SMB Digest Volume 19 Issue 14

SMB DIGEST ISSN 1086-6566 
April 10, 2019
This issue’s editor:


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Issue’s Topics:
NIMBioS Announces New Support for Short-term Visits
VipIMAGE 2019, Porto, Oct 16-18
ESMTB Summer School: Modelling in Marine Ecology, Palermo, Sep 8-21
Call for proposals to host CNS*2021
CfP: DECOR 2019, Macau, Apr 8
Bulletin of Mathematical Biology, Vol. 81, Issue 5 – New Issue Alert
ToC: Wiley, Systems Biology & Medicine, Vol 11, Issue 3
PhD Position: ER-Stress response, Dublin
PhD Position: Molecular Evolution, Uppsala
PhD Positions: Joint Graduate Program, Muenster
Senior Research Technician in Development Cell Biology…, Leiden
New NSF funding opportunity: Models for Uncovering Rules…
NIH Update: FY 2018 By the Numbers, K Awards and Future…
SMBnet Reminders


From: Catherine Crawley <>
Date: Apr 4, 2019, 2:30 PM
Subject: NIMBioS Announces New Support for Short-term Visits

NIMBioS is offering support for visits of up to one week for groups of
one to six people working on projects that conform to the NIMBioS
mission to foster interdisciplinary collaborations, research and
education at the interface of the quantitative and life sciences.
Visitors work onsite at NIMBioS, may link the visit to a previous
Working Group or other activity at NIMBioS, or to collaborations with
our affiliated Centers (DySoC, NISER,
and SAL Support is focused on US-based
researchers. We particularly welcome collaborative projects involving
NIMBioS resident or local researchers; joint applications from two or
more researchers to spend time together at NIMBioS; or applications
from participants in other NIMBioS activities to work on their project
with NIMBioS computational science staff. Visits must be concluded by
August 2020. Applications will be considered monthly.

For more information and the online application, visit


From: “João Manuel R. S. Tavares” <>
Date: Apr 7, 2019, 4:58 PM
Subject: VipIMAGE 2019, Porto, Oct 16-18

We are pleased to announce the International Conference VipIMAGE 2019
IMAGE PROCESSING ( to be held in October 16-18,
2019, in Axis Vermar Conference & Beach Hotel, Porto, Portugal.

For further details, please, have a look in the conference website at:, the Facebook page at:, or join the LinkedIn group at:

We are looking forward to see you in Porto in October, 2019,
João Manuel R. S. Tavares
Renato Natal Jorge
(VipIMAGE 2019 co-chairs)


From: Berec Luděk <>
Date: Apr 5, 2019, 9:10 AM
Subject: ESMTB Summer School: Modelling in Marine Ecology, Palermo, Sep 8-21

Biomathematics ESMTB Summer School 2019
Modelling in Marine Ecology
Isola delle Femmine (PA) Sicily, Italy 8-21 September 2019

The biomathematics “2019 ESMTB Summer School: Modelling in Marine
Ecology” will take place in Italy (Isola delle Femmine, Palermo,
Sicily) between 8th and 21st September 2019.

The school is mainly addressed to PhD and Post-Doc students interested
in modelling of marine systems and with background in applied
mathematics, bioengineering or physics.

For more details, please visit the web page of the summer school at:

Looking forward to seeing you in Palermo,
The management and scientific committee of the ESMTB Summer School 2019:
Ludek Berec, University of South Bohemia, Ceske Budejovice, Czech
Jean-Christophe Poggiale, Aix-Marseille University, Marseille, France,
Simona Panunzi, Italian National Research Council (CNR), Institute for
Systems Analysis and Computer Science, Rome, Italy,


From: Sharon Crook <>
Date: Apr 3, 2019, 6:52 PM
Subject: Call for proposals to host CNS*2021

The Organization for Computational Neurosciences requests proposals
from candidate local organizers to hold CNS*2021, preferably at a
location in Europe, but all applications will be considered.

Groups or individuals interested in organizing the 2021 meeting should
submit a proposal following the on-line instructions and using the
on-line templates at:

Proposals should be submitted by email to OCNS President Volker
Steuber at no later than October 1, 2019. The
OCNS Board Members will consider the proposals, contact local
organizers for more information if necessary, and select a location in
a timely agreement between OCNS and the potential local organizers.
As usual, the selected location will be officially announced in at the
CNS Meeting in July of 2020.

An earlier email to the OCNS President declaring the intent to submit
a proposal would be appreciated, but is not required.

The OCNS Board thanks you for your support.


From: Maria Leite <>
Date: Apr 2, 2019, 3:42 AM
Subject: CfP: DECOR 2019, Macau, Apr 8

Join and enjoy DECOR 2019 – The Second International Workshop on Data
Engineering meets Intelligent Food & Cooking Recipes,

When: April 8, 2019; Where: Macau SAR, China

It is a premier international workshop providing concrete
contributions in developing model design, technologies and presenting
intelligent data management tools supporting Intelligent Food and
Cooking Recipes processes. Co-sponsored by the IEEE International
Conference on Data Engineering (ICDE), a leading international
conference in the field of Data Science.

Register now @


From: Springer <>
Date: Apr 7, 2019, 9:44 PM
Subject: Bulletin of Mathematical Biology, Vol. 81, Issue 5 – New Issue Alert

Please see:


From: Wiley: Systems Biology and Medicine <>
Date: Apr 6, 2019, 8:03 AM
Subject: ToC: Wiley, Systems Biology & Medicine, Vol 11, Issue 3

For the Wiley Interdisciplinary Reviews: Systems Biology and Medicine,
Volume 11, Issue 3, see


From: Marc Sturrock <>
Date: Apr 8, 2019, 6:27 PM
Subject: PhD Position: ER-Stress response, Dublin

Project title: Dissecting the ER-Stress response using mathematical
models and protein expression data
Location: Royal College of Surgeons in Ireland (RCSI)
Supervisors: Professor Jochen Prehn ( and Dr Marc
Sturrock (

Project Summary: ER-stress is induced by the accumulation of unfolded
proteins and is observed especially in secretory cells and triggers a
protective signalling pathway termed the unfolded protein response
(UPR). The UPR is activated via its three main signalling branches
(ATF-6, PERK and IRE1α) which induce cellular adaptation to ER-Stress.
The UPR attempts to re-establish folding homeostasis or commits the
cell to apoptosis. Dysfunctions of this signalling pathway are
considered to be an important factor in diseases such as autoimmune,
neurodegenerative & liver disorders, cancer, diabetes and obesity.
However, the complex signalling that determines the cell fate upon
ER-Stress is still poorly understood, and in order to develop
therapeutic target strategies, a detailed understanding of the UPR is
essential. Such complex signalling pathways are difficult to
disentangle through mere thought experiments, and the careful
construction of a mathematical model can aid enormously in the
understanding of the pathway reaction to certain stimulations as well
as guiding future experiments.

This PhD project aims to build upon previous modelling studies and
develop a novel holistic stochastic model of the UPR signalling
pathway which aims to reproduce experimental data of our own in house
reporter cell lines, specifically time series data from an SH-SY5Y
reporter cell line for the ATF6 branch and SH-SY5Y cell lines for the
PERK and IRE1α branch of the UPR. The model will be calibrated using
summary statistics acquired from these time series data sets,
essentially the model will aim to first reproduce the means and
variance of signal intensity captured in the experimental reporter
cell lines, in response to 48 hour exposure to different dosages of
Thapsigargin or Tunicamycin. The model will then try to make
predictions using various additional knock-out experiments.

Further details can be found here:


From: Ema Shollenberger <>
Date: Apr 10, 2019, 5:57 AM
Subject: PhD Position: Molecular Evolution, Uppsala

Project description: One of the major objectives in evolutionary
genetics is to understand the molecular basis and mechanisms of
phenotypic variation and differentiation between species. Two
classical candidates underlying phenotypic change are protein coding
sequences and functional sequences that regulate gene expression.
Here, changes of the DNA sequence itself or epigenetic modifications
can influence the phenotype. However, the relative importance of these
two sequence classes and the role of epigenetic modifications is still
unclear. Flycatchers provide a good model system to study this
question. Collared flycatcher (Ficedula albicollis) and pied
flycatcher (Ficedula hypoleuca) have been a model of speciation
research for decades, and a rich source of genomic, transcriptomic and
epigenomic data have become available. In particular, data on
naturally occurring hybrids provides the opportunity to study the
molecular basis and mechanisms of reproductive isolation in an
ecologically relevant setting. Moreover, genomic data of the more
distantly related Taiga flycatcher (Ficedula albicilla) permits
studying molecular evolution also at larger time-scales.

For more details and instructions on how to apply, please refer to:


From: Martin Wild <>
Date: Apr 10, 2019, 11:04 AM
Subject: PhD Positions: Joint Graduate Program, Muenster

16 PhD Positions in Life Sciences, Mathematical Modelling and Image Analysis

The joint graduate program of the Research Cluster Cells in Motion
(CiM) and the International Max Planck Research School – Molecular
Biomedicine (IMPRS-MBM) offers positions to pursue PhD projects in the
areas of biology, chemistry, physics, mathematics or computer science.
We are looking for young scientists with a vivid interest in
interdisciplinary projects to image cell dynamics from the subcellular
to the patient level. PhD projects range from the analysis of basic
cellular processes to clinical translation, from the application of
novel biophysical approaches and the generation of mathematical models
to the development of new imaging-related techniques and compounds.

Research areas:
Cell and Molecular Biology * Developmental and Stem Cell Biology
Vascular Biology * Immunology
Microbiology * Neurobiology
In vivo Imaging * High Resolution Optical Imaging
Biophysics * Chemical Biology
Label Chemistry * Mathematical Modelling
and more.

Applications for the PhD program can be submitted from 1 March – 26
April 2019. Projects start in October 2019 (earlier start possible if
desired). Applications can only be submitted via our online system.
For online application and further information go to



From: Merks, R.M.H. <>
Date: Apr 10, 2019, 9:57 AM
Subject: Senior Research Technician in Development Cell Biology…, Leiden

Senior Research Technician in Development Cell Biology and Imaging to
test mathematical models at the Institute of Biology Leiden, The

As senior technician you will actively participate in the
interdisciplinary research of our group. You will be responsible for
setting up and running experimental work to test our mathematical
models in collaboration with an experimental PhD student and with a
number of PhD students in mathematical modeling.

For details, see:

A related vacancy for a mathematical modeller is still open at:


From: Henry Warchall <>
Date: Apr 8, 2019, 3:04 PM
Subject: New NSF funding opportunity: Models for Uncovering Rules…

New NSF funding opportunity: Models for Uncovering Rules and
Unexpected Phenomena in Biological Systems (MODULUS)

For more details, see Dear Colleague Letter at:


From: NIH Extramural Nexus (NIH/OD) <>
Date: Apr 3, 2019, 2:49 PM
Subject: NIH Update: FY 2018 By the Numbers, K Awards and Future…

NIH Update: FY 2018 By the Numbers, K Awards and Future Research
Support, Protocol Template for Behavioral and Social Sciences
Research, and more!



Subject: SMBnet Reminders

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