68,425 research outputs found
The computer revolution in science: steps towards the realization of computer-supported discovery environments
The tools that scientists use in their search processes together form so-called discovery environments. The promise of artificial intelligence and other branches of computer science is to radically transform conventional discovery environments by equipping scientists with a range of powerful computer tools including large-scale, shared knowledge bases and discovery programs. We will describe the future computer-supported discovery environments that may result, and illustrate by means of a realistic scenario how scientists come to new discoveries in these environments. In order to make the step from the current generation of discovery tools to computer-supported discovery environments like the one presented in the scenario, developers should realize that such environments are large-scale sociotechnical systems. They should not just focus on isolated computer programs, but also pay attention to the question how these programs will be used and maintained by scientists in research practices. In order to help developers of discovery programs in achieving the integration of their tools in discovery environments, we will formulate a set of guidelines that developers could follow
Towards Understanding the Origin of Genetic Languages
Molecular biology is a nanotechnology that works--it has worked for billions
of years and in an amazing variety of circumstances. At its core is a system
for acquiring, processing and communicating information that is universal, from
viruses and bacteria to human beings. Advances in genetics and experience in
designing computers have taken us to a stage where we can understand the
optimisation principles at the root of this system, from the availability of
basic building blocks to the execution of tasks. The languages of DNA and
proteins are argued to be the optimal solutions to the information processing
tasks they carry out. The analysis also suggests simpler predecessors to these
languages, and provides fascinating clues about their origin. Obviously, a
comprehensive unraveling of the puzzle of life would have a lot to say about
what we may design or convert ourselves into.Comment: (v1) 33 pages, contributed chapter to "Quantum Aspects of Life",
edited by D. Abbott, P. Davies and A. Pati, (v2) published version with some
editin
Quantum fluctuations and life
There have been many claims that quantum mechanics plays a key role in the
origin and/or operation of biological organisms, beyond merely providing the
basis for the shapes and sizes of biological molecules and their chemical
affinities. These range from the suggestion by Schrodinger that quantum
fluctuations produce mutations, to the conjecture by Hameroff and Penrose that
quantum coherence in microtubules is linked to consciousness. I review some of
these claims in this paper, and discuss the serious problem of decoherence. I
advance some further conjectures about quantum information processing in
bio-systems. Some possible experiments are suggested.Comment: 10 pages, no figures, conference pape
McGenus: A Monte Carlo algorithm to predict RNA secondary structures with pseudoknots
We present McGenus, an algorithm to predict RNA secondary structures with
pseudoknots. The method is based on a classification of RNA structures
according to their topological genus. McGenus can treat sequences of up to 1000
bases and performs an advanced stochastic search of their minimum free energy
structure allowing for non trivial pseudoknot topologies. Specifically, McGenus
employs a multiple Markov chain scheme for minimizing a general scoring
function which includes not only free energy contributions for pair stacking,
loop penalties, etc. but also a phenomenological penalty for the genus of the
pairing graph. The good performance of the stochastic search strategy was
successfully validated against TT2NE which uses the same free energy
parametrization and performs exhaustive or partially exhaustive structure
search, albeit for much shorter sequences (up to 200 bases). Next, the method
was applied to other RNA sets, including an extensive tmRNA database, yielding
results that are competitive with existing algorithms. Finally, it is shown
that McGenus highlights possible limitations in the free energy scoring
function. The algorithm is available as a web-server at
http://ipht.cea.fr/rna/mcgenus.php .Comment: 6 pages, 1 figur
Ab initio RNA folding
RNA molecules are essential cellular machines performing a wide variety of
functions for which a specific three-dimensional structure is required. Over
the last several years, experimental determination of RNA structures through
X-ray crystallography and NMR seems to have reached a plateau in the number of
structures resolved each year, but as more and more RNA sequences are being
discovered, need for structure prediction tools to complement experimental data
is strong. Theoretical approaches to RNA folding have been developed since the
late nineties when the first algorithms for secondary structure prediction
appeared. Over the last 10 years a number of prediction methods for 3D
structures have been developed, first based on bioinformatics and data-mining,
and more recently based on a coarse-grained physical representation of the
systems. In this review we are going to present the challenges of RNA structure
prediction and the main ideas behind bioinformatic approaches and physics-based
approaches. We will focus on the description of the more recent physics-based
phenomenological models and on how they are built to include the specificity of
the interactions of RNA bases, whose role is critical in folding. Through
examples from different models, we will point out the strengths of
physics-based approaches, which are able not only to predict equilibrium
structures, but also to investigate dynamical and thermodynamical behavior, and
the open challenges to include more key interactions ruling RNA folding.Comment: 28 pages, 18 figure
Grid Added Value to Address Malaria
Through this paper, we call for a distributed, internet-based collaboration
to address one of the worst plagues of our present world, malaria. The spirit
is a non-proprietary peer-production of information-embedding goods. And we
propose to use the grid technology to enable such a world wide "open source"
like collaboration. The first step towards this vision has been achieved during
the summer on the EGEE grid infrastructure where 46 million ligands were docked
for a total amount of 80 CPU years in 6 weeks in the quest for new drugs.Comment: 7 pages, 1 figure, 6th IEEE International Symposium on Cluster
Computing and the Grid, Singapore, 16-19 may 2006, to appear in the
proceeding
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