Combined 2020 Network Modeling Summer School and Hackathon and Multicell Virtual-Tissue Modeling Summer School and Hackathon.
Indiana University, Bloomington, Indiana.
Dates: Sunday July 26th, 2020 - Sun. Aug 9.
AUDIENCE: Mathematical Biologists, Computational Biologists, Experimental Biologists, Medical Scientists and Biophysicists, from undergraduates to senior faculty, with a current or potential interest in mechanistic modeling of biological systems. The first half covers modeling biochemical networks, including metabolic, signaling and gene regulatory networks. The second half covers multicellular modeling, which applies to developmental and tissue biology, tissue engineering, developmental diseases like cancer and tissue-level toxicology. No specific programming or mathematical experience is required.
Summer school attendance guarantees admission to the Model-Building Hackathons.
The Hackathons will group attendees by topic of interest. Experienced modelers will be embedded within each group. Everyone will leave with a functioning core model that they can further customize. Advanced modelers can apply to attend just the Hackathons.
AIM AND FOCUS:
An Introductory Python Tutorial will take place on July 26th, 2020. If you already know Python, you may skip this Tutorial or take this material as a review
Network Modeling Summer School (July 27-July 30, 2020) and Hackathon (July 31-August 2, 2020): Text on Network Modeling Here!
Multicell Virtual-Tissue Modeling Summer School (August 3-August 6, 2020) and Hackathon (August 7-August 9,2020):
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 the Summer Schools and Hackathons, 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.
Summer schools will include four days of lectures and hands-on computer tutorials. In the modeling Hackathons teams of advanced and beginner modelers will develop research-quality models of their systems of interest. Each attendee will also present a mini-talk on their problem of interest. We will provide after-hackathon support to assist users in the development of these models in their research.
Principles of modeling biological and biomedical problems
Python and Antimony scripting
Dynamic Network Modeling with Tellurium
Multicellular Virtual-Tissue simulations with CompuCell3D
Combining network models with virtual-tissue models in multiscale models
Prof. Julio Belmonte (North Carolina State University), Mr. Juliano Gianlupi (Indiana University), Prof. James A. Glazier (Indiana University), Dr. Bobby Madamanchi (Purdue University), Prof. Herbert Sauro (University of Washington, Tellurium lead developer), Dr. T.J. Sego (Indiana University, CompuCell3D lead developer), Dr. James Sluka (Indiana University), Dr. Endre Somogyi (Indiana University, Tellurium lead developer), Dr. Maciek Swat (CompuCell3D lead developer), Prof. Gilberto Thomas (Federal University of Rio Grande do Sul, Brazil)
Because the number of places is limited, admission is by application only. To apply for admission, please visit the school websitewww.compucell3d.org or email firstname.lastname@example.org
DEADLINE for APPLICATIONS:
April 1st, 2020. 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.
The workshop is partially supported by grants from the US National Institutes of Health. Enrollment is free and includes breakfast and lunches. However, participants are expected to cover their own travel and accommodation costs and the optional group dinners. The workshop may be able to assist participants who are interested in sharing accommodations.
VENUE and TRAVEL INFORMATION:
The workshop will be held in the Woodburn Hall Conference Facility, on the campus of Indiana University, Bloomington. The nearest airport to Bloomington is Indianapolis International Airport (IND). A scheduled bus service runs between IND airport and Indiana University. Numerous hotels and rental options and a wide variety of restaurants are located within walking distance of Woodburn Hall.
James A. Glazier
Department of Intelligent Systems Engineering
Indiana University, Bloomington
Advanced School on Applied Dynamical Systems to Synthetic and Systems Biology . 15-19 February 2021
The goal of this summer school is to bring together senior researchers working within the fields of dynamical systems and complex systems. The school is directed to PhD students and postdocs mainly.
Maíra Aguiar, BCAM
Jordi Garcia-Ojalvo, UPF
Imma Baldomà, UPC
Tomàs Lázaro, UPC
For inquiries about the program please contact the research programme's coordinator Ms. Núria Hernandez at email@example.com
THE HELSINKI SUMMER SCHOOL ON MATHEMATICAL ECOLOGY AND EVOLUTION 2020
We are glad to invite applications to the 2020 edition of The Helsinki Summer School on Mathematical Ecology and Evolution, an EMS-ESMTB School in Applied Mathematics to be held between 8 and 15 August 2020 in Turku, Finland.
The core program consists of five series of lectures:
Josef Hofbauer (University of Vienna): Dynamical systems in mathematical ecology
Julia Gog (University of Cambridge): The mathematics of infectious diseases
Pieter Trapman (Stockholm University): Stochastic models of epidemics
Jarno Vanhatalo (University of Helsinki): Linking ecological models to data through Bayesian statistics
Christian Hilbe (Max Planck Institute for Evolutionary Biology): Dynamics of social behaviour
All young researchers working in mathematical ecology can apply from all countries, especially from Europe and the Mediterranean. The school is aimed at graduate students of mathematics, but we also welcome students of biology with sufficient background in mathematics, as well as advanced undergraduates and postdocs.
For more information and details of the application procedure, please visit the school's webpage
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