SMB Digest Volume 19 Issue 22

July 5, 2019
This issue’s editor:


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Issue’s Topics:
Workshop: Devel…. Simul. w/CompuCell3D, Aug 11-17, Indiana U
Special Session: Comp. Proteomics, NETTAB, Nov 11-13, Italy
PhD Position: Machine Learn. & PRRSv Epid., North Carolina St U
PhD Position: Environmental Science, Lund U, Sweden
PhD/Post-doc Positions: HIV Latency Modelling, UNSW Sydney
Post-doc: Intra-cellular Viral Dynamics, U Leeds, UK
Post-doc: Gene Network Evol. & Anatomical Complexity, Barcelona
Post-doc: Mathematical Modelling of the Thymus, U Oxford
Post-doc: Utilising Data Assimilation to Model…, U Nottingham
Senior Researcher: Math Biology, QIMR Berghofer, Australia
Positions: Math Modeling, Applied BioMath, US
SMBnet Reminders


from: Andy Somogyi <>
date: Jun 29, 2019, 1:11 PM
subject: Workshop: Devel…. Simul. w/CompuCell3D, Aug 11-17, Indiana U

We are pleased to announce the 14th User Training Workshop: Developing
Multi-Scale, Virtual-Tissue Simulations with CompuCell3D, which will
take place at Indiana University, Bloomington, Indiana, USA between
August 11th and August 17th, 2019. This workshop should be of interest
to SIAM members in the areas of Life Sciences, Dynamical Systems,
Supercomputing and Computers in Science and Engineering.

Mechanistic modeling is an integral part of contemporary bioscience,
used for hypothesis generation and testing, experiment design and
interpretation and the design of therapeutic interventions. The
CompuCell3D modeling environment allow researchers with modest
programing experience to rapidly build and execute complex Virtual
Tissue simulations of development, homeostasis, toxicity and disease in
tissues, organs and organisms, covering sub-cellular, multi-cell and
continuum tissue scales. Virtual-Tissue simulations developed using
CompuCell3D run on Windows, Mac and Linux. CompuCell3D is open source,
allowing users to extend, improve, validate, modify and share the core
software. By the end of this one-week course, participants will have
implemented a basic simulation of their particular biological problem of
interest. Post-course support and collaboration will be available to
continue simulation development.

Because the number of places is limited, admission is by application
only. To apply for admission, please visit the school website

July 20th, 2019. However, we strongly encourage early applications.
Applications will be processed as received. Please do not make travel
arrangements until you have received a notice that your application for
admission has been accepted.

For more information, please see our announcement at


from: Romano Paolo <>
date: Jul 2, 2019, 5:08 AM
subject: Special Session: Comp. Proteomics, NETTAB, Nov 11-13, Italy

I’m glad to inform you that the NETTAB/BBCC 2019 joint meeting has
recently been recognized as ISCB Affiliated Conference. Moreover, we
have just established a collaboration with the ELIXIR Proteomics
Community that will support participation of ELIXIR members to the

As a consequence, the deadline for submitting four-page abstracts for
oral presentations has been postponed to Monday July 15, 2019.

For further information, see last week’s announcement.


from: Gustavo Machado <>
date: Jun 26, 2019, 11:44 AM
subject: PhD Position: Machine Learn. & PRRSv Epid., North Carolina St U

PhD opportunity on machine learning and porcine reproductive and
respiratory syndrome virus (PRRSv) epidemiology

An exciting USDA-NIFA-PhD funded position is offered at the Department
of Population Health and Pathobiology at North Carolina State University
College of Veterinary Medicine, is now open.

This research aims the development of new machine learning algorithms to
predict the risk of porcine reproductive and respiratory syndrome virus
(PRRSv) spread and further introduction to promote informed and targeted
disease management and prevention.

This PhD project is research and extension integrated:
a) Research (80%) includes the selection and validation of
machine-learning algorithms to calculate the predicted risk of PRRSv
introduction, and to generate ranked lists by relevance of each
biosecurity measure for each farm (Machado et al., 2015, 2019).
b) Extension (20%) includes the promotion of the use of PRRSv risk of
introduction in disease management and prevention through
producer-oriented extension and by building online reporting system for
data sharing and reporting.

Candidates must provide advanced skills in epidemiology or quantitative
discipline (ecology, epidemiology, applied mathematics, physics,
statistics) (master level or equivalent) and scientific writing.
Shortlisted candidates will be invited for interview (by distance if

The position is based within Dr. Gustavo Machado laboratory at NCSU with
collaboration from Iowa State University Dr. Daniel Linhares and
Dr. Derald J Holtkamp.

Applications shall include:
1) a cover letter of no more than two pages that highlights your
research interests, interest in graduate school, interest in infectious
diseases, and why we should consider your application
2) curriculum vitae
3) unofficial transcripts
4) sample of scientific writing (e.g., a manuscript in preparation,
an undergraduate thesis, published manuscript as the first author)
5) contact information for 3 references who can explain your research
skills and interests. References will only be contacted after applicants
are notified.

If you have questions specific to the positions please contact
Gustavo Machado at


from: Mikael Pontarp <>
date: Jul 1, 2019, 9:45 AM
subject: PhD Position: Environmental Science, Lund U, Sweden

Doctoral student in environmental science
Lund University, Centre for Environmental and Climate Research

Modelling effects of eco-evolutionary dynamics on ecosystem services in
heterogeneous agricultural landscapes

Sustainable agriculture is promoted by ecosystem services like
pollination and natural biological control of pests. Strengthening such
services may result in increased yields and reduced agro-chemical
inputs. Our ability to study and optimise ecosystem services is,
however, limited. The project aim is to study the mechanistic link
between farmland heterogeneity at various spatial scales and
spatiotemporal dynamics of service providing organisms (e.g. spiders,
ground beetles, and parasitoid wasps). We will answer calls for an
eco-evolutionary, trait-based, and spatially explicit perspective on
ecosystem services and the student should thus have knowledge of how
ecological interactions, evolution, and dispersal of organisms may
affect population dynamics. An important project component is to test
models against empirical patterns through parametrization and validation
of the models. There will be a focus on data on agro-ecosystems,
including crop rotation, functional traits and insect population
dynamics. The student should thus have knowledge in database handling
and data analysis. By fitting models to data, the aim is to quantify the
processes that are active in the study system and to communicate ways of
optimizing biological control to stakeholders and policymakers.

Last application date: 2019-08-30
Link to ad for more details:


from: Miles Davenport <>
date: Jun 27, 2019, 11:17 PM
subject: PhD/Post-doc Positions: HIV Latency Modelling, UNSW Sydney

PhD studentship and Post-doc in modelling HIV latency.

The infection Analytics team at UNSW Sydney is seeking both a PhD
student and a post-doc / research fellow in mathematical biology, to
model infection dynamics in HIV infection.

The Infection Analytics Program at the Kirby Institute is an
interdisciplinary team including applied mathematicians, physicists, and
computer scientists, who collaborate widely with around 30 experimental
groups around the world to model within-host and epidemiological aspects
of infection and immunity. The group has a high publication output and a
strong history in successful interdisciplinary training. It is an ideal
venue for students with a quantitative background (mathematics/physics/
statistics) aiming to establish themselves in mathematical biology.

UNSW Sydney is a ‘top 50’ ranked global university, situated 5 km (3
miles) from Central Sydney, and 1.5 km (1 mile) from Sydney’s beaches.

More information on the group’s research is available at the Infection
Analytics website:

PhD studentship:
Applicants are sought for both local and International student
scholarships for PhD studies. These scholarships cover tuition and
living expenses (with stipends ranging from approx. $35,000 – $40,000
p.a., depending on scholarship). PhD studies generally last 3.5 years.

The scholarships are highly competitive. For local students, first class
honors is usually required. For international students, a high GPA
(first class honors or equivalent. High ranking in class)
+/- publications are required.

Applications for January 2020 close on early September for International

Interested students should forward a CV and outline of interests to
Professor Miles Davenport (

Post-doctoral Fellow

About the role
$75k- $123k p.a. plus 17% superannuation and leave loading
3 years
Full-time or part-time.

The position of Post-Doctoral Fellow will be responsible for
mathematical modelling of experimental data from animal models and human
infection. This will involve developing familiarity with the HIV
literature and underlying biology, biostatistical analysis, and ODE and
stochastic modelling.

To be successful in this role you will:
-Demonstrated mathematics, statistics, or computer programming skills
relevant to modelling of experimental data.
-Interest in modelling in immunology and infection dynamics.
-Proven evidence of publications in peer reviewed journals.
-Success in funding applications, student supervision and superior
publication output required at the higher levels.
-PhD in mathematics / physics/statistics or other quantitative

The advertisement can be found on the UNSW website:

Closing date: 16 August 2019


from: Carmen Molina-Paris <>
date: Jun 29, 2019, 4:21 AM
subject: Post-doc: Intra-cellular Viral Dynamics, U Leeds, UK

We are looking for a Research Fellow in Mathematical and Statistical
Models of intra-cellular viral dynamics to join our project on the
estimation of a human dose range for VH244 for the prevention and
treatment of respiratory infections. You will work together with teams
at the University of Leeds and Virion Biotherapeutics (VB) to
mathematically, statistically and computationally characterise the
dynamics of respiratory virus infection and a therapeutic interfering
particle (TIP), making use of experimental data.

You will have a PhD in Applied Mathematics, Physics or a closely allied
discipline. You will also have a strong background in mathematical
biology, multi-scale modelling, agent-based modelling, and statistical
inference and multi-variate analysis; as well as in theoretical
immunology and infection, and mathematical, statistical and
computational modelling of immune responses. In addition, you will have
the ability to conduct independent research and a developing track
record of publications in international journals, alongside excellent
communication, planning and team working skills.


from: Isaac Salazar Ciudad <>
date: Jul 1, 2019, 4:29 AM
subject: Post-doc: Gene Network Evol. & Anatomical Complexity, Barcelona

Barcelona_Postdoc: Mathematical biology: Evolution of gene networks and
the origins of organismal complexity.

2,5 years postdoc in mathematical evolutionary and developmental biology
in Barcelona.

The job is the Autonomous University of Barcelona (UAB) and in the
Centre de Recerca Matemàtica (CRM). The CRM is in the UAB campus.

The main project questions are:
How should gene networks and cell interactions be organized to lead to
biological complexity?
How is such organization achieved in evolution?
How does gene network organization affect variational properties of the
phenotype (e.g. evolvability)?
Any other question of the applicants interest that is related to the
previous questions.

We will use computational models of the genotype-phenotype map and
computational models of evolution by natural selection to study such
questions for the case of organismic complexity (e.g. anatomy). The
genotype-phenotype maps models we develop are based on realistic gene
network models of pattern formation and morphogenesis that lead to
realistic 3D multicellular phenotypes.

The position is in Salazar-Ciudad’s group. Salazar-Ciudad’s group is
between the Genetics department in the UAB ( and the CRM: and

Job description
The main tasks of the post-doc include using and modifying existing
models of embryonic development (e.g. EmbryoMaker) in order to simulate
the development of complex phenotypes. These models will be combined
with models of evolution, in a population context with mutation, genetic
drift and natural selection on morphology (see for example
Salazar-Ciudad and Marin-Riera, 2013). The gene networks found to lead
to the development of complex and robust phenotypes in evolution would
be analyzed to extract general regularities, if any, these gene networks
need to fulfill. The main tasks, thus, consist in simulation,
theorizing, data analysis, scientific programming, literature searching,
writing and presenting results in conferences. The post-doc is expected
to lead part of the project and develop his/her own research questions
within the general framework of the project. We, thus, seek candidates
highly motivated for theoretical work and data analysis with a broad
understanding of the evolutionary theory and/or developmental biology
and/or modeling.

-The applicant should hold a PhD in either mathematical biology,
evolutionary biology, developmental biology, systems biology, biophysics
or theoretical biology.
-Scientific programming skills or a willingness to acquire them is
-The most important requirement is a strong interest and motivation.
A capacity for creative and critical thinking is also required.

The application must include:
-Application letter including a statement of interests and motivation.
-CV (including publications, the contribution of the applicant in each
publication, degrees obtained, subjects included in degree and grades,
average grade).

Foreign applicants, especially non-EU applicants, should attach an
explanation of their University’s grading system. All documents should
be in English, no official translation is required in the initial
application but may be requested afterwards.

-Applications should be sent to Isaac Salazar-Ciudad by email:

The start date is negotiable between autumn 2019 and early 2020.


from: S. Jon Chapman <>
date: Jul 2, 2019, 9:35 AM
subject: Post-doc: Mathematical Modelling of the Thymus, U Oxford


This is a 30 month fixed-term position to work with Prof Jon Chapman,
part of a large multidisciplinary project, and is available for an
immediate start.

The overall aim of the project is to create a fully functional thymus in
the lab, by using cutting-edge stem cell biology with biomaterials
engineering and advanced mathematics. This holder of this position will
develop quantitative mathematical models of thymus development, informed
by experimental results and guiding the tissue engineering approaches. A
wide range of mathematical ideas will be explored. A network analysis of
gene expression data will be used to identify key checkpoints associated
with cell differentiation. This will be used to develop and inform
population dynamics (ordinary differential equation) models of cell
growth and differentiation. In turn these will be extended to include
spatial effects such as cell-cell and cell-substrate signalling to
develop partial differential equation models of tissue development. The
analysis of these models will involve a combination of asymptotic and
numerical methods.

Candidates should be familiar with either differential equations and
asymptotic methods, or network analysis and statistical methods, and be
prepared to learn techniques they are unfamiliar with.

Applications for this vacancy are to be made online. To apply for this
post and for further details, including the job description and
selection criteria, please click on the link below:

Only applications received before 12:00 noon UK time on Friday 2nd
August 2019 can be considered.


from: Stephen Coombes <>
date: Jul 4, 2019, 12:07 PM
subject: Post-doc: Utilising Data Assimilation to Model…, U Nottingham

Fellowship in Mathematical modelling of physiological dynamics utilising
data assimilation

This is an exciting opportunity to join the research team in the
Precision Imaging Beacon of Excellence and Sir Peter Mansfield Imaging
Centre, who are driving the discovery and translation of new imaging
tools that will transform non-invasive diagnosis, improve the outcomes
for patients, and better evaluate the success of medical interventions.

Our Precision Imaging Fellowship scheme is aimed at early career
researchers from any discipline who have recently completed their
doctoral studies and show promise for an outstanding career in medical
imaging research. Fellows are expected to undertake a substantive piece
of independent work that contributes to the aims of the Beacon Research
Programme, and to complete a newly designed portfolio training
programme to support the transition to an externally-funded fellowship.
Supervision and individual mentorship will be offered by a range of
world-leading experts in imaging, clinical research, mathematical
modelling and computer science.

Strategic areas
To be eligible, candidates should have a research background, skill-set
and strong interest supporting translational and clinical imaging
research in one or more of the following areas:
-Mathematical modelling of physiological dynamics utilising data
-Under sampling in MRI
-Physiological MRI (e.g., perfusion and/or CEST MRI)
Each fellowship offers:
-Two years of independent funding (which may be extended by one year
subject to performance), to conduct research and develop an
externally-funded fellowship application, to be held at the University
of Nottingham.
-Salary at a level on the R&T4 University salary scale dependent on
-Extensive career development support, including individual mentoring
and participation in the FAST training scheme.
-Pump-priming research support of £10,000.
-The opportunity to spend up to 3 months abroad to develop international

Eligibility: Candidates must have been awarded their PhD. This scheme is
aimed at early career researchers, and candidates do not normally have
more than 4 year’s postdoctoral experience. However, there are no
eligibility rules based on years of post-doctoral experience as this
doesn’t allow for variations of career paths across disciplines.
Candidates will be assessed on their quality, potential and track
record, relative to their career stage.

To apply please go to our vacancies page here.


from: Peter ORourke <>
date: Jul 1, 2019, 12:30 AM
subject: Senior Researcher: Math Biology, QIMR Berghofer, Australia

We have advertised for a senior researcher to lead mathematical biology
(Ref No 12552) in our unit at QIMR Berghofer, Australia. The
advertisement can be accessed through SEEK and the QIMRB Careers Page.


from: Helen Moore <>
date: Jul 1, 2019, 4:09 PM
subject: Positions: Math Modeling, Applied BioMath, US

We’re hiring math modelers! Do you have (or will you soon have) a PhD in
math, applied math, math biology, biomedical engineering, or related
areas? Have you created ODE models of diseases and drug dynamics? Are
you passionate about making a difference in the lives of patients? Then
we want to talk with you!

Applied BioMath (currently 30 people and growing steadily) provides math
modeling support to biopharma companies in finding and developing
therapies for patients. If you have strong mathematical, computational,
and communication skills, and some knowledge/interest in biology, you
could be a good candidate for one of our current or future openings
( We’re hiring in both
Oakland, CA and Concord, MA. We value work-life balance, diversity, and
inclusiveness in the workplace.

Email me if you’d like more info about our openings or what it’s like to
be a mathematician in industry. Also, I will be attending the SMB
meeting in Montreal July 22-25 and would be happy to meet with you

Helen Moore, PhD
Director of Applied Mathematics
Applied BioMath
561 Virginia Road, Suite 220
Concord, MA 01742


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