ISSN 1086-6566
March 29, 2017

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Issue's Topics:

  Correction: Data Challenges in Systems Immunology, Cardiff
  Modeling Immunology Summer School, Emory University
  Workshop Making Meaning Through Modeling
  Short Course: Model Fitting & Inference, Infectious Disease Dynamics
  International Neural Dynamics Summer School 2017, Bristol U
  Special Issue on Molecular Based Mathematical Biology
  New DARPA program Lifelong Learning Machines
  NIH Regional Seminar on Funding and Grants Administration
  Postdoc: Individual-Based Models of Microbial Communities
  Postdoc: Wellcome Trust Sanger Institute
  Lecturer/Senior: Applied Mathematics, Liverpool John Moores U
  Bioinformatician Position: Ragon Institute of MGH, MIT and Harvard
  SMBnet Reminders


From: Barbara Szomolay <>
Date: March 22, 2017 at 2:30:45 PM CDT
Subject: Correction: Data Challenges in Systems Immunology, Cardiff

Data Challenges in Systems Immunology, Jun 6th, Cardiff, UK


From: Andreas Handel <>
Date: 2017-03-24 12:49 GMT-03:00
Subject: Modeling Immunology Summer School, Emory University

The ?Modeling Immunity to Influenza Infection? (MITII) Center at Emory
University, which is the part of an NIH/NIAID funded program on Modeling
Immunity for Biodefense (MIB), is hosting a summer school on "Modeling
Immunology?  on May 21-24, 2017 at Emory University in Atlanta.
There is no fee to attend the summer school. Admitted students will be
provided with accommodation at Emory, and their travel expenses will be
reimbursed up to $500.
The main target audience for the summer school are individuals who are early
in their career (advanced undergraduate or graduate students and postdocs),
have solid training in the lab/bench-sciences, but not much mathematical/
statistical modeling background, and want to get an introduction to modeling
in immunology, virology, and related areas.
More details about the summer school and how to apply can be found at:


From: Kristin Jenkins <>
Date: 2017-03-24 15:32 GMT-03:00
Subject: Workshop Making Meaning Through Modeling

Applications are now open for the 2017 Summer Workshop ?Making Meaning through
Models: Problem solving in biology? to be held July 23-28 at Michigan State
University.  More information about the workshop is available here:  or see the attached flier.
At this summer?s workshop we will delve into how to engage our students more
productively with models and the process of modeling.  Join us as we consider
how to enhance the skills students need to understand and build models, how to
expand upon models already in our curriculum, and ultimately how to enhance
student understanding of the nature and process of science with modeling.  We
will discuss effective pedagogical approaches, share excellent resources, and
build community around effective use of models.  The intensive week-long
workshop is followed by the opportunity to continue to work with colleagues on
the QUBESHub through the fall semester to develop and implement new approaches
or materials.
The summer workshop is appropriate for two and four year faculty teaching all
levels of undergraduate biology, quantitative biology, and life science-
oriented mathematics.  We encourage future faculty, full and part time faculty
and teams of faculty from the same or affiliated institutions to apply.
Please share this information with any of your colleagues who might be


From: Sebastian Funk <>
Date: 2017-03-27 8:45 GMT-03:00
Subject: Short Course: Model Fitting & Inference, Infectious Disease Dynamics

The Centre for the Mathematical Modelling of Infectious Diseases (CMMID) at
the London School of Hygiene & Tropical Medicine is pleased to invite
applications for the fourth instalment of our a 4-day course on
*Model fitting and inference for infectious disease dynamics* taught by
Sebastian Funk and Anton Camacho

The course will be held from 25-28 July, 2017. Course material will range from
the basics of model fitting to methods such as Markov-Chain Monte Carlo (MCMC)
and particle filtering, and will introduce methods used within CMMID to
analyse and forecast the recent Ebola epidemic and Zika virus outbreaks.
The course fee varies from £500 (students) to £650 (academics) and £850 (non-
For more information, contact details, and to apply, please visit


From: Tsaneva-Atanasova, Krasimira <>
Date: 2017-03-27 11:30 GMT-03:00
Subject: International Neural Dynamics Summer School 2017, Bristol U

The 1st International Neural Dynamics Summer School 2017
Experience experimental and computational neuroscience research 30/08/2017 ?
01/09/2017 Bristol University, UK
We are offering twelve fully funded positions on the Wellcome Trust sponsored
summer school for training and research experience in neural dynamics(TRENDs).
The training and research in neural dynamics summer school is an exciting
Wellcome Trust funded course held at the University of Bristol.
The aim is to introduce young scientists to experimental and computational
techniques used in neuroscience research.
The summer school will be a three-day course made up of a series of seminars
and lab visits where successful candidates will get first hand experience of
electrophysiological recordings (bothin vitro and in vivo), EEG recordings,
brain imaging, optogenetics, data analysis workshops and practical classes on
learning to code in Python. No prior experience is necessary, but a keen
interest is essential!
We welcome applications from science undergraduates from a wide range of
For successful applicants all costs to attend the course, including travel
expenses within the UK, accommodation and food will be
covered. Overseas travel expenses will be considered on a case by case basis.
Deadline 15th May, 2017

Please send a completed application form, along with a cover letter, a copy of
your CV and one academic reference or the name of one referee to
The application form is available as .doc at
or as a LaTeX template at
Please submit either .doc or .pdf


From: Duan Chen <>
Date: 2017-03-27 22:26 GMT-03:00
Subject: Special Issue on Molecular Based Mathematical Biology

The journal Molecular Based Mathematical Biology (MBMB) will publish a special
issue entitled ?Microscopic charge/particle transport at molecular level?. The
purpose of this special issue is to create a medium for researchers from
mathematical and biological sciences and other related disciplines to report
novel mathematical models, analysis, computational algorithms, and biological
applications to the dynamics of charge or biological particle transport, in
ion channel, industrial nano-devices, or complicated cellular environment.
More details can be found at
MBMB ( is a recently established
journal, whose aim is to promote the mathematical study and findings of
biological structure, functions and dynamics at the molecular scale. Original
papers and high-quality review articles on the aforementioned topics are
solicited for this special issue.


From: Whang, Kenneth C. <>
Date: 2017-03-27 15:25 GMT-03:00
Subject: New DARPA program Lifelong Learning Machines

DARPA-MTO is delighted to announce a new program, Lifelong Learning Machines
(L2M).  The program will develop new machine learning systems that continue to
learn during operation with strong ties to biology.
A Special Notice for the L2M Proposers' Day on March 30th at DARPA has been
published at
Registration was filled up, largely by the AI community, within the first day;
however, we are very interested in biologists and computational biologists to
join the program, and everyone writing to the email at the link above will be
put on a waiting list for possible future proposer day and will get copies of
the slides and video.
For further information please contact:
Dr. Hava Siegelmann,
MTO Program Manager


From: NIH OER Communications Office (NIH/OD) <>
Date: Wed, Mar 29, 2017 at 2:47 PM
Subject: NIH Regional Seminar on Funding and Grants Administration

Meet Face-to-Face & Talk with Experts from NIH & HHS in 2017



From: Paolo Zuliani <>
Date: 2017-03-27 7:55 GMT-03:00
Subject: Postdoc: Individual-Based Models of Microbial Communities

The EPSRC-funded NUFEB project at Newcastle University (UK) is looking for a
talented computational modeller. The post-holder will join NUFEB's Large Scale
Modelling Team, an interdisciplinary environment with microbiologists,
engineers, statisticians and mathematicians. Application deadline: 11th April,
For more information and to apply, visit


From: Francesca Saccone <>
Date: 2017-03-27 12:52 GMT-03:00
Subject: Postdoc: Wellcome Trust Sanger Institute

The Wellcome Trust Sanger Institute is seeking a highly motivated researcher
with strong skills in computational genomics to fill a postdoctoral fellow
position. The aim of the fellow is to develop a quantitative framework for
predicting antimicrobial resistance spread in clinical bacterial isolates from
diverse generated large-scale genetic and phenotypic data.
The goal of the encompassing international collaborative project is to predict
and map drug targets for cell-to-cell horizontal transmission of antibiotics
resistance. To this end, we are generating data from three different types of
bacterial strains. First, we are performing large-scale experimental evolution
experiments to map de novo mutations that confer changes to transmission
ability. Second, we are phenotyping comprehensive collections of knockout and
overexpression mutants to identify determinants of adaptation. Finally, we
will sequence full genomes of, gather gene expression and proteomics data for,
and deeply phenotype thousands of clinical isolates from the largest
collection in Europe to find variants likely to alter resistance transmission
properties. The first sets of experiments have been executed, and the bulk of
the assays are expected to complete in 2017.
The successful candidate will perform original research in quantitative
modeling of these multimodal high throughput data to predict antimicrobial
transmission for previously unobserved clinical isolates. It is important you
have the ability to bridge from understanding the processes generating the
measured data, to implementing computational pipelines to extract information,
as well as creating and applying correct models for analysis. You are expected
to make progress on your project as the first priority, while budgeting time
for training in further skills, piloting new leads, and potentially
collaborating on other related projects. To function effectively in a
multidisciplinary, collaborative setting, you have to be able to communicate
well with scientists from diverse backgrounds, and be a pleasant colleague.

The application link is:


From: Webb, Steven <>
Date: 2017-03-29 11:18 GMT-03:00
Subject: Lecturer/Senior: Applied Mathematics, Liverpool John Moores U

There is a vacancy for a lecturer/senior lecturer (grade 8, £39,324-£48,327
per annum) in Applied Mathematics at Liverpool John Moores University,
Liverpool, UK, with expertise in mathematical biology in particular relating
to quantitative systems pharmacology. The closing date is 23/04/2017. Informal
enquiries may be made to the Head of Department, Prof Paulo Lisboa, email: Full details can be found at


From: Gasca-Lozano, Angela Marin <>
Date: 2017-03-23 16:51 GMT-03:00
Subject: Bioinformatician Position: Ragon Institute of MGH, MIT and Harvard



Subject: SMBnet Reminders

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