Subject: Society for Mathematical Biology Digest

SMB Digest  August 9, Volume 16  Issue 32
ISSN 1086-6566

Editor: Ray Mejía ray(at)smb(dot)org

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:
   COMBINE & de.NBI tutorial, satellite meeting of the ICSB2016
   Highlights from Springer's collection in Math and Comp Biology
   Postdoctoral Investigator: Metacommunity Dynamics, Woods Hole ...
   IC2016 SUMMER International Call for Postdocs, BCAM
   Job: Open systems pharmacology modeling/mathematical biology, Sanofi
   Metabolic Network Modeling Research Scientist (211875)
   Research Director (Synthetic Portabolomics)
   NIH Update: criterion scores and funding outcomes, data ...
   SMBnet Reminders


From: Juergen Pahle <juergen.pahle@bioquant.uni-heidelberg.de>
Date: Tue, Aug 9, 2016 at 5:15 AM
Subject: COMBINE & de.NBI tutorial, satellite meeting of the ICSB2016

We will organize a
COMBINE & de.NBI Tutorial
'Modelling and Simulation Tools in Systems Biology'
on Friday,16 September, 2016 (8:30 - 13:30)

as a a satellite of the 17th International Conference on Systems Biology

Participation is free of charge and registration is open until August 25th:

Please note that the tutorial is at the opening day of the ICSB conference. It
will finish in time to allow participants to join the ICSB opening ceremony
in the afternoon.

Participants will learn how to set up computer models of biological systems
(e.g. metabolic or signalling networks) using experimental kinetic data
and how to simulate them in different systems biology platforms. Hands-on
sessions, lectures and software demonstrations will be included, providing
attendees with the necessary skills to access experimental kinetics data
from available resources, to assemble computer models with these data,
and finally to simulate the generated models using simulation tools. Also
handling and exchange of biological models based on existing community
standards will be demonstrated along with the basic principles of the
underlying standard formats.

The topics will include:

 * Model setup using different software tools and systems biology
 * Using experimental data for setting up quantitative models
 * Parameter estimation, optimization and model fitting
 * Simulation, analysis and visualization of biochemical models
 * Database supported modelling: integrated data management and model
 * Community standards and formats for systems biology models

Covered tools, platforms and databases

 * BioModels database: http://www.ebi.ac.uk/biomodels-main/
 * CellDesigner: http://www.celldesigner.org/
 * COPASI: http://www.copasi.org
 * JWS Online: http://jjj.biochem.sun.ac.za/
 * SABIO-RK: http://sabio.h-its.org/
 * SEEK: http://fair-dom.org/platform/seek/
 * SYCAMORE: http://sycamore.eml.org

You are invited to join us and/or send your students. The target audience are
experimentalists and modellers with some very basic experience in modelling
and simulation of biological networks and everybody who would like to learn
more about the tools and standards.

Please feel free to forward this invitation to anybody you would think
could be interested to attend.

Best regards,
Martin Golebiewski
(on behalf of all tutors)


From: Divya Laul | Springer <springer@news.springer.com>
Date: Thu, Aug 4, 2016 at 6:03 AM
Subject: Highlights from Springer's collection in Math and Comp Biology

Springer publishes key books in Mathematical and Computational
Biology - take a look inside!

We offer a free preview for all titles:

Mathematical Models for Therapeutic Approaches to Control HIV
Author: Priti Kumar Roy

The Mathematics Behind Biological Invasions
Authors: Mark A. Lewis, Sergei V. Petrovskii, Jonathan R. Potts

An Introduction to Mathematical Epidemiology
Author: Maia Martcheva

Stochastic Processes in Cell Biology
Author: Paul C. Bressloff

Computing Characterizations of Drugs for Ion Channels & Receptors
Authors: Aslak Tveito, Glenn T. Lines

Models of Calcium Signalling
Authors: G. Dupont, M. Falcke, V. Kirk, J. Sneyd

Cellular Automaton Modeling of Biological Pattern Formation
Authors: Andreas Deutsch, Sabine Dormann

Data-driven Modelling of Structured Populations
Authors: Stephen P. Ellner, Dylan Z. Childs, Mark Rees


From: Michael Neubert <mneubert@whoi.edu>
Date: Wed, Aug 3, 2016 at 4:09 PM
Subject: Postdoctoral Investigator: Metacommunity Dynamics, Woods Hole ...

Postdoctoral Investigator: Hydrothermal Vent Metacommunity Dynamics
Biology Department, Woods Hole Oceanographic Institution

We seek a postdoctoral investigator to develop and analyze mathematical
models describing the processes that generate patterns of species diversity
observed at deep-sea hydrothermal vents. We are particularly interested
in how metacommunity processes - including dispersal, disturbance, and
succession - interact to drive patterns of diversity.

The ideal candidate will have completed a Ph.D. in Applied Mathematics,
Biological Oceanography, Ecology, or a related discipline and have
demonstrable expertise in mathematical ecology (in particular, the
mathematical modelling of population and/or community dynamics). The
successful applicant will work with the three PIs (Michael Neubert, Lauren
Mullineaux, and Julie Kellner) at the Woods Hole Oceanographic Institution,
in Woods Hole, Massachusetts. The Institution has a top-rated postdoctoral
program (www.whoi.edu/postdoctoral/) that supports a dynamic postdoctoral
community with formal mentoring and career guidance programs. While the
primary focus of the work will be on research, the postdoctoral investigator
will have an opportunity to participate in educational and outreach activities
associated with the project.

We will begin reviewing applications August 15, 2016 and the position will
remain open until filled (preferably by the end of the year). The initial
appointment will be for one year, with the possibility of extension for a
second year based upon performance.

Please contact Michael Neubert (mneubert@whoi.edu), Lauren Mullineaux
(lmullineaux@whoi.edu), or Julie Kellner (jkellner@whoi.edu), with
questions about the project. To apply, please submit, as a single pdf
file, an application (including a short cover letter, a curriculum vita,
a statement of past research experience and future interests, contact
information for three references, and at most two relevant manuscripts),
to Michael Neubert and online (bit.ly/1Rj2zKj).

WHOI is an Affirmative Action/Equal Opportunity
Employer/Disabled/Veterans/M/F.  We encourage veterans and those with
disabilities to apply. Applications are reviewed confidentially. Applicants
that require accommodation in the job application process are encouraged
to contact the Human Resources Department at (508) 289-2253 or email
eeo@whoi.edu for assistance. WHOI is a member of the Higher Education
Recruitment Consortium (HERC). We are sensitive to the issues of dual career
candidates and we will work with applicants to address them.  Please visit
HERC for more information.


From: Miguel A. Benitez <benitez@bcamath.org>
Date: Wed, Aug 3, 2016 at 6:07 AM
Subject: IC2016 SUMMER International Call for Postdocs, BCAM

BCAM, the Basque Center for Applied Mathematics http://www.bcamath.org whose
mission is to develop high quality interdisciplinary research in the frontiers
of Applied Mathematics, has opened the following positions:

ONE Postdoctoral Fellowship in Modelling and Simulation in Life and Materials
Deadline for submission: September 20 2016, 17:00 [UTC/GMT + 1 hour]. All
applications must be submitted on-line at:

We kindly ask you to distribute this call among colleagues and potential
candidates. Please, do not hesitate to contact us if you need further
information: recruitment@bcamath.org.


From: <Karim.Azer@sanofi.com>
Date: Thu, Aug 4, 2016 at 8:16 AM
Subject: Job: Open systems pharmacology modeling/mathematical biology, Sanofi

Dear readers,

Posting: Open systems pharmacology modeling/mathematical biology - Principal
scientist position at Sanofi. Please contact karim.azer@sanofi.com or, to
see a description and apply online, search for Position 75034404-0001 at


From: <jpeters@hjf.org>
Date: Tue, Aug 9, 2016 at 10:32 AM
Subject: Metabolic Network Modeling Research Scientist (211875)

Metabolic Network Modeling Research Scientist (211875)

The Henry M. Jackson Foundation for the Advancement of Military Medicine,
Inc.  (HJF) is seeking a Metabolic Network Modeling Research Scientist to
provide support to the U.S. Army Medical Research and Materiel Command's
Biotechnology High Performance Computing Software Applications Institute
(BHSAI) [www.BHSAI.org]. HJF provides scientific, technical, and programmatic
support services to the BHSAI. Working in an interdisciplinary environment
with focus on the development and application of computational solutions to
biomedical problems, including toxicology, drug resistance, and infectious


Use computational modeling to integrate transcriptomic and metabolomics
data with metabolic networks to understand malaria host/pathogen responses
to different physiological stressors, including drug treatment.

 1. Perform both basic and applied research in close collaboration with
    experimental laboratories.
 2. Simultaneously work on multiple projects, involving a diverse and
    interdisciplinary team of scientists across multiple laboratories.
 3. Collaborates with other scientists and computational staff on research
    projects and development of new approaches to existing research problems.
 4. Prepares research proposals, progress reports, and manuscripts for
    submission to scientific journals.
 5. Presents research methods and findings at appropriate scientific
 6. Completes other projects as needed.

Required Knowledge, Skills, and Abilities: Experience in high-performance
computing, biostatistics or population genomics, mathematical modeling
and biological network analysis is a plus. Expertise in at least one of C,
C++, Java, Python or Pen is a must. PLEASE ONLY APPLY IF YOU HAVE PROVEN
COMPUTATIONAL BIOLOGY EXPERIENCE. The candidate is expected to simultaneously
work on multiple projects, involving a diverse and interdisciplinary team
of scientists across multiple laboratories

Minimum Education/Training Requirements: Ph.D. in a related discipline,
post-graduate experience, and a strong publication record.

Minimum Experience: 4 - 6 years

HJF is an equal opportunity and affirmative action employer. All qualified
applicants will receive consideration for employment without regard to race,
color, religion, sex, sexual orientation, gender identity, national origin,
disability, or protected veteran status.

TO APPLY Please copy and paste the following URL into your web browser:


From: Paolo Zuliani <paolo.zuliani@newcastle.ac.uk>
Date: Tue, Aug 9, 2016 at 6:24 AM
Subject: Research Director (Synthetic Portabolomics)

The EPSRC project Synthetic Portabolomics is a looking for a Senior Research
Associate to act as Research Director, supporting the PI in the delivery of
the project objectives including (but not limited to) coordinate and carry
out its management activities including all reporting activities, e.g. to
EPSRC, stakeholders, REF related, UKRC related (e.g. research fish), etc.

The Research Director will also be lead in the execution and further
development of Pathways to Impact plan and carry out translational
research activities. In addition, the post holder will work closely with
Prof. Krasnogor in (a) the exploration, dissemination and exploitation
of IP generated by the project and, more generally, the Interdisciplinary
Computing and Complex Systems (ICOS) research group and (b) the conception,
design and implementation of funding opportunities for ICOS from UKRC,
Innovate UK, H2020, etc.

This post is fixed term for two years.

For informal enquiries please contact Professor Natalio Krasnogor

For further information and to apply:

The ICOS group http://ico2s.org


From: NIH Extramural Nexus (NIH/OD) <ExtramuralNexus@mail.nih.gov>
Date: Mon, Aug 1, 2016 at 5:05 PM
Subject: NIH Update: criterion scores and funding outcomes, data ...

NIH Update: criterion scores and funding outcomes, data on model organism
funding, fellowship application tips and more.  See


Subject: SMBnet Reminders

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