Bøger af Corrado Priami

Inresponsetothecallforpapers39weresubmittedtoCMSB2003. Allthe submittedpaperswerereviewedandtheprogrammecommittee(listedbelow) selected11high-qualitypapersforpublicationinthisvolume. Thecareofthe reviewersandoftheprogrammecommitteemembersinreviewingthepapers wassurelyvaluable. Afurther11paperswereselectedonlyforpresentationat theworkshopinordertostimulatediscussions(anabstractisincluded). AttheworkshopEhudShapiroandMichaelSterngavetwoinvited talks whosetopicsaredescribedinpapersincludedinthisvolume. Theprogramme committeedecidedtoacceptforpublicationinthisvolumealsosomeposition papers that highlight the research trends in this new ?eld of computational methodsinsystemsbiology. Thereasonisthatbecausethisisthe?rstedition ofaworkshopinthisfast-growing?eldalargeviewofpotentialtopicsofresearch wasconsideredextremelyimportant. Rovereto,December2002 CorradoPriami ProgrammeCommitteeofCMSB 2003 CorradoPriami(Chair),UniversityofTrento(Italy), CharlesAu?ray,CNRS,Villejuif(France), CosimaBaldari,Universit`adiSiena(Italy), AlexanderBockmayr,Universit¿eHenriPoincar¿e(France), LucaCardelli,MicrosoftResearchCambridge(UK), VincentDanos,Universit¿eParisVII(France), PierpaoloDegano,Universitad ` iPisa(Italy), Francois ¿ Fages,INRIA,Rocquencourt(France), DrabløsFinn,NorwegianUniversityofScienceandTechnology,Trondheim(N- way), MonikaHeiner,BrandenburgUniversityofTechnologyatCottbus(Germany), InaKoch,UniversityofAppliedSciencesBerlin,(Germany), JohnE. Ladbury,UniversityCollegeLondon(UK), PatrickLincoln,SRI(USA), SatoruMiyano,UniversityofTokyo(Japan), GordonPlotkin,UniversityofEdinburgh(UK), SimonPlyte,PharmaciaCorporation(Italy), AvivRegev,WeizmannInstituteofScience(Israel), MagaliRoux-Rouqui¿e,BSMIPasteurInstitute(France), VincentSchachter,HybrigenicsParis(France), MasaruTomita,KeioUniversity(Japan), AdelindeUhrmacher,UniversityofRostock(Germany), AlfonsoValencia,CNB-CSIC,CentroNacionaldeBiotecnologia(Spain), OlafWolkenhauer,UMIST,Manchester(UK) Local Organizing Committee Corrado

The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences. It supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena. The six papers selected for this special issue cover a broad range of topics.

The goal of the IST/FET proactive initiative on Global Computing is to - tain models, frameworks, methods, algorithms to build systems that are ?exible, dependable, secure, robust and e?cient. The dominant concerns are those of handling the co-ordination and interaction, security, reliability, robustness, fa- uremodes,andcontrolofriskoftheentitiesinthesystemandtheoveralldesign, descriptionandperformanceofthesystemitself.Completelydi?erentparadigms of computer science may have to be developed to tackle these issues e?ectively. The research should concentrate on systems having the following characteristics: - The systems are composed of autonomous computational entities where - tivity is not centrally controlled, either because global control is impossible or impractical, or because the entities are controlled by di?erent owners. - The computational entities are mobile, due to the movement of the physical platforms or movement of the entity from one platform to another. - The con?guration varies over time. For instance, the system is open to the introduction of new computational entities and likewise their deletion. The behavior of the entities may vary over time. - The systems operate with incomplete information about the environment. For instance, information becomes rapidly out of date and mobility requires information about the environment to be discovered. Theultimategoaloftheresearchactionistoprovideasolidscienti?cfoundation for the design of such systems, and to lay the groundwork for achieving e?ective principles for building and analyzing such systems.

It gives me great pleasure to present the Special Issue of LNCS Transactions on Computational Systems Biology devoted to considerably extended versions of selected papers presented at the International Workshop on Bioinformatics Research and Applications (IWBRA 2005). The IWBRA workshop was a part of the International Conference on Computational Science (ICCS 2005) which took place in Emory University, Atlanta, Georgia, USA, May 22-24, 2005. See http://www.cs.gsu.edu/pan/ iwbra.htm for more details. The 10 papers selected for the special issue cover a wide range of bioinformatics research. The first papers are devoted to problems in RNA structure prediction: Blin et al. contribute to the arc-preserving subsequence problem and Liu et al. develop an efficient search of pseudoknots. The coding schemes and structural alphabets for protein structure prediction are discussed in the contributions of Lei and Dai, and Zheng and Liu, respectively. Song et al. propose a novel technique for efficient extraction of biomedical information. Nakhleh and Wang discuss introducing hybrid speciation and horizontal gene transfer in phylogenetic networks. Practical algorithms minimizing recombinations in pedigree phasing are proposed by Zhang et al. Kolliet al. propose a new parallel implementation in OpenMP for finding the edit distance between two signed gene permutations. The issue is concluded with two papers devoted to bioinformatics problems that arise in DNA microarrays: improved tag set design for universal tag arrays is suggested by Mandoiu et al. and a new method of gene selection is discussed by Xu and Zhang.

Starting from basic simulation algorithms, the book also introduces more advanced techniques that support delays, diffusion in space, or that are based on hybrid simulation strategies.This is a valuable self-contained resource for graduate students and practitioners in computer science, biology and bioinformatics.