterosexual Settings in Sub-Saharan African Communities
N. J. Malunguza, S. D. Hove-Musekwa, G. Musuka & Z. Mukandavire
A Note on the Derivation of Epidemic Final Sizes
Joel C. Miller
Uni-directional Interaction and Plant?Pollinator?Robber Coexistence
Yuanshi Wang, Donald L. DeAngelis & J. Nathaniel Holland
A Differential Equation Model of Collagen Accumulation in a
Healing Wound
Rebecca A. Segal, Robert F. Diegelmann, Kevin R. Ward & Angela Reynolds
A Model of Oscillatory Protein Dynamics in Bacteria
Peter Rashkov, Bernhard A. Schmitt, Lotte Søgaard-Andersen, Peter Lenz &
Stephan Dahlke
Re-evaluating the Use of Voronoi Tessellations in the Assessment of
Oxygen Supply from Capillaries in Muscle
A. A. Al-Shammari, E. A. Gaffney & S. Egginton
Carrying BioMath Education in a Leaky Bucket
James A. Powell, Brynja R. Kohler, James W. Haefner & Janice Bodily
----------------------------------------------------
From: Sue Risseeuw <risseeuw@beloit.edu>
Date: August 2, 2012 10:43:58 AM
Subject: Math Survey
The UK's Higher Education Academy is working on a report comparing the
pedagogical approaches and curricula used in the US and the UK when
teaching math and quantitative methods (including statistics) to
undergraduates and postgraduates who are majoring in Biology. When the
report is published at the end of this year, we're hoping that the it
will be a useful tool to educational practitioners in both the UK and
the US. To make sure that our observations and conclusions are as
relevant and generalizable as possible, we'd be hugely grateful if you
could help us by completing a very short online survey ( just ten
questions long). This survey can be found here: http://bit.ly/biomaths
Please rest assured that all responses will be examined only in
aggregate and will be treated with absolute anonymity. That said, if you
would like to receive a copy of the report once it is published, please
do enter your email address into the form.
----------------------------------------------------
From: Catherine Crawley <ccrawley@nimbios.org>
Date: August 2, 2012 1:51:15 PM
Subject: Support Activities, Deadline Sep 1, NIMBioS, UT, Knoxville
September 1st deadline for applications of support for research
activities at the National Institute for Mathematical and Biological
Synthesis is fast approaching.
September 1, 2012 is the deadline for requests for support for Working
Groups, Investigative Workshops, Postdoctoral Fellows, Sabbaticals, and
Short-term Visitors for activities beginning spring 2013 at the National
Institute for Mathematical and Biological Synthesis (NIMBioS). All areas
of research at the interface of biology and mathematics will be
considered. NIMBioS, located at the University of Tennessee-Knoxville,
is an NSF-sponsored initiative to foster interdisciplinary research at
the interface between mathematical and biological sciences. The
institute's mission is to cultivate cross-disciplinary approaches in
mathematical biology and to develop a cadre of researchers who address
fundamental and applied biological problems in creative ways. Other
NIMBioS sponsors include DHS and USDA, with additional support from the
University of Tennessee-Knoxville. More details are posted at
http://www.nimbios.org
Related Links:
NIMBioS Working Groups http://www.nimbios.org/workinggroups/
NIMBioS Investigative Workshops http://www.nimbios.org/workshops/
Postdoctoral Fellowships http://www.nimbios.org/postdocs/
Sabbaticals http://www.nimbios.org/visitors/sabbatical
Short-term Visits http://www.nimbios.org/visitors/
----------------------------------------------------
From: Catherine Crawley <ccrawley@nimbios.org>
Date: August 2, 2012 1:42:54 PM
Subject: Post-docs: NIMBioS, UT, Knoxville
The September 1st deadline for applications for postdoctoral fellowships
at NIMBioS is fast approaching.
The National Institute for Mathematical and Biological Synthesis
(NIMBioS), located at the Univ. of Tennessee, Knoxville, is currently
accepting applications for postdoctoral scholarship at the interface
between mathematics and biology. Highest priority will be given to those
with explicit plans to develop their ability to effectively carry on
research across these fields. We are particularly interested in requests
to support research that integrates diverse fields, requires synthesis
at multiple scales, and/or makes use of or requires development of new
mathematical/computational approaches. NIMBioS Postdoctoral Fellows are
chosen based upon indications that the applicant's research plans are
consistent with the mission of NIMBioS, the applicant has the
demonstrated ability to carry out the proposed research, and the
opportunities provided through NIMBioS will enhance the capacity for the
research to be completed in an efficient and timely manner. Support:
annual stipend of $51,000, full University of Tennessee employee fringe
benefits, and an annual travel allowance of $2,000.
How to apply: Complete the online application and submit a brief project
description, references, and CV following the guidelines available at
http://www.nimbios.org/postdocs/
Deadline: NIMBioS postdoctoral requests for support are reviewed three
times per year, and the selected researchers are offered positions at
NIMBioS where they conduct research that is mostly self-directed. The
deadline for activities beginning in winter/spring 2013 is September 1,
2012. All letters of recommendation must be submitted before the
request deadline.
The National Institute for Mathematical and Biological Synthesis
(NIMBioS) (http://www.nimbios.org) brings together researchers from
around the world to collaborate across disciplinary boundaries to
investigate solutions to basic and applied problems in the life
sciences. NIMBioS is sponsored by the National Science Foundation, the
U.S. Department of Homeland Security, and the U.S. Department of
Agriculture with additional support from The University of Tennessee,
Knoxville.
----------------------------------------------------
From: Reiko Tanaka <r.tanaka@imperial.ac.uk>
Date: August 2, 2012 5:09:04 PM
Subject: Post-doc: Design Principles of Biological Control, Imperial Col
PostDoc position available in Imperial College London
Applications are invited for the post of Research Associate in the
Department of Bioengineering at Imperial College working under the
supervision of Dr Reiko Tanaka.
This post is for a project aimed at understanding design principles of
biological control systems. We will employ a diverse range of
theoretical/engineering methodologies to model and elucidate the
regulatory mechanisms for skin barrier homeostasis and inflammatory
signalling. The project will include collaboration with experimentalists
and clinicians. The main responsibilities of this post will include
development of mathematical models for skin barrier homeostasis and
inflammation, proposition of the experiments, coordination, integration
and analysis of experimental data, and the statistical analysis and
reformulations of these models in light of the collected data. More
information on research activities in Dr Tanaka's group is found in
http://www.bg.ic.ac.uk/research/r.tanaka.
Applicants should hold a PhD or equivalent in a relevant area
(Computational Biology, Control Engineering, Mathematics, Applied
Mathematics, or closely aligned disciplines) to undertake this project.
You should also have experience in modelling and analysis of biological
systems, expertise in modelling with differential equations and
numerical methods, and strong interest in biology. We look for highly
motivated applicants with excellent interpersonal, written and oral
communication skills and enthusiasm for exposure to a diversity of
scientific projects.
For further details of the post contact Dr Reiko Tanaka
(r.tanaka@imperial.ac.uk). Interested applicants should send a current
curriculum vitae and research statement to Dr Tanaka by e-mail.
Candidates will be required to apply online via the Imperial College
website at http://www3.imperial.ac.uk/employment where you will find a
job description and person specification for this post. Please select
"Job Search", then enter the job title or vacancy reference number
EN20120212FH into "Keywords". Complete and upload an application form as
directed.
Closing date: September 5th 2012
Start date: as soon as possible
A fixed term appointment for up to 16 months
----------------------------------------------------
From: Junghyo Jo <jojunghyo@gmail.com>
Date: August 3, 2012 1:19:12 PM
Subject: Post-docs/PhDs: Computat. Biology, Pohang U Sci & Tech, Korea
APCTP launches a new Junior Research Group (JRG), lead by Dr. Junghyo
Jo, to investigate design principles in biological systems. JRGs at
APCTP are funded by the Max Planck Society of Germany, Korean
Government, and Pohang University of Science and Technology (POSTECH).
The new group will be located on the POSTECH campus.
The Design Principles of Cellular Networks group seeks for two
postdocs/PhD students who have strong interest in computational biology,
particularly in cell-to-cell communication for biological functions.
Details on our research can be found at
https://www.apctp.org/jrg/blogindex.php?JrgId=13.
The postdoctoral positions are initially for two years with possible
extensions. Applicants should send a curriculum vitae, description of
research interests, and list of two references to Dr. Junghyo Jo
(jojunghyo@gmail.com) by email. The screening of applications will begin
in September, 2012 and last until the positions are filled. If you have
any questions about the group or the positions, please feel free to
contact us.
----------------------------------------------------
From: Owens, Roland (NIH/OD) [E] <owensrol@mail.nih.gov>
Date: August 6, 2012 10:09:53 AM
Re-Sent From: Raymond Mejía <mejiar@helix.nih.gov>
Subject: NIH Research and Scientific/Clinical Positions - August Update
Staff Scientist
Center for Cardiovascular Genomics, NHLBI
(deadline: August 20)
The Center for Cardiovascular Genomics (CCVG) of the National Heart,
Lung, and Blood Institute (NHLBI) at the National Institutes of Health
invites applications for a Staff Scientist position. We seek a highly
motivated, creative and bright individual with expertise in statistical
genetics and/or bioinformatics who is interested in a range of human
epidemiology and genetic epidemiology studies. The candidates must hold
a Ph.D. degree or equivalent with at least 5 years of postdoctoral
experience. A good track record of productivity judged by peer-reviewed
publications is recommended. The successful candidate must have a strong
background in statistical genetic analysis and/or bioinformatics
analyses of genetic/genomic epidemiology research projects.
Specialized experience should include significant experience in
large-scale data analysis, data integration, data mining, optimization
techniques, algorithm design and development, and data visualization as
evidenced by citable publications. Additionally, expertise in
statistical work, such as computing and analyzing large genotype and
phenotype datasets, managing large-scale human genome sequence data,
and applying known statistical techniques to epidemiology and genetic
data, including genomewide association data from human populations is
required. Experience with analysis of gene expression, metabolomic
and/or proteomic data is recommended but not required.
In addition to innovative and independent research in integrative
computational biology and/or cutting edge statistical genetics, the
successful candidate will take an active role in supporting other
members of the Center and will participate in a cooperative effort to
accomplish program, division, and Institute goals.
The successful candidate will be offered a competitive salary
commensurate with experience and qualifications. The initial appointment
will be for a minimum of 2 years, with possible appointment renewals in
1-year increments. Appointees must be US citizens, resident aliens, or
nonresident aliens with a valid employment visa. Applicants should
submit a cover letter highlighting key qualifications, a current
curriculum vitae with complete bibliography, three reference letters, a
one-page summary of the applicant's philosophy of core facility
operation, and a list of three publications that provide evidence of
relevant skills along with corresponding PDF copies of these
publications by August 20 to: Marcia Lobos, Executive Assistant to
Dr. Christopher J. O'Donnell, CCVG, NHLBI at:
NHLBI_CCVG_RecruitStaffScientist@mail.nih.gov. The advertisement will
remain open until the position is filled. PDF versions of documents sent
by electronic mail are strongly preferred. HHS and NIH are Equal
Opportunity Employers.
Applications from women, minorities and persons with disabilities are
strongly encouraged to apply. The NHLBI/NIH is a smoke-free workplace.
Trans-NIH Earl Stadtman Tenure-Track Investigator Search
(deadline: October 1)
The National Institutes of Health, the U.S. government's premier
biomedical and behavioral research enterprise, is pleased to announce
its fourth annual call for "NIH Earl Stadtman Investigators." Scientific
discoveries from our intramural laboratories, with their extensive
infrastructure and critical mass of expertise, have a crucial role in
both maintaining America's research excellence and advancing medical
treatments and cures.
Come join the team whose hallmarks are stable funding, intellectual
freedom, shared resources, and access to a broad range of scientific
expertise. We seek creative and independent thinkers eager to take on
high-risk, high impact research in tenure-track positions.
A variety of basic and translational/clinical positions are available,
with areas of active recruitment including (but not limited to):
Biostatistics/Bioinformatics; Chromatin Biology/Epigenetics; DNA
Replication, Repair and Recombination; Molecular Epidemiology and
Population Genetics; Molecular Immunology; Molecular Pharmacology and
Toxicology; Neuroscience; Population Science; Stem Cells/iPS Cells;
Structural Biology and Systems Biology; and Virology.
Who we are: Among our approximately 1,200 principal investigators and
4,000 trainees are world-renowned experts in basic, translational and
clinical research. Our strength is our diversity in pursuit of a common
goal, to alleviate human suffering from disease. Similar to academia, we
offer our scientists the opportunity to mentor outstanding trainees at
all levels (e.g., graduate students and postdoctoral fellows) in a
research setting.
Whom we seek: For this broad, trans-NIH recruitment effort, we seek
talented, early-career scientists with a clear and creative research
vision who wish to contribute to the nation's health.
Qualifications/eligibility: Candidates must have an M.D., Ph.D.,
D.D.S./D.M.D., D.V.M, D.O., R.N./Ph.D., or equivalent doctoral degree
and have an outstanding record of research accomplishments as evidenced
by publications in major peer-reviewed journals. Applicants may be in
early stages of their research careers or non-tenured early-to-mid
career scientists. Appointees may be U.S. citizens, resident aliens, or
non-resident aliens with, or eligible to obtain, a valid
employment-authorization visa.
How to apply: Applicants must submit a CV, a three-page research plan, a
one-page description of their vision for future research and its
potential impact, and contact information for three professional
references through our online application system at
http://irp.nih.gov/stadtman between August 1 and October 1, 2012. You
will be asked to designate a primary and secondary scientific area of
expertise to aid in assigning your application to the appropriate review
committee. Requests for letters of recommendation will be sent to your
references when you submit your application. Reference letters will be
accepted via upload to the website until 11:59 p.m. EDT October 15,
2012. We cannot accept paper applications.
What to expect: Search committees of subject-matter experts will review
and evaluate applicants based on the following criteria: publication
record, scientific vision and potential scientific impact of current and
proposed research, demonstrated independence, awards and references. The
committees will identify the most highly qualified candidates to invite
to the NIH for a lecture in November or December 2012, which will be
open to the NIH scientific staff, and for subsequent interviews with the
search committees. The search committee chairs and NIH Scientific
Directors, who lead our intramural programs, will identify finalists to
be recruited as Earl Stadtman Investigators. Candidates not selected as
Stadtman finalists can still be considered for other open NIH research
positions. The entire process from application review to job offer may
take several months, depending on the volume of applications.
We call upon individuals who will open our eyes to possibilities we
haven't yet envisioned, to complement our scientific mission and enhance
our research efforts. More information about our program is at
http://irp.nih.gov. The inspiring story of Earl and Thressa Stadtman's
research at the NIH is at http://history.nih.gov/exhibits/stadtman.
Specific questions regarding this recruitment effort may be directed to
Dr. Roland Owens, Assistant Director, NIH Office of Intramural Research,
at owensrol@mail.nih.gov. DHHS and NIH are Equal Opportunity Employers.
Systems Biology/Bioinformatics Staff Scientist
Neuro-Oncology Branch, NCI-NINDS
(deadline: open-ended)
The Neuro-Oncology Branch, a trans-institute program of the National
Cancer Institute and the National Institute of Neurological Disorders and
Stroke of the National Institutes of Health is seeking an outstanding
candidate to work in the area of cancer genomics, bioinformatics and
systems biology, particularly on computational modeling of signaling and
gene networks in cancer cells. Ongoing projects include the integration
of -omics and clinical data in the exploration of signaling and
transcriptional networks that govern cell differentiation, proliferation
and migration in primary brain tumors, cancer tumor stem cells and
normal embryonic neural stem cells and the translation of those
discoveries to patients through the highly integrated clinical brain
tumor research program. Applicants should have a strong background in
mathematical and computational modeling and be expected to carry out an
interdisciplinary project with experimental groups.
The Staff Scientist candidate will take a lead role in the mentorship
and scientific management of a team of bioinformatics research fellows.
The following skills and qualifications are required: 1) PhD in computer
science, mathematics, bioinformatics, or related fields, and at least 3
years of post-doctoral training in bioinformatics and/or systems
biology; 2) experience in machine learning and network generation
algorithms; 3) basic knowledge of cell/molecular biology; 4) experience
in genome-wide genetic and gene expression data analysis.
Please send curriculum vitae, statement of research interests and two
letters of reference to: Howard A. Fine, Chief; Neuro-Oncology Branch,
National Cancer Institute; MSC 8200, Room 225; 9030 Old Georgetown Road;
Bethesda, MD 20892-8200 or to smithj9@mail.nih.gov. Candidates may be
U.S. citizens, resident aliens, or nonresident aliens. DHHS, NIH, the
National Cancer Institute and the National Institute of Neurological
Disorders and Stroke are Equal Employment Opportunity and Affirmative
Action employers that value and foster diversity throughout the entire
organization.
----------------------------------------------------
Subject: SMBnet Reminders
To subscribe to the SMB Digest please point your browser at
http://list.auckland.ac.nz/mailman/listinfo/math-smbnet
and complete the subscription information. Alternatively, if you prefer
to simply receive notice when the next issue is available, send mail to
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in the body of the mail (omit the quotes and include your name).
After you subscribe, you will receive a greeting with additional
information.
Submissions to appear in the SMB Digest may be sent to
SMBnet(at)smb(dot)org .
Items of interest to the mathematical biology community may be submitted
for inclusion in the SMBnet archive. See instructions at:
http://smb.org/publications/SMBnet/pubs/fyi .
The SMB Digest is also available on the SMB Home Page at
http://smb.org/publications/SMBnet/digest/
The contents of this publication may be reproduced in whole or in part
with attribution.
End of SMB Digest
****************************************************