ISSN 1086-6566
MAY 11, 2017


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Issue's Topics:
  12th Annual CompuCell3D User Training Workshop, Jul 30- Aug 4
  Postdoc: Membrane dynamics in health and disease, Alabama
  Group Leaders in Computational and System Biology, Toulouse
  Two Visiting Professorships at Virginia Commonwealth University
  NSF Employment Opportunity: Division Director, DMS
  NIH Update: implementing limits on grant support to strengthen...
  SMBnet Reminders


From: Andy Somogyi <>
Date: Wed, May 10, 2017 at 8:15 PM
Subject: 12th Annual CompuCell3D User Training Workshop, Jul 30- Aug 4

July 30th-August 4th, 2017
Indiana University, Bloomington, IN, USA

Background: 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 learn to 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.
Simulations written using these environments are compact and run on Windows,
Mac and Linux, desktops. CompuCell3D is open source, allowing users to extend,
improve, validate, modify and share the core software. For more information
please visit:

Goal: 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

Topics: Python scripting. Introduction to Reaction-Kinetics (RK) models.
Introduction to SBML. Introduction to Virtual-Tissue simulations. Introduction
to CompuCell3D. Basics of model building. Combining RK and Virtual-Tissue
models. Extending CompuCell3D. Building a basic simulation of your system.

Format: The workshop will include a limited number of lectures and numerous
hands-on computer tutorials. Each attendee will also  present a  mini-talk on
her/his problem of interest.

Instructors: Julio Belmonte, James A. Glazier, Andy Somogyi

Target Audience: Experimental Biologists, Medical Scientists, Biophysicists,
Mathematical Biologists and Computational Biologists from advanced
undergraduates to senior faculty, who have an interest in developing
multi-scale Virtual-Tissue simulations, or learning how such simulations might
help their research. No specific programming or mathematical experience is
required, though familiarity with a modeling environment (e.g. Mathematica®,
Maple®, Python, or Matlab®) and how to represent basic concepts like diffusion
and chemical reactions mathematically, will be helpful. Important: An
Introductory Python Tutorial will take place on July 30th. If you already know
Python you may skip this part of the workshop.

Fees: There is no registration fee. We will provide coffee, tea, snacks and
workshop materials.

Application and Registration: Enrollment is limited and by application only.
To apply, please send a c.v., a brief statement describing your current
research interests and the specific problem you would like to model. Students
should also include a letter of support from their current advisor. Please
submit all application materials electronically to Andy Somogyi
( by June 30th, 2017.

Facilities: The workshop will be held at Indiana University, Bloomington.
Participants will be able to connect to the Internet using their own laptops.

For more information, please contact: Andy Somogyi (


From: Andre Leier <>
Date: Tue, May 9, 2017 at 7:24 PM
Subject: Postdoc: Membrane dynamics in health and disease, Alabama

A postdoctoral position is available for a highly-motivated individual in the
group of Dr. André Leier at the Informatics Institute, University of Alabama
at Birmingham, to work in predictive modeling of spatiotemporal processes on
endo-membranes. The successful candidate will perform original research in
quantitative modeling of membrane-localized protein complex formation,
receptor-lipid and lipid-lipid interactions, and other associated processes,
integrating experimental data from different sources.

For further details, see:


From: Isabelle Saves <>
Date: Fri, May 5, 2017 at 10:02 AM
Subject: Group Leaders in Computational and System Biology, Toulouse

Application deadline: June 15, 2017

The Centre for Integrative Biology of Toulouse (CBI;
launches two international calls for the recruitment of outstanding group

In order to reinforce its research endeavors in an inspiring, collaborative
and cutting-edge environment, the CBI is seeking new talented group leaders,
at junior or midcareer level, addressing Computational biology and data
modeling, including computational analysis of large data-sets, network
analyses, physics and mathematical modeling connected to research themes of
the CBI.

Applications (about 10 pages, in English) should be sent before June 15, 2017,
as a single file named LASTNAME_CBI2017_open call or specific call.pdf to and should include (i) a cover letter, (ii) a CV, (iii)
three reference letters and (iv) a summary of achievements and future research

Tentative calendar
Mid-July: Preselection of candidates
Mid-September: Interview of preselected candidates by the selection committee
and presentation of research project at CBI.
Late-September: Outcome of the selection process.

More information:


From: Angela M Reynolds <>
Date: Mon, May 8, 2017 at 7:58 PM
Subject: Two Visiting Professorships at Virginia Commonwealth University

Positions: Two faculty positions (9-month) as Visiting Assistant Professor of
Mathematics in the Dept. of Mathematics and Applied Mathematics beginning
August 16, 2017, subject to availability of funding. The Department and
University Web pages may be found at and Position responsibilities: To teach two upper level
courses each per semester and engage in research with current faculty.
How to Apply for the Position: To apply, candidates must submit electronically
through the following: a cover letter
that clearly delineates how they meet the qualifications outlined above, an
AMS Standard Cover Sheet, a current curriculum vitae, detailed teaching and
research statements, and four letters of recommendation, of which one must
support the applicant's effectiveness as a teacher.


From: Henry Warchall <>
Date: Thu, May 4, 2017 at 2:03 PM
Subject: NSF Employment Opportunity: Division Director, DMS

The Directorate for Mathematical and Physical Sciences (MPS) announces a
nationwide search to fill the position of Director, Division of Mathematical
Sciences (DMS).

Please see:
for details.


From: NIH Extramural Nexus (NIH/OD) <>
Resent-from: Raymond Mejía <>
Date: Thu, May 4, 2017 at 1:59 AM
Subject: NIH Update: implementing limits on grant support to strengthen...

NIH Update: implementing limits on grant support to strengthen biomedical
workforce; forms updates ahead; new resources



Subject: SMBnet Reminders

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