BCI 2010 Summer School - extended deadline
by
12 July 2010
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SIXTH INTERNATIONAL SCHOOL ON BIOLOGY,
COMPUTATION AND INFORMATION (BCI 2010)
 
 
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September 20-24, 2010, Dobbiaco (BZ), Italy
 
 
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CALL FOR PARTICIPATION
 
 
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The School of Biology, Computation, and Information (BCI), 
reaching this year its sixth edition, 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 discuss the 
different points of view on Bioinformatics typical of 
the two main sub-communities of computationally oriented 
scientists working in the field. 
The central question that will be addressed is wether 
the more algorithmic or more systemic approach to Bioinformatics 
is going to lead the way in the future.
 
The three distinguished speakers for this year's edition 
are Jasmin Fisher (Biology), Eugene Myers 
(Computer Science), and Bud Mishra (Mathematics) and 
the school will take place during the fourth week of 
September (September 20-24, 2010).
 
 
 
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COURSES
 
Main topic: algorithmic vs systemic approach to bioinformatics
 
 
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Area: Mathematics
Lecturer: Prof. Bud Mishra,
Courant Institute of Mathematical Sciences,  New York University, USA.
Mt. Sinai School of Medicine, New York, USA.
NYU School of Medicine,  New York University, USA.
 
Prof. Bud Mishra is a professor of computer science and mathematics at 
NYU's Courant Institute of Mathematical Sciences, professor of human 
genetics at Mt. Sinai School of Medicine, and a professor of cell biology 
at NYU School of Medicine. He founded the NYU/Courant Bioinformatics Group, 
a multi-disciplinary group working on research at the interface of computer 
science, applied mathematics, biology, biomedicine and bio/nano-technologies. 
Prof. Mishra has a degree in Physics from Utkal University, in Electronics 
and Communication Engineering from IIT, Kharagpur, and MS and PhD degrees in 
Computer Science from Carnegie-Mellon University. He has industrial experience 
in Computer Science (Tartan Laboratories, and ATTAP), Finance (Tudor Investment 
and PRF, LLC), Robotics and Bio- and Nanotechnologies (OpGen, and Bioarrays). 
He is editor of Molecular Cancer Therapeutics, AMRX (Applied Mathematics 
Research Exchange), Nanotechnology, Science and Applications, and Transactions 
on Systems Biology, and author of a textbook on algorithmic algebra and more 
than two hundred archived publications. He has advised and mentored more than 
35 graduate students and post-docs in the areas of computer science, robotics 
and control engineering, applied mathematics, finance, biology and medicine. 
He is an inventor of Optical Mapping and Sequencing (SMASH), Array Mapping, 
Copy-Number Variation Mapping, Model Checker for circuit verification, Robot 
Grasping and Fixturing devices and algorithms, Reactive Robotics, and 
Nanotechnology for DNA profiling. He is a fellow of both IEEE and ACM fellow 
and a NYSTAR Distinguished Professor (2001). He also holds adjunct professorship 
at Tata Institute of Fundamental Research in Mumbai, India. From 2001-04, he was 
a professor at the Watson School of Biological Sciences, Cold Spring Harbor Lab; 
currently he is a visiting scholar at the Center of Quantitative Biology at CSHL
 
 
Abstract.
Solved and Unsolved Problems in Biology
 
In this talk, I will describe a few classical and recent open problems in 
biology that require careful reasoning (Thought Biology). 
It is interesting  to ask how areas such as systems biology, model checking 
and quantitative biology may be able to tackle these problems. 
To address these questions, we will develop a model of causality that is based 
on the work of various philosophers, starting with John Stuart Mill and David Hume, 
but more recently by Skyrms, Suppes and Eells. Examples from biology, neuroscience, 
finance, and web applications will illustrate how we hope to exploit this technology. 
This is joint work with Samantha Kleinberg.
 
 
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Area: Computer Science
Lecturer: Prof. Eugene Myers, 
HHMI Janelia Farm Research Campus, USA 
 
Gene Myers is a group leader at the HHMI Janelia Farm Research Campus
near Washington DC.  He was the Vice President of Informatics Research at
Celera Genomics and has been on the computer science and biology faculties
of UC Berkeley and the University of Arizona for most of his career.
 
He is best known for the development of BLAST -- the most widely used
tool in bioinformatics -- and for the paired-end whole genome shotgun
sequencing protocol and the assembler he developed at Celera that
delivered the fly, human, and mouse genomes in a three year period.  He
has also written many seminal papers on the theory of sequence comparison.
He is a member of the National Academies of the United States and Germany.
 
Abstract.
While there have been a few interesting discoveries based on prediction,
my own sense is that most of the knowledge accumulated in molecular
biology has been based on observation, the more direct, the better.  I
believe that the main contribution of the genome project(s) has been that
we can now do recombinant genetics on a genome-wide scale.  The output of
such studies are typically images produced by light or EM microscopy.
I will describe the growing sub-field of "bio-image informatics" and
illustrate projects underway to directly model and measure the cellular
anatomy of organs, the meso-scale anatomy of cells, and the developmental
trajectory of a genome.
 
 
 
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Area: Biology
Lecturer: Prof. Jasmin Fisher
Cambridge University, UK.
Microsoft Research Center, Cambridge, UK.
 
Dr. Jasmin Fisher received her PhD in Neuroimmunology from the Weizmann Institute of Science and is currently an affiliated Lecturer at the Centre for Systems Biology in Cambridge University and a Research Scientist at Microsoft Research Cambridge. Her research focuses on the applications of formal methods to biological modelling, as well as on the development of novel formalisms and tools to better understand complex biological systems. She is mainly interested in processes of cell fate determination and signalling networks operating during normal animal development and cancer. Her e-mail address is jasmin.fisher@microsoft.com and her webpage is http://research.microsoft.com/en-us/people/jfisher/  
 
Abstract.
Executable Biology: Successes and Challenges
 
Understanding living systems remains one of the greatest challenges in science, despite an explosion of data in the Biological Sciences.  Computational modelling of biological systems is consequently becoming increasingly important in efforts to better understand complex biological behaviours. In my talks I will outline one branch of research aiming to address this important challenge. We distinguish between two types of biological models -mathematical and computational- which differ in their representations of biological phenomena. We call the approach of constructing computational models of biological systems Executable Biology, as it focuses on the design of executable computer algorithms that mimic biological phenomena. In the talks I will survey the main modelling efforts in this direction (e.g., Boolean networks, process calculi, Petri nets, interacting state-machines), emphasize the applicability and benefits of executable models in biological research, mainly through 
models o
f cancer-related signalling pathways, and highlight some of the main challenges that executable biology poses for Biology and Computer Science.
 
 
 
 
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REGISTRATION
 
 
*Early registration deadline (extended): July 15, 2010*.
Late registration deadline:  August 31, 2010. 
 
 
We can provide accommodation for 40 participants,
assigned on a first-come first-served basis. To apply use
the online registration form available at school's website
 
         LINK
 
Acceptance of more participants will be evaluated by the
organizers.
 
Early registration fee: EUR 500.
Late registration fee: EUR 600.
Supplement for single room: EUR 100.
 
 
The registration fee covers participation at all lectures,
course materials, coffee break, and full board accommodation.
 
 
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ACCOMODATION
 
Participants will be lodged at the Apparthotel Germania
(http://www.apparthotel-germania.com/), located in Dobbiaco, 
just in front of the conference center. 
Accommodation includes five nights with breakfasts, lunches
and dinners, including the dinner on Sunday 19, 2010 h20:00,
and the lunch on Friday 24, 2010.
Students will be accomodated in double rooms, shared with
other participants. Single room accomodation is possible by paying 
a supplementary fee.
 
For persons accompanying the School participants, please,
contact the organizing committee.
 
 
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LOCATION
 
The school will take place in Dobbiaco, an inspiring village in the italian Alps, 
called "the door to the Dolomiti".
Lessons will be held at the congress center Centro
Culturale Grandhotel Dobbiaco, via Dolomiti 31, I-39040 Dobbiaco.
The congress center is close to the railway station.
 
 
 
 
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WEBSITE AND CONTACT
 
 
For all additional information, please visit the website:
http://www.dmi.units.it/bci2010/
 
 
You can also contact the school organizers by writing to bci2010@dmi.units.it
 
 
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SPONSORS
 
 
 
- Department of Mathematics and Computer Science, University of Trieste.
- Department of Mathematics and Computer Science,  University of Udine.
- GNCS, INdAM (National Institute of High Mathematics)
- IEEE
 
 
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ORGANIZING AND SCIENTIFIC COMMITTEE
 
 
- Alberto Policriti, University of Udine (school director)
- Luca Bortolussi, University of Trieste (school co-director)
- Alberto Casagrande, University of Trieste
- Cristian Del Fabbro, Istituto di Genomica Applicata (IGA), Udine
- Agostino Dovier, University of Udine 
- Francesco Fabris, University of Trieste
- Eugenio Omodeo, University of Trieste
- Carla Piazza, University of Udine 
- Simone Scalabrin, Istituto di Genomica Applicata (IGA), Udine
- Andrea Sgarro, University of Trieste
- Alexandru Tomescu, University of Udine
- Francesco Vezzi, University of Udine
- Nicola Vitacolonna, University of Udine
 
 
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