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Conferencias

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International Workshop on High Performance Computational Systems Biology

(HiBi 2009)

Trento, Italy, October 14-16, 2009

http://www.cosbi.eu/hibi09/

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The HiBi (High performance computational systems Biology) workshop

establishes a forum to link researchers in the areas of parallel computing

and computational systems biology.

One of the main limitations in managing models of biological systems comes

from the fundamental difference between the high parallelism evident in

biochemical reactions and the sequential environments employed for the

analysis of these reactions. Such limitations affect all varieties of

continuous, deterministic, discrete and stochastic models; undermining the

applicability of simulation techniques and analysis of biological models.

The goal of HiBi is therefore to bring together researchers in the fields

of high performance computing and computational systems biology. Experts from

around the world will present their current work, discuss profound

challenges, new ideas, results, applications and their experience relating

to key aspects of high performance computing in biology.

IMPORTANT DEADLINES:

paper submission deadline (abstract only) April 24, 2009

paper submission deadline May 1, 2009

acceptance notification June 23, 2009

revised papers due July 15, 2009

early registration deadline July 31, 2009

Best regards,

HiBi organizing committee

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We apologize if you received multiple copies of this Call for Papers.

Please feel free to distribute it to those who might be interested.

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International Workshop on

High Performance Computational Systems Biology

(HiBi 2009)

October 14-16, 2009

Trento, Italy

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1st Call for Papers (http://www.cosbi.eu/hibi09/cfp.pdf)

*****************

The HiBi (High performance computational systems Biology) workshop

establishes a forum to link researchers in the areas of parallel computing

and computational systems biology.

One of the main limitations in managing models of biological systems comes

from the fundamental difference between the high parallelism evident in

biochemical reactions and the sequential environments employed for the

analysis of these reactions. Such limitations affect all varieties of

continuous, deterministic, discrete and stochastic models; undermining the

applicability of simulation techniques and analysis of biological models.

The goal of HiBi is therefore to bring together researchers in the fields

of high performance computing and computational systems biology. Experts from

around the world will present their current work, discuss profound

challenges, new ideas, results, applications and their experience relating

to key aspects of high performance computing in biology.

Topics of interest include high performance algorithms, systems,

architecture, and tools for the following: (but are not limited to the

following list)

- Parallel and distributed Stochastic simulation

- Biological and Numerical parallel computing

- Parallel and distributed architectures

- Emerging processing architectures (Cell processors, GPUs, mixed CPU-FPGA)

- Parallel Model Checking techniques

- Parallel parameters estimation

- Parallel algorithms for biological analysis

- Application of concurrency theory to biology

- Parallel visualization algorithms

- Web-services and internet computing for e-Science

- Tools and applications

SUBMISSION INFORMATION:

HiBi welcomes submissions for:

- *full research papers* describing recent advances at the border

between parallel computing and systems biology;

- *short tool papers* describing implemented parallel techniques

and tools for systems biology.

PROCEEDINGS:

All submitted papers will be reviewed by the Program Committee. The review

process will include a rebuttal phase whereby authors will be given the

possibility to send their comments on the received review. Full papers as

well as short (tool) papers will be published in the proceedings of the

workshop. Detailed information about papers format and publisher will be

available soon. A selection of best (full) papers will also be published on

a dedicated special issue of the Briefings in Bioinformatics journal.

Submission of papers to HiBi09 will be through the EasyChair conference

system.

PROGRAM COMMITTEE MEMBERS:

- Tommaso Mazza (CoSBi, Italy) - chair

- Mateo Valero (Technical University of Catalonia, Spain) - co-chair

- Yutaka Akiyama (Tokyo Institute of Technology, Japan)

- Paolo Ballarini (CoSBi, Italy)

- Gianfranco Balbo (University of Torino, Italy)

- Lubos Brim (Masaryk University, Czech Republic)

- Kevin Burrage (University of Oxford, UK)

- Hidde De Jong (INRIA Rhône-Alpes, France)

- François Fages (INRIA Paris-Rocquencourt, France)

- Fabrizio Gagliardi (Microsoft Research Cambridge, United Kingdom)

- Martin Leucker (Technische Universität München, Germany)

- Gethin Norman (Oxford University Computing Laboratory, United Kingdom)

- Dave Parker (Oxford University Computing Laboratory, United Kingdom)

- Davide Prandi (CoSBi, Italy)

- Assaf Schuster (Israel Institute of Technology, Israel)

- Koichi Takahashi (RIKEN, Japan)

- David Torrents Arenales (Barcelona Supercomputing Center, Spain)

- Adelinde Uhrmacher (University of Rostock, Germany)

Information related to HiBi 2009 is available at the official HiBi 2009 Web

site: http://www.cosbi.eu/hibi09/

Textos Legais

STUART KAUFFMAN
Director, The Institute for Biocomplexity and Informatics, The University of Calgary; Author, Reinventing the Sacred

THE OPEN UNIVERSE

John Brockman's question is dramatic: What will change everything? Of course, no one knows. But the fact that no one knows may be the feature of our lives and the universe that does change everything. Reductionism has reigned as our dominant world view for 350 years in Western society. Physicist Steven Weinberg states that when the science shall have been done, all the explanatory arrows will point downward, from societies to people, to organs, to cells, to biochemistry, to chemistry and ultimately to physics and the final theory.

I think he is wrong: the evolution of the biosphere, the economy, our human culture and perhaps aspects of the abiotic world, stand partially free of physical law and are not entailed by fundamental physics. The universe is open.

Many physicists now doubt the adequacy of reductionism, including Philip Anderson, and Robert Laughlin. Laughlin argues for laws of organization that need not derive from the fundamental laws of physics. I give one example. Consider a sufficiently diverse collection of molecular species, such as peptides, RNA, or small molecules, that can undergo reactions and are also candidates to catalyze those very reactions. It can be shown analytically that at a sufficient diversity of molecular species and reactions, so many of these reactions are expected to be catalyzed by members of the system that a giant catalyzed reaction network arises that is collectively autocatalytic. It reproduces itself.

The central point about the autocatalytic set theory is that it is a mathematical theory, not reducible to the laws of physics, even if any specific instantiation of it requires actual physical "stuff". It is a law of organization that may play a role in the origin of life.

Consider next the number of proteins with 200 amino acids: 20 to the 200th power. Were the 10 to the 80th particles in the known universe doing nothing but making proteins length 200 on the Planck time scale, and the universe is some 10 to the 17th seconds old, it would require 10 to the 39th lifetimes of the universe to make all possible proteins length 200 just once. But this means that, above the level of atoms, the universe is on a unique trajectory. It is vastly non-ergodic. Then we will never make all complex molecules, organs, organisms, or social systems.

In this second sense, the universe is indefinitely open "upward" in complexity.

Consider the human heart, which evolved in the non-ergodic universe. I claim the physicist can neither deduce nor simulate the evolutionary becoming of the heart. Simulation, given all the quantum throws of the dice, for example cosmic rays from somewhere mutating genes, seems out of the question. And were such infinitely or vastly many simulations carried out there would be no way to confirm which one captured the evolution of this biosphere.

Suppose we asked Darwin the function of the heart. "Pumping blood" is his brief reply. But there is more. Darwin noted that features of an organism of no selective use in the current environment might be selected in a different environment. These are called Darwinian "preadaptations" or "exaptations". Here is an example: Some fish have swim bladders, partially filled with air and partially with water, that adjust neutral bouyancy in the water column. They arose from lung fish. Water got into the lungs of some fish, and now there was a sac partially filled with air, partially filled with water, poised to become a swim bladder. Three questions arise: Did a new function arise in the biosphere? Yes, neutral bouyancy in the water column. Did it have cascading consequences for the evolution of the biosphere? Yes, new species, proteins and so forth.

Now comes the essential third question: Do you think you could say ahead of time all the possible Darwinian preadaptations of all organisms alive now, or just for humans? We all seem to agree that the answer is a clear "No". Pause. We cannot say ahead of time what the possible preadaptations are. As in the first paragraph, we really do not know what will happen. Part of the problem seems to be that we cannot prespecify all possible selective environments. How would we know we had succeeded? Nor can we prespecify the feature(s) of one or several organisms that might become preadaptations.

Then we can make no probability statement about such preadaptations: We do not know the space of possibilities, the sample space, so can construct no probability measure.

Can we have a natural law that describes the evolution of the swim bladder? If a natural law is a compact description available beforehand, the answer seems a clear No. But then it is not true that the unfolding of the universe is entirely describable by natural law. This contradicts our views since Descartes, Galileo and Newton. The unfolding of the universe seems to be partially lawless. In its place is a radically creative becoming.

Let me point to the Adjacent Possible of the biosphere. Once there were lung fish, swim bladders were in the Adjacent Possible of the biosphere. Before there were multicelled organisms, the swim bladder was not in the Adjacent Possible of the biosphere. Something wonderful is happening right in front of us: When the swim bladder arose it was of selective advantage in its context. It changed what was Actual in the biosphere, which in turn created a new Adjacent Possible of the biosphere. The biosphere self consistently co-constructs itself into its every changing, unstatable Adjacent Possible.

If the becoming of the swim bladder is partially lawless, it certainly is not entailed by the fundamental laws of physics, so cannot be deduced from physics. Then its existence in the non-ergodic universe requires an explanation that cannot be had by that missing entailment. The universe is open.

Part of the explanation rests in the fact that life seems to be evolving ever more positive sum games. As organismic diversity increases, and the "features" per organism increase, there are more ways for selection to select for mutualisms that become the conditions of joint existence in the universe. The humming bird, sticking her beak in the flower for nectar, rubs pollen off the flower, flies to a next flower for nectar, and pollen rubs off on the stamen of the next flower, pollinating the flower. But these mutualistic features are the very conditions of one another's existence in the open universe. The biosphere is rife with mutualisms. In biologist Scott Gilbert's fine phrase, these are codependent origination—an ancient Buddhist phrase. In this open universe, beyond entailment by fundamental physics, we have partial lawlessness, ceaseless creativity, and forever co-dependent origination that changes the Actual and the ever new Adjacent Possible we ceaselessly self-consistently co-construct. More, the way this unfolds is neither fully lawful, nor is it random. We need to re-envision ourselves and the universe.