[SocBiN] BCI 2013 summer school

Luca Bortolussi luca.bortolussi at gmail.com
Thu Jul 11 12:44:22 CEST 2013


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Joint Third FVG International Summer School on Bioinformatics
Eighth International Summer School on 
Biology, Computation and Information 
BCI 2013

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September 09-13, 2013, Trieste, Italy

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CALL FOR PARTICIPATION

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The School of Biology, Computation, and Information (BCI), 
reaching this year its eighth edition, as a joint event 
with the third FVG summer school on bioinformatics,
aims at bringing  together teachers and students in 
Biology, Mathematics,  and Computer Science. 
The main goal of the School is to 
give an updated overview of interdisciplinary techniques 
and problems cross-bordering the three fields.

This year's edition will be dedicated to the study of 
cancer bioinformatics, with emphasis on  genetic and protein
interaction networks involved and on multi-scale modeling
of cancer tissues.
The topics of the school will cover such issues as production 
and analysis of experimental data and construction and validation
of mathematical and computational models.

The three distinguished speakers for this year's edition 
are Francesca Ciccarelli (Biology), Pietro Liò
(Computer Science), and Luigi Preziosi (Mathematics) and 
the school will take place during the second week of 
September (September 09-13, 2013).

A workshop will take place during the last day of the summer school,
while poster session will be organized throughout the conference.

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COURSES

Main topic: cancer modelling

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Area: Mathematics
Lecturer: Prof. Luigi Preziosi,
Politecnico di Torino, Italy.

Bio: Luigi Preziosi is full professor of Mathematical Physics at 
the Politecnico di Torino, where he is also head of the School of 
Mathematical Engineering. He got a Master degree in Mathematics 
cum laude at the University of Naples, a Ph.D. in Mechanics 
with minor in Mathematics at the University of Minnesota and a
Ph. D. in Mathematics at the University of Naples.
He is author of more than 100 publications in the international 
literature  in several fields of Applied Mathematics, such as dynamics 
of immiscible fluid and viscoelasticity, kinetic models in gas and 
population dynamics, cancer modelling, biomechanics of living tissues, 
and deformable porous media applied to bio-mathematics, composite 
materials manufacturing processes, and soil mechanics.

Abstract: Multiscale Developments of Cellular Potts Models and 
Individual Cell-based Models in Cancer Modelling.
All biological phenomena emerge from an intricate interconnection of 
multiple processes occurring at different levels of organization: namely, 
at the molecular, the cellular and the tissue level. These natural levels 
can approximately be connected to a microscopic, mesoscopic, and macroscopic 
scale, respectively. The microscopic scale refers to those processes that 
occur at the subcellular level, such as DNA synthesis and duplication, gene
dynamics, activation of receptors, transduction of chemical signals and 
diffusion of ions. The mesoscopic scale, on the other hand, can refer to 
cell-level phenomena, such as adhesive interactions between cells or between 
cells and ECM components, cell duplication and death and cell motion. 
The macroscopic scale finally corresponds to those processes that are 
typical of multicellular behavior, such as population dynamics, tissue 
mechanics and organ growth and development.
One of the most widespread hybrid approaches, that is particularly suitable 
for cancer modelling and other biological problems, is the Cellular Potts 
Model, a stochastic Monte Carlo method based on energy minimization principles.
The scope of the series of lectures is to present some innovative multiscale 
extensions of the Cellular Potts models and of Individual Cell-based models. 
In particular, we focus on ways to integrate and interface the standard method 
with detailed descriptions of microscopic dynamics located not only in the 
external space but also within the simulated elements. We aim therefore to 
introduce some nested characteristics in the basic hybrid environment, that 
realistically reproduce the multiscale organization typical of biological 
development, where the individual behavior is driven by the constant interplay 
between different levels of description. 

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Area: Computer Science
Lecturer: Dr. Pietro Liò, 
University of Cambridge, UK.

Bio: Dr. Pietro  Liò research activities focus in several areas of computational medicine and biology. He is Senior Lecturer in the Computer Laboratory which is the department of Computer Science of the University of Cambridge where he supervises a group of four PhD students and one postdoc. He teaches Bioinformatics algorithms (undergraduates) at the Computer Laboratory and Model and Methods in Genomics at the MPhil in Computational Biology, Dept. of Mathematics and Applied Physics. He is affiliated staff of the Systems Biology tripos. Dr. Liò holds a PhD in Complex Systems and Non Linear Dynamics (School of Informatics, dept of Engineering of the University of Firenze, Italy) and a PhD in Genetics (University of Pavia, Italy). 

Abstract: Medicine is moving from reacting to a disease to a proactive P4 medicine: personalized, predictive, preventive and participatory medicine. A difficult step is to bridge the actual distance between biomedical research and clinical practice. I would like to focus on the challenges in data analysis and modeling in cancer bioinformatics. In particular I would like to discuss the following issues:
* Multi omics (1 lecture)
Expensive and complex data are gathered and analysed in a rather simple way that completely misses the opportunity to uncover combinations of predictive and meaningful profiles among the omics data. Novel methodological frameworks, beyond single datasets, should integrate multilevel omics data to bring biological understanding to the next level. "Super-Meta" methods combining multilevel data across populations need to be developed. Omics may include HI-C, epigenetic, gene expression and sequence data; they are not independent each other. I will provide details of the algorithms and the software
* Multi scale modeling (1 lecture)
A disease manifests first as a dysfunction at the cell level and is then translated at the tissue level due to a change in the cell response. Here I am considering tgb-beta as a coupling factors for modeling breast cancer at different scales (from molecules to tissues).
* Multi morbidities (1 lecture)
Comorbidity addresses the occurrence of different medical conditions or diseases, usually complex and often chronic ones, in the same patient.
I am addressing bone diseases as a secondary effect of several types of cancers.
* Multi objective optimisation (1 lecture) 
If there is time I will show use multi objective optimisation to investigate how energetic factors enters the tissue dynamics.



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Area: Biology
Lecturer:Dr. Francesca Ciccarelli
IEO-IFOM Milano, Italy.

Bio: Francesca Ciccarelli is group leader at the European Institute 
of Oncology (IEO) in Milan. She earned a PhD in Natural Science 
at the University of Heidelberg. Her expertise is in computational 
biology and her research focuses on applying computational methods 
to study cancer genetics and to model tumor evolution. She is also 
the scientific coordinator of the PhD program in computational biology 
at the European School of Molecular Medicine (SEMM) in Milan.

Abstract: In this series of lectures I will discuss the recent advances 
in on our understanding of cancer genetics and evolution. I will start 
by reviewing the accumulating evidence of cancer heterogeneity in terms 
of acquired genetic mutations and genomic rearrangements. I will then 
describe the impact of these novel results on our modeling of cancer 
networks. In the last lectures, I will focus on the current attempts 
of using large-scale genomics data for rebuilding tumor evolution and
 how this is changing also anti-cancer therapeutic approaches.


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WORKSHOP

A workshop, will take place during the last day of the summer school, 
with title "Cancer Bioinformatics".
Invited speakers for the workshop are:
* Marco Antoniotti (University of Milano Bicocca)
* Silvio Bicciato (University of Modena-Reggio Emilia)
* Barbara Di Camillo (University of Padova)
* Erez Persi (Tel Aviv University)
* Francesca Demichelis (University of Trento) 
* Michele Caselle (University of Torino)

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REGISTRATION

Registration deadline: 31 August.

To apply use the online registration form available 
at school's website

          http://bci2013.units.it/

Acceptance of more participants will be evaluated by the
organizers.

Registration fee: EUR 100 (#)

The registration fee covers participation at all lectures,
course materials, coffee break, and lunches.
Accommodation is not included. Please contact the organization 
or visit the web site for additional information.

(#) The registration is free for students and staff of the 
University of Udine, University of Trieste, SISSA, and other FVG
research institutions.

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LOCATION

The school will take place in Trieste, Friuli Venezia Giulia, Italy. 
Lessons will be held at the University Building of Androna Baciocchi,
Via Elisa Baciocchi, Trieste 
(in the city centre, in a side street of Via del Lazzaretto Vecchio).
The congress center is 10 minutes by bus from the train station (line 8).

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WEBSITE AND CONTACT

For all additional information, please visit the website:
http://bci2013.units.it/

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SPONSORS

- Regione Autonoma del Friuli Venezia Giulia
- University of Trieste.
- University of Udine.
- SISSA, Trieste.
 
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ORGANIZING AND SCIENTIFIC COMMITTEE

- Luca Bortolussi, University of Trieste (school co-director)
- Alberto Policriti, University of Udine (school co-director)
- Claudio Altafini, SISSA, Trieste (school co-director)
- Alberto Casagrande, University of Trieste

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