Subject: Society for Mathematical Biology Digest

SMB Digest      June 8, 2016   Volume 16  Issue 23
ISSN 1086-6566

Editor: Alex Fletcher digest.alex(at)gmail(dot)com

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Issue's Topics:
    ECMTB/SMB 2016 Pre-conference Workshop, July 10, UK
    Society for Experimental Biology Cell Symposium, Sept 14-15, UK
    Workshop: COMBINE 2016, Sept 19-23, Newcastle, UK
    Workshop: BIOMAT-2016, Oct 30 - Nov 5, People's Republic of China
    PhD Position: Bioinformatics/Computational Biology, UNSW, Australia
    PhD Position: Cardiac Modelling, Maastricht University, Netherlands
    Request for Information from the NIH Common Fund
    Selected NIH Intramural Research and other job openings - June 2016
    SMBnet Reminders


From: Adriana T. Dawes <dawes.33@math.ohio-state.edu>
Date: Thu, Jun 2, 2016 at 5:38 PM
Subject: ECMTB/SMB 2016 Pre-conference Workshop, July 10, UK

ECMTB/SMB 2016 Pre-conference Workshop

Please join us before the start of the scientific meeting for a variety of 
presentations and discussions around careers in mathematical biology. The 
workshop has four main components:

1. For graduate students and postdoctoral fellows, there will be a session 
   led by Robert Smith? and Christina Cobbold about strategies for the 
   academic job market.
2. This will be followed by a career panel with professionals from industry 
   and academia to discuss alternative career paths. The panel will be 
   moderated by early career scientists Linus Schumacher (postdoctoral 
   fellow) and Alexandra Hogan (graduate student).
3. The last formal part of the workshop will be a session for researchers at 
   all career levels about the philosophical and administrative challenges 
   of multidisciplinary appointments. The interactive panel discussion will 
   be lead by Christina Cobbold, Adriana Dawes, Elissa Schwartz and Rebecca 
   Tyson, who either currently have joint appointments, or who have served 
   in an administrative capacity on joint appointments. This will be 
   followed by an open discussion for people to discuss some of the 
   potential obstacles and solutions for scientists who wish to 
   substantively bridge more than one academic discipline.
4. The workshop will conclude with dinner and informal discussions and 


From: Alexander Fletcher <a.g.fletcher@sheffield.ac.uk>
Date: Fri, Jun 3, 2016 at 5:45 PM
Subject: Society for Experimental Biology Cell Symposium, Sept 14-15, UK

Society for Experimental Biology Cell Symposium
"Bridging Scale in Models of Cell to Tissue Behaviour: Recent Progress and 
Future Challenges"
13-15 September 2016; Lady Margaret Hall, University of Oxford

Recent years have witnessed remarkable progress in molecular and 
live-imaging studies of cell and tissue biology, leading to large datasets 
that require careful interpretation. There has also been a dramatic increase 
in computational power. As a result, mathematical models play an ever 
greater role in helping us understand how subcellular phenomena, cell 
mechanical interactions and long-range signalling collectively give rise to 
tissue-level function. To understand tissue-level function, one must be able 
to integrate across temporal and spatial scales in addition to understanding 
each scale. Modelling at each scale can require very different areas of 
technical skills, while integration across scales necessitates the solution 
to novel mathematical and computational problems.

By bringing together interdisciplinary researchers working in a variety of 
different application areas, this workshop aims to identify the common 
mathematical challenges arising in the development of 'multiscale' models of 
biological systems and accelerate progress in this area. Immediately 
preceding the workshop there will be an optional one-day tutorial on Chaste 
(http://www.cs.ox.ac.uk/chaste), an open-source software tool for the 
simulation of multicellular models.

Confirmed keynote speakers:
 * Dr Katie Bentley (Beth Israel Deaconess Medical Center, USA)
 * Dr Jordi Garcia-Ojalvo (Universitat Pompeu Fabra, Spain)
 * Prof Henrik Jönsson (University of Cambridge, UK)
 * Prof Stanislav Shvartsman (Princeton University, USA)

Organised by: 
 * Prof Ruth Baker (University of Oxford, UK)
 * Dr Alexander Fletcher (University of Sheffield, UK)  

The Society for Experimental Biology (SEB), Multi-Scale Biology (MSB) 
Network and 2020 Science have some funding available to help support PhD 
students and early career scientists attend this symposium. For further 
details and to register, visit:


From: Paolo Zuliani <paolo.zuliani@newcastle.ac.uk>
Date: Sun, Jun 5, 2016 at 12:18 PM
Subject: Workshop: COMBINE 2016, Sept 19-23, Newcastle, UK

COMBINE 2016: 7th Computational Modeling in Biology Network Workshop
19-23 September 2016, Newcastle upon Tyne, UK

The "Computational Modeling in Biology" Network (COMBINE) is an initiative 
to coordinate the development of the various community standards and formats 
in systems biology and related fields. COMBINE 2016 will be a workshop-style 
event with oral presentations, posters, and breakout sessions. The five 
meeting days will include talks about the COMBINE standards and associated 
or related standardization efforts, as well as presentations of tools using 
these standards. Oral presentations will be selected from the submitted
abstracts. In addition, poster sessions will allow people to inform each 
other about their software and other projects in a setting that fosters 
interaction and in-depth discussion.

Abstract submission: 8 July 2016
Scholarship application: 8 July 2016
Notification: 15 July 2016
COMBINE Workshop: 19-23 September 2016

- Alfonso Bueno-Orovio (Oxford)
- Carole Goble (Manchester)
- Michael Hucka (Caltech)
- Dagmar Iber (ETH Zurich)
- Andrew Millar (Edinburgh)
- Chris J. Myers (Utah)
- Yujiang Wang (Newcastle)

Topics include, but are not limited to:
- Data exchange and model standards for systems biology
- Graphical notation standards for systems biology
- Standards for sharing and analysing biological pathway data
- Standards for computational biological models
More on the COMBINE standards at http://co.mbine.org/standards

We solicit high-quality abstracts, to be refereed by the COMBINE 
Coordinators below, for either oral or poster presentation at the Workshop. 
Abstracts will appear on the COMBINE website only, there will be no formal 

Please see the COMBINE website for submission instructions.

PhD students and postdocs may apply for travel funds to attend COMBINE. More 
information on the COMBINE website.

COMBINE 2016 is generously supported by:
- Engineering and Physical Sciences Research Council (UK) [AUDACIOUS project 
- Interdisciplinary Computing and Complex BioSystems Group (ICOS)
- School of Computing Science, Newcastle University
- National Science Foundation (USA)

Paolo Zuliani & Anil Wipat, ICOS Group, School of Computing Science, 
Newcastle University.

Gary Bader (Toronto)
Martin Golebiewski (Heidelberg)
Michael Hucka (Caltech)
Nicolas Le Novère (Babraham)
Chris J. Myers (Utah)
David Nickerson (Auckland)
Falk Schreiber (Monash)
Dagmar Waltemath (Rostock)


From: Ezio Venturino <ezio.venturino@unito.it>
Date: Wed, Jun 1, 2016 at 2:59 PM
Subject: Workshop: BIOMAT-2016, Oct 30 - Nov 5, People's Republic of China

Dear colleague,

I would like to draw your attention to the International Conference BIOMAT 
2016, which will be held in Tianjin, People's Republic of China, October 
30th - November 5th, 2016.

We stress that the BIOMAT 2016 will be held at the Chern Institute of 
Mathematics in Tianjin, People's Republic of China.

For this conference, the BIOMAT Consortium is offering 50 to 60 FELLOWSHIPS 
to support the local expenses. The deadline for abstract and full papers 
submission has been extended.

For the specific link to the 2016 conference, please see

Latex and Word templates for extended abstract and paper submissions are 
also available at this website.

The BIOMAT Consortium is an international non-profit association of 
scientific faculty members of universities and research institutions 
worldwide, their scientific research students as well as other interested
scientific practitioners on the areas of Mathematical Biology, Biological
Physics and the generic mathematical modelling of biosystems.

The fundamental mission of the BIOMAT Consortium is the enhancement of the
scientific activity of these areas on developing countries, by assembling 
together professionals, from mathematicians and physicists to biologists, 
research physicians and engineers in high level conferences. The only link 
which is supposed to exist among the attendees is the scientific interest on 
the mathematical and computational modelling of biological phenomena and on 
biologically-inspired approaches to these interdisciplinary fields.

For more information please visit the website http://biomat.org/

BIOMAT 2016 is the sixteenth event of the series, which took place in 
several countries in the past. for the full list, please visit

If interested in joining the event, please contact 

Ezio Venturino


From: Fabio Luciani <luciani@unsw.edu.au>
Date: Wed, Jun 8, 2016 at 11:37 AM
Subject: PhD Position: Bioinformatics/Computational Biology, UNSW, Australia

The Viral Immunology Systems Program (VISP) at the Kirby Institute for 
Infection and Immunity at the University of New South Wales, Sydney 
Australia is looking for PhD students to work on research projects in the 
area of bioinformatics / computational biology as well as statistical 
analyses that are aimed at understanding viral evolution and the role of 
host immune response. These projects and will involve high- throughput data, 
such as next-generation sequencing, as well as immunological data (flow-
cytometry, single cell sorting and sequencing of T and B cell repertoire).
The group has recently established single cell genomics laboratory assays to 
study antigen specific T cell responses and their subtype evolution during 
an infection.
Computational projects are suited to students with a strong background in 
quantitative disciplines such as Bioinformatics, Computer Science, Physics, 
Statistics, Mathematics or similar.  Successful applicants will join a team 
of researchers at the Kirby Institute and The School of Medical Sciences, 
which hosts > 140 PhD and Masters students and researchers in various field 
of Medical Sciences. There is also a great opportunity to interact with 
researchers involved in wet-lab activities.

We have recently established the VISP program and the web page is under 
construction. Additional information on the Computational Biology Group's 
research interests is available at:
Please include a cover letter and CV that provide details about research 
interests, education, employment history (if any), skills.
Post-graduate scholarships are available to support tuition and living 
expenses for domestic (Australian Postgraduate Award APA)

and overseas PhD students to study in Australia. More information on the 
postgraduate research scholarships is available at:
Top-up scholarships are available in our group for USD5-10K.

Interested applicants should contact Dr Fabio Luciani: luciani@unsw.edu.au.


From: John Walmsley <j.walmsley@maastrichtuniversity.nl>
Date: Tue, Jun 7, 2016 at 8:58 AM
Subject: PhD Position: Cardiac Modelling, Maastricht University, Netherlands

We have a PhD position in Maastricht with a closing date coming very soon. 
In this project, computer simulation of the failing heart will be combined 
with data from patients and animal experiments to determine how pacemaker 
therapy can be optimally delivered in the individual patient.

This would be a great opportunity for an applied mathematics / engineering 
masters student with an interest in cardiac research who's interested in 
working in a different country. The student will be based in Maastricht and 
collaborate closely with Bordeaux and Graz.

For further details, visit: http://www.academictransfer.com/33732

Interested candidates will need to send a cover letter and your CV to Joost 
Lumens, PhD (joost.lumens@maastrichtuniversity.nl) before June 10, 2016.


From: Ellie Murcia <murciae@OD.NIH.GOV>
Date: Tue, 31 May 2016 14:50:35 +0000
Resent-from: Raymond Mejía <mejiar@helix.nih.gov>
Subject: Request for Information from the NIH Common Fund

Request for Information from the NIH Common Fund: Characterizing and
Understanding the Organization of Individual Cells within Human Tissues

The NIH Common Fund has released a Request for Information (RFI) to
solicit input regarding a proposal for a new Common Fund program aimed at
characterizing and understanding organization of large numbers of primary
cells in human tissues using high throughput approaches. Recent advances in
multiplexed imaging, proteomics, genomics and transcriptomics are starting
to reveal that cells in tissues and organs are more heterogeneous and have
much richer organizational structure than previously thought. There is now
the opportunity to increase the throughput and apply these technologies
to identify the foundational principles underlying cellular organization
in human tissues that could lead to a new level of understanding in many
scientific areas.

The NIH seeks input from researchers, academic institutions, professional
societies, businesses, non-profit organizations, other government
agencies, and other stakeholders on the opportunities and challenges
with applying methods, approaches and technologies to enable the study of
entire organs at the individual cell level and cell interactions in situ
that form a functional tissue. The deadline for submitting information
is June 22, 2016. For further information, please see the RFI notice

The NIH Common Fund <http://commonfund.nih.gov/> (formerly the NIH Roadmap)
encourages collaboration and supports a series of exceptionally high impact,
trans-NIH programs. These programs are supported by the Common Fund, and
managed by the NIH Office of the Director in partnership with the various
NIH Institutes, Centers, and Offices.

The National Institutes of Health (NIH) - "The Nation's Medical Research
Agency" - includes 27 Institutes and Centers and is a component of the
U. S. Department of Health and Human Services. It is the primary federal
agency for conducting and supporting basic, clinical and translational
medical research, and it investigates the causes, treatments and cures for
both common and rare diseases. For more information about the NIH and its
programs, visit the NIH website <http://www.nih.gov/>.


From: Roland Owens <owensrol@mail.nih.gov>
Date: Wed, 1 Jun 2016 13:46:42 +0000
Resent-from: Raymond Mejía <mejiar@helix.nih.gov>
Subject: Selected NIH Intramural Research and other job openings - June 2016

Staff Scientist
Section on Development and Affective Neuroscience, NIMH
(Review of applications begins: July 1)

The Section on Development and Affective Neuroscience (SDAN) in the 
Intramural Research Program (IRP), National Institute on Mental Health 
(NIMH), seeks a Staff Scientist.

Research in SDAN is designed to achieve an integrated understanding of
brain system perturbations that occur in pediatric emotional disorders,
particularly anxiety disorders. SDAN then attempts to use this understanding
to identify children at particularly high risk, to improve current treatments,
and to develop new ones. Current projects in SDAN examine the predictive
utility of functional magnetic imaging (fMRI) profiles for diverse clinical
outcomes, applied in research on children and adolescents at temperamental
risk for anxiety or receiving treatment for anxiety.

The NIMH IRP brings together a highly interactive and dynamic group of
collaboratively focused scientists. These individuals are at the forefront
of research on mental disorders. SDAN is housed on the main NIH campus in
Bethesda, Maryland.

The SDAN Staff Scientist serves as a laboratory leader who contributes
to mentoring of postdoctoral fellows and other laboratory staff and
trainees. The position requires specific expertise in the analysis of
fMRI data, as reflected in training and publication record. The successful
candidate should have a doctoral degree, postdoctoral research experience,
and an outstanding publication record. Requisite expertise includes basic
analysis of fMRI data using the general linear model as well as expertise in
more advanced approaches to fMRI data. The main job of the Staff Scientist
will be to be the leader of data analytic approaches in SDAN and to apply
advanced analytic approaches in particular, with a focus on computational
neuroscience, multivoxal pattern analysis (MVPA), and machine learning. 
Salary is commensurate with experience.

Applicants should submit their curriculum vitae with bibliography, statement
of interest, and names and contact information for three references to Daniel
Pine at daniel.pine@nih.gov. Applications will be reviewed starting July 1,
2016, and accepted until the position is filled. HHS, NIH, and NIMH are 
equal opportunity employers.

The NIH Intramural Research Program

Link to Fellowships and Positions of Interest to fellows

Link to NIH Jobs


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