Details .:. BITS Bioinformatics Italian Society

courses

BCI 2010 Summer School - extended deadline

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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