SMB Digest Volume 18 Issue 7

February 14, 2018
This issue’s editor:

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Issue’s Topics:
Peer Networking Event for Early Career Women in Mathematical Biology
Summer School on Quantitative Biology, June 25-29, Nice, France
Boston University Summer Institute in Biostatistics
CBMS Conference: Computational Methods in Optimal Control, July 23-27
5th International Conference on Algorithms for Computational Biology
Graduate Student Modeling Workshop (IMSM 2018), July 15-25
Bi-Monthly News from NIMBioS
Call for Chapters: Automated Reasoning for Systems Biology and Medicine
PhD Position: Computational Biology, Systems Medicines
PhD Studentship: Systems Biology of Psoriasis: Bridging the Gap …
Up to 8 PhD Fellowships: Cognitive Neuroscience at SISSA, Trieste
Postdoc Position: Multiscale Modeling, UConn Health
Postdoc Position: fruit modeling, INRA Avignon, France
NIH HPC Group is Hiring Systems Administrators and Scientists
SMBnet Reminders


from: Natalie Lemanski <>
date: Sat, Feb 10, 2018 at 12:17 AM
subject: Peer Networking Event for Early Career Women in Mathematical Biology


We are seeking undergraduate and graduate women in mathematics or mathematical
biology to participate in a peer networking workshop at The University of
Tennessee, Knoxville, coinciding with the Applications of Spatial Data:
Ecological Niche Modeling tutorial taking place at NIMBioS(National Institute
for Mathematical and Biological Synthesis) from May 16th-18th.

This workshop, fully funded by the Association for Women in Mathematics, will
provide early-career women with the opportunity to meet with female mentors in
a small group setting. During the workshop, participating students will
collaborate to interview mentors and produce videos documenting their career
trajectories and research. Mentors will be selected from faculty attending the
tutorial, University of Tennessee – Knoxville faculty, and Oak Ridge National
Laboratory researchers. If you or someone you know are interested in
attending, please go to to apply. Any
questions regarding the event or application can be directed to Applications are due March 30th.

Thank you,

Jessica Beck and Natalie Lemanski


from: Fai, Thomas <>
date: Sat, Feb 10, 2018 at 3:23 PM
subject: Summer School on Quantitative Biology, June 25-29, Nice, France

We are excited to announce the program for our international summer school on
quantitative biology from June 25-29, held at hotel Saint Paul right on the
water in Nice, France. The main goal of this school is to engage the students
in truly interdisciplinary science, and lead a cooperative reflection on the
goal of quantitative efforts in biology. We welcome an interdisciplinary crowd
of students and researchers and propose a variety of formats, including
lectures, discussions, talks, flash presentations, poster sessions and group
work. Twelve fellowships are available to support participation of students
from developing countries.


Apply by March 1st:

Agnese Seminara, Chris Rycroft, Thomas Fai, and Madalena Neri

Questions? Email


from: Hicks, Jacqueline Milton <>  
date: Sat, Feb 10, 2018 at 8:12 PM
subject: Boston University Summer Institute in Biostatistics

My colleague and I run the Boston University Summer Institute for Research
Education in Biostatistics (BU SIBS) which introduces students to the field of
Biostatistics; a vibrant and growing career path that they may not have
considered. This program is motivated by the shortage of statisticians working
in health and science related fields. BU SIBS introduces students to the field
of Biostatistics with modules in statistics, epidemiology, statistical genetics
and clinical trials. The program is hands on and includes teaching data sets
and speakers from the Framingham Heart Study (a study of mostly Caucasian
individuals ongoing since 1948) and the Jackson Heart Study (the largest
genetic study of African American individuals) and encompasses relevant topics
such as obesity, health disparities, big data, research ethics, and career
development. Travel, tuition (4 credits earned), room and board are funded for
all students attending. We are seeking to engage a diverse group of students to
participate. We welcome faculty or students with interest or questions about
the program to contact one of us via email (
Applications will be evaluated on a rolling basis with priority given to those
received prior to March 5, 2018.

We would appreciate it if you would share this information with your students
and any colleagues who have contact with undergraduate students with math,
science or other quantitative backgrounds.


from: Liu, Jun <>
date: Sun, Feb 11, 2018 at 1:41 PM
subject: CBMS Conference: Computational Methods in Optimal Control, July 23-27

The NSF-CBMS conference on “Computational Methods in Optimal Control”, will be
held at the Jackson State University, Jackson, Mississippi, during July 23-27,
2018. The principal lecturer will be Dr. William W. Hager from the University
of Florida. Dr. Hager will deliver ten lectures on state-of-the-art
computational methods on optimal control in the morning sessions, which are
accompanied with lab sessions in the afternoon. The lectures and labs are
designed to provide both the background needed to analyze convergence of
discrete approximations and solution techniques in optimal control, and
practical experience in solving real-world problems. Additional invited
speakers will give introductory talks that focus on computational methods for
PDE optimal control problems. The anticipated participants include faculty,
postdoctoral fellows, and graduate students.

This conference is supported by a grant from the National Science Foundation
(DMS-1743826). Limited travel support is available to selected participants.
Graduate students, recent PhDs, and members of under-represented groups in
mathematics and related disciplines are especially encouraged to apply.

The registration form for attending this conference is now open, participants
can register at the conference website:

Deadline for requesting travel support: May 1, 2018.
Deadline for attendance registration: July 1, 2018.

Should you have any questions,
please feel free to contact Dr. Jun Liu via email:


from: GRLMC <>
date: Thu, Feb 8, 2018 at 2:43 AM
subject: 5th International Conference on Algorithms for Computational Biology



AlCoB 2018 Hong Kong June 25-27, 2018 Co-organized by: The Hong Kong
Polytechnic University Department of Computing

Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University


from: Mansoor Haider <>
date: Tue, Feb 13, 2018 at 4:08 PM
subject: Graduate Student Modeling Workshop (IMSM 2018), July 15-25

The 24th Industrial Mathematical & Statistical Modeling (IMSM) Workshop for
Graduate Students will take place at North Carolina State University, between
15-25 July 2018. The workshop is sponsored by the Statistical and Applied
Mathematical Sciences Institute (SAMSI) together with the Center for Research
in Scientific Computation (CRSC) and the Department of Mathematics at North
Carolina State University.

The IMSM workshop exposes graduate students in mathematics, engineering, and
statistics to exciting real-world problems from industry and government. The
workshop provides students with experience in a research team environment and
exposure to possible career opportunities. On the first day, a Software
Carpentry bootcamp will bring students up-to-date on their programming skills
in Python/Matlab and R, and introduce them to version control systems and
software repositories.

Local expenses and travel expenses will be covered for students at US
The application deadline is April 15, 2018.
Information is available at
and questions can be directed to

With best regards,
Mansoor Haider, Ilse Ipsen, Pierre Gremaud, and Ralph Smith


from: (NIMBioS) <>
date: Thu, Feb 8, 2018 at 9:49 AM
subject: Bi-Monthly News from NIMBioS



from: Paolo Zuliani <>
date: Sat, Feb 10, 2018 at 11:20 AM
subject: Call for Chapters: Automated Reasoning for Systems Biology and Medicine

Book title: Automated Reasoning for Systems Biology and Medicine

Editors: Pietro Lio’ (University of Cambridge, UK) and
Paolo Zuliani (Newcastle University, UK)

Publisher: Springer (Computational Biology Series), Summer 2018.

Deadline: 15 April 2018

The aim of this volume is to present the very best research in an exciting new,
multidisciplinary area: the application of formal, automated reasoning
techniques for the analysis of complex models in systems biology and systems
medicine. We believe this volume will facilitate and foster the cross talk
between physicians, statisticians, and computer scientists. For this purpose,
we also welcome contributions from medical statisticians, machine learning
researchers, and physicians.

Automated reasoning is the field of computer science devoted to the development
of algorithms that return trusted answers, so that sound logical reasoning can
be built upon. For example, formal verification is instrumental in the
semiconductor industry to make sure that chip designs are free from defects (or
‘bugs’). Systems biology and systems medicine are recent attempts at
understanding the enormous complexity of life from a computational point of
view. They have generated a wealth of new knowledge in the form of
computational models whose staggering complexity makes manual analysis methods
unfeasible. Sound, trusted, and automated ways to analyse such models are thus
required in order to be able to trust the models’ conclusions. Overall, this is
crucial to engineering safe biomedical devices and to reducing our reliance on
wet-lab experiments and clinical trials, thus reducing both economic and
societal costs.

Some examples of the questions tackled in the area include: can we
automatically revise medications in patients with multiple chronic conditions?
Again, can we verify that an artificial pancreas system delivers insulin in a
way that Type 1 diabetic patients never suffer from hyperglycaemia or
hypoglycaemia? Can we predict the phenotype given the genotype? Can we model
the evolution of an acute or chronic disease and marker remodulation?

This volume aims at bringing together researchers from a number of highly
interdisciplinary areas including, but not limited to (in alphabetical order):

– Artificial organs: principles and models
– Big data analytics in precision medicine
– Cost-effectiveness analysis alongside clinical trials
– Decision making in health care
– Digital pathology
– Disease, multimorbidity and comorbidity management
– Drug repurposing, proof-of-concept trials, and pharmacoepidemiology
– Formal methods for systems biology
– Hypothesis generation from experimental data
– Inductive logic
– In silico trials analysis
– Machine learning (including deep learning)
– Mathematical models in health care and systems biology
– Medical ontologies
– Model selection
– Network structure identification, network meta-analysis
– Parameter inference from time series and longitudinal data
– Precision/Personalised medicine
– Synthetic biology
– Systems biology
– Systems medicine
– Verification for healthcare technologies (e.g., biomedical devices)
– Virtual patient modelling and repositories
– Whole-cell models


Extended abstract due: 28 February 2018
Feedback on abstract: within 3-4 days from submission
Full submission due: 15 April 2018

Page limit: 25 (excluding references)

Prospective authors should submit an extended abstract (max 500 words) of their
planned contribution, in order for the Editors to advise authors whether their
contribution fits the volume’s scope and aims, and to facilitate the reviewing
process. The Editors reserve the right to reject without review any
contribution deemed unfit. Submissions within the scope and aims of the volume
will be rigorously reviewed by at least two anonymous referees.

Abstracts and (original, previously unpublished) manuscripts should be
submitted for consideration through EasyChair at the page:

Please prepare your manuscript following the Volume Manuscript Guidelines, with
reference style Basic:


from: Esteban Vargas <>
date: Fri, Feb 9, 2018 at 6:42 AM
subject: PhD Position: Computational Biology, Systems Medicines

PhD Position in Computational Biology

The group of Systems Medicine ( invites applications
for a full-time PhD position in Computational biology. The successful
candidate will receive a scholarship for 3 years. Major duties: · Develop
mathematical models describing diseases using deterministic models, stochastic
models, and compartmental models. · Analyze clinical and experimental data
from collaborators using machine learning and bioinformatics approaches. ·
Develop novel algorithms to treat diseases. · Publish research findings in
scientific journals and present them at major scientific meetings.
Qualifications: · A bachelor/MSc degree in a quantitatively-oriented field,
such as engineering, computer science or applied mathematics. · Excellent
command of English. · Knowledge in analytical and quantitative methods. ·
Experience in MATLAB or R, and LaTex. · Knowledge of immunology is a plus.

Please send questions or your application with a motivation letter, outlining
your interest in a PhD position, along with your curriculum vitae which should
include the names and contact details of three referees, to

Positions are open until filled. The planned start date is in September 2018
but can be negotiated.


from: Paolo Zuliani <>
date: Sat, Feb 10, 2018 at 11:28 AM
subject: PhD Studentship: Systems Biology of Psoriasis: Bridging the Gap …

At the School of Computing of Newcastle University (UK) I have available a PhD
studentship on ‘Systems Biology of Psoriasis: Bridging the Gap between Computer
and Clinic’. The project involves 1) the development and use of machine
learning techniques for identifying personalised phototherapy treatments for
psoriasis; and 2) the clinical evaluation of the treatments, in collaboration
with a local hospital (Royal Victoria Infirmary).

For more information and to apply:


from: Alessandro Treves <>
date: Tue, Feb 13, 2018 at 12:15 PM
subject: Up to 8 PhD Fellowships: Cognitive Neuroscience at SISSA, Trieste

SISSA is an elite postgraduate research institution, focused on Maths, Physics
and Neuroscience. It operates in English: many among its students and faculty
are not Italian. Campus above Trieste, overlooking the Gulf. Research
approaches in the CNS PhD span the range from
cognitive psychology and imaging in humans to behavioural neuroscience and
multiple single-unit recording in rats, mathematical and computational
modeling; with research groups led by Domenica Bueti, Davide Crepaldi, Mathew
Diamond, Chris Mathys, Raffaella Rumiati, Alessandro Treves and Davide
Zoccolan. Allied approaches are pursued in other SISSA PhDs. All admitted
students receive a 4-year fellowship and engage full-time in research based in
Trieste, with limited coursework in the first few months, talks and seminars
throughout the year and a TEX event in the summer, see

First deadline for EU candidates: March 2, 2018, for nonEU: March 31, 2018


from: Laubenbacher,Reinhard C. <>
date: Thu, Feb 8, 2018 at 10:54 AM
subject: Postdoc Position: Multiscale Modeling, UConn Health


The Laubenbacher Research Group at UConn Health and the Jackson Laboratory for
Genomic Medicine has an immediate opening for a postdoctoral researcher to join
an interdisciplinary team focused on an NIH-funded project to develop new
software design approaches to multiscale computational modeling. The
application area is the innate immune response to fungal infections in the
lung. For more details see
The project team combines expertise in mathematical modeling, pulmonary
immunology, and scientific visualization. The position is for two years, with
the possibility of an extension. The researcher to fill this position will play
an important leadership role in the development of innovative approaches to
disease models in biomedicine. The Laubenbacher Group has several other ongoing
and planned multiscale disease modeling projects that will also benefit from
this research.

An important focus of the project is on the design of novel software
architectures for multiscale models, combining a strongly modular design with
Dockerization to build models that are easily extendable, modifiable,
shareable, and whose output is reproducible. Innovative visualization
techniques will make the models usable by non-modelers.

We are looking for a researcher who has experience with up-to-date software
design approaches in the context of multiscale mathematical and computational
modeling, the use of Docker containers, and familiarity with popular
programming languages, such as Java, Python, and C++. Previous experience in
implementing parallel and multithreaded applications is required. A strong
mathematical background related to various aspects of dynamic models would be a
great plus.

Please direct inquiries to Reinhard Laubenbacher,


from: valentina baldazzi <>
date: Thu, Feb 1, 2018 at 3:51 AM
subject: Postdoc Position: fruit modeling, INRA Avignon, France

Key words : plant physiology, apple, modeling, optimisation, post-harvest, fruit quality, fruit processing

The proposal is part of a research project (Interfaces) which deals with the
interface between raw material production and processing. The post-doctorate
will have to improve the understanding of fruit quality build-up from the raw
material to the processed product (i.e., from the pre-harvest stage in the
field to fruit storage and processing stages).
He/she will focus on two specific points: macronutrients (sugars and acids) and
structural material (as relevant for texture), and consider their control by
climatic conditions and agronomical and processing factors. The impact of
practices, maturity and storage (temperature and/or duration effect), and
process, on the availability of carbon and water and on the mechanical and
chemical properties of cells and cell wall, will be looked upon.
The approach will be based on modelling. The post-doctorate will first
contribute to deliver an agro-ecophysiological model of fresh apple fruit based
on an existing virtual fruit model (Fishman and Génard, 1998; Génard et al.,
2010). The model will predict growth and the accumulation of macronutrients and
structural material.

The post-doctorate will parameterize and test the model during the pre-harvest
phase. With such a model it will become possible to simulate the allocation of
assimilates and water to the fruit and to predict the effect of environment and
management on fruit quality at harvest. The model will also be adapted and
tested for its ability to predict the evolution of apple fruit quality during
the post-harvest storage period. A focus will be on the impact of storage
conditions (mostly storage duration) on the evolution of maturity and quality
traits after harvest and prior to processing. The post-harvest model for fruit
storage will focus on changes in water balance, turgor pressure, cell adhesion,
starch degradation and acids metabolism.
This agro-ecophysiological model of fresh apple fruit will be then connected to
a product processing model relying the characteristics of processed apples to
those of fresh apple. This product processing model will be done by another
team involved in the interface project.

Finally, the modeling framework will be used to find in silico the orchard
management practices and the fruit storage – ripening conditions that optimise
quality criteria of interest for processed apple fruits.

The postdoctoral scientist will benefit from a strong scientific background of
the host institution in plant sciences, in particular crop ecophysiology. He/
she will have access to a computing cluster for intensive calculation used for
He/she will have access to continuing training, scientific and technical
information, editorial online resources, as well as all scientific computing
tools of INRA. He/she will benefit from the social policies of the Institute in
the enjoyable campus of Avignon. Scientists at Avignon campus have access to a
broader science environment, conducive to cross disciplinary research.

Required Skills
We are looking for a self-motivated individual with strong communication and
organization skills, who will have completed a Ph.D. thesis in Plant Sciences,
Information Sciences, Agronomy or Horticulture, with an experience in modeling
and a publication record. Knowledge of programming languages (Java, Python, C+
+,…) and experience in statistical tools (R) will be an asset. Ability to
communicate in English both orally and in writing is essential.

Growth, Architecture and Quality (CRAQ)) team, Research Unit 1115 «
Horticultural Plants and culture Systems », INRA, Domaine Saint Paul, Site
Agroparc, CS 40509, 84914 Avignon Cedex 9, France

Between 2200€ and 2900€ gross, depending on prior experience.

12 months (initially 6 months, extension of contract after revision of goals).
The position will start in mid-2018. Open until filled.

Your application should include a cover letter, with a brief description of
your research interests, a detailed CV (including a list of publications) and
the names and addresses of at least two references. The deadline to send your
application is April 15th, 2018.


from: Fellini, Steve (NIH/CIT) [E] <>
date: Monday, February 12, 2018 10:35
resent-from: Mejia, Raymond (NIH/NHLBI) [E] <>
subject: NIH HPC Group is Hiring Systems Administrators and Scientists

Join the NIH High Performance Computing team and help support biomedical
research on one of the 100 most powerful supercomputers in the world.

The NIH HPC staff advances research at NIH by planning, managing, and
supporting the NIH High Performance Computing (HPC) Facility, including the
94,000-core Biowulf cluster, 25 PB of storage, and the 600+ biomedical
applications used by over 2000 users in the NIH intramural program.

We are currently looking for enthusiastic systems administrators and scientists
to expand our existing team.

Please see for details.

Qualified individuals who are interested in these positions should send resumes
to Steve Bailey at


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