The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and 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. This, the 14th Transactions on Computational Systems Biology volume, guest edited by Ion Petre and Erik de Vink, focuses on Computational Models for Cell Processes and features a number of carefully selected and enhanced contributions, initially presented at the CompMod workshop, which took place in Aachen, Germany, in September 2011. The papers, written from different points of view and following various approaches, cover a wide range of topics within the field of modeling and analysis of biological systems. In addition, two regular submissions deal with models of self-assembling systems and metabolic constraints on the evolution of genetic codes.

The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and 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. This, the 13th Transactions on Computational Systems Biology volume, guest edited by Ralph-Johan Back, Ion Petre, and Erik de Vink, focuses on Computational Models for Cell Processes and features a number of carefully selected and enhanced contributions initially presented at the CompMod workshop, which took place in Eindhoven, The Netherlands, in November 2009. From different points of view and following various approaches, the papers cover a wide range of topics in systems biology, addressing the dynamics and the computational principles of this emerging field.

Inspired by the interesting contributions to the 6th Conference on Compu- tional Methods in Systems Biology (CMSB 2008) and the Dagstuhl Seminar 09091on"FormalMethods inMolecular Biology"inFebruary2009, papershave been selected for this special issue of the journal TransactionsonComputational Systems Biology, under the title Modeling Methodologies. The special issue starts with a position paper on "Biomodel Engineering - from Structure to Behavior," which discusses the potential that concepts from traditional computing science hold for creating more powerful models of biol- ical systems and identi?es venues for challenging future research. The technical contributions of the special issue covera broadrangeof mod- ing methodologies that have recently been developed in computational systems biology. First, twonewmodelinglanguagesarepresented.The"Attributed?-Calculus withPriorities"presentsacombinationofaconcurrentprocesslanguage, i.e., the ?-calculus, and a sequential core language, i.e., the ?-calculus; being equipped withprioritiesthelanguageenablesthedescriptionofdiversespatialphenomena, di?erent kinetics, as well as an individual-based and population-based modeling of biological systems. It is shown how the di?erent dialects of the ? calculus, including the pi@-calculus, can be expressed. Its stochastic semantic is ?rmly rooted in CMTC's and is re?ected in the stochastic simulator.

Biology is witnessing a transformation towards a more quantitative science, based on the major technological breakthroughs of the past decade. In this transformation, biology is incorporating mathematical modeling techniques and computational approaches towards numerical simulations, model analysis, and quantitativepredictions.An importantgoalis to formalizeandanalyzethe ev- changing inter-connections between components (often on di?erent time and space scales), their in?uence on one another, regulatory patterns, alternative pathways, etc. Formal reasoning rather than empirical observations is the main driving force in this new type of biological research.At the same time, computer science and applied mathematics are faced with considerable methodological challenges in handling an unprecedented level of concurrency, stochastic e?ects, amixoflargeandsmallpopulations,combinatorialexplosionsinthe statespace, model re?nement, and model (de)composition, etc. ThisspecialissueofTransactionsonComputationalSystemsBiologyonC- putationalModels forCellProcessesisbasedonaworkshopwith thesamename that took place in Turku, Finland, on May 27, 2008. The workshop was or- nized as a satellite event of the 15th International Symposium on Formal Me- ods that took place in Turku in the period May 28-31, 2008. This special issue however had an open call for paper submissions, with a separate peer-review process. The accepted papers span an interesting mix of approaches to systems biology, ranging from quantitative to qualitative techniques, from continuous to discrete mathematics, from deterministic to stochastic methods, from compu- tional models for biology to computing paradigms inspired by biology. Overall, they give a good glimpse into some of the exciting current research avenues in computational systems biology.

This issue of the journal reports regular papers. The ?rst contribution is by ParasChopra and Andreas Bender and discusses quantitative modelling aspects of the bgl operon for E. coli. The second contribution is by Rodrick Wallace and Deborah Wallace and deals with ecosystem transitions a?ecting phenotype - pressions and selection mechanisms. The techniques used are statistical models. The thirdcontributionis byRoberto Barbuti, Andrea Maggiolo-Schettini, Paolo Milazzo, Paolo Tiberi and Angelo Troina and presents the Stochastic Calculus of Looping Sequences (SCLS) suitable for the description of microbiologicals- tems, such as cellular pathways, and their evolution. The last contribution is by Federica Ciocchetta and describes the use of biological transactions to make atomic sequences of interactions in the BlenX language. May 2008 Corrado Priami LNCS Transactions on Computational Systems Biology - Editorial Board Corrado Priami, Editor-in-chief University of Trento, Italy Charles Au?ray Genexpress, CNRS and Pierre & Marie Curie University, France Matthew Bellgard Murdoch University, Australia Soren Brunak Technical University of Denmark, Denmark Luca Cardelli Microsoft Research Cambridge, UK Zhu Chen Shanghai Institute of Hematology, China Vincent Danos CNRS, University of Paris VII, France Eytan Domany Center for Systems Biology, Weizmann Institute, Israel Walter Fontana Santa Fe Institute, USA Takashi Gojobori National Institute of Genetics, Japan Martijn A.

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 5th Transactions on Computational Systems Biology volume, edited by Gordon Plotkin, features carefully selected and enhanced contributions initially presented at the 2005 IEEE International Conference on Granular Computing. The 9 papers selected for this special issue discuss various aspects of computational methods, algorithm and techniques in bioinformatics such as gene expression analysis, biomedical literature mining and natural language processing, protein structure prediction, biological database management and biomedical information retrieval.

This volume, the 7th in the Transactions on Computational Systems Biology series, contains a fully refereed and carefully selected set of papers from two workshops: BioConcur 2004 held in London, UK in August 2004 and BioConcur 2005 held in San Francisco, CA, USA in August 2005.

The 8 papers chosen for this special issue are devoted to various aspects of computational methods, algorithms, and techniques in bioinformatics.

This book constitutes the refereed proceedings of the International Conference on Computational Methods in Systems Biology, CMSB 2006, held in Trento, Italy, in October 2006. The 22 fully revised papers presented together with 2 invited talks were carefully reviewed and selected from 68 submissions. The papers present a variety of techniques from computer sciences, such as language design, concurrency theory, software engineering, and formal methods.

This, the 4th Transactions on Computational Systems Biology volume, contains carefully selected and enhanced contributions presented at the first Converging Science conference held at the University of Trento, Italy, in December 2004.

Dedicated especially to models and metaphors from biology to bioinformatics tools, the 11 papers selected for the special issue cover a wide range of bioinformatics research, such as foundations of global computing, interdisciplinarity in innovation initiatives, biodiversity, and more.

In the last few decades, advances in molecular biology and in the research - frastructure in this ?eld has given rise to the omics revolution in molecular biology, alongwiththeexplosionofdatabases: fromgenomicstotranscriptomics, proteomics, interactomics, and metabolomics. However, the huge amount of b- logicalinformationavailablehasleftabottleneckindataprocessing: information over?ow has called for innovative techniques for their visualization, modelling, interpretationandanalysis.The manyresultsfromthe ?eldsofcomputerscience andengineeringhavethenmetwithbiology, leadingto new, emergingdisciplines such as bioinformatics and systems biology. So, for instance, as the result of - plicationoftechniquessuchasmachinelearning, self-organizingmaps, statistical algorithms, clusteringalgorithmsandmulti-agentsystemstomodernbiology, we can actually model and simulate some functions of the cell (e.g., protein inter- tion, gene expression and gene regulation), make inferences from the molecular biology database, make connections among biological data, and derive useful predictions. Today, and more generally, two di?erent scenarios characterize the po- genomic era. On the one hand, the huge amount of datasets made available by biological research all over the world mandates for suitable techniques, tools and methods meant at modelling biological processes and analyzing biological sequences. On the other hand, biological systems work as the sources of a wide range of new computational models and paradigms, which are now ready to be applied in the context of computer-based syst

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."

Thisisthe?rstissueofanewjournaloftheLNCSjournalsubline.Theaimofthe journal is to encourage inter- and multidisciplinary research in the ?elds of c- puter science and life sciences. The recent paradigmatic shift in biology towards a system view of biological phenomena requires a corresponding paradigmatic shift in the techniques from computer science that can face the new challenges. Classical tools usually used in bioinformatics are no longer up to date and new ideas are needed. The convergence of sciences and technologies we are experiencing these days is changing the classical terms of reference for research activities. In fact clear distinctions between disciplines no longer exist because advances in one ?eld permit advances in others and vice versa, thus establishing a positive feedback loop between sciences. The potential impact of the convergence of sciences and technologies is so huge that we must consider how to control and correctly drive our future activities. International and national funding agencies are looking at interdisciplinary research as a key issue for the coming years, especially in the intersection of life sciences and information technology. To speed up this process, we surely need to establish relationships between researchers of di?erent communities and to de?ne a common language that will allow them to exchange ideas and - sults. Furthermore, expectations of di?erent communities can be merged only by running activities like common projects and experiences. TheTransactionsonComputationalSystemsBiologycouldbeagoodforumto helplifescientistsandcomputerscientiststodiscusstogethertheircommongoals.

This volume collects revised versions of some of the papers presented at the S- ond IST/FET International Workshop on Global Computing held in Rovereto, Italy (9-12 March, 2004). The workshop involved all the thirteen projects funded under the IST/FET proactive initiative on GLOBAL COMPUTING: AGILE; CRESCCO; DART; DBGLOBE;DEGAS;FLAGS;MIKADO;MRG;MYTHS;PEPITO;PROFUN- DIS; SECURE; SOCS. The ?rst aim of the GLOBAL COMPUTING initiative is the development of paradigms for building ?exible, dependable, secure, robust and e?cient systems. Primaryresearchconcernsaretheco-ordination, interaction, security, reliability, robustness, and risk control of the entities in the global system. The ultimate goaloftheresearchactionistoprovideasolidscienti?cfoundationforthedesign of such systems, and to lay the groundwork for achieving e?ective principles for building and analysing them. Theworkshopcoveredtopicsrelatedtoprogrammingenvironments, dynamic recon?guration, resource guarantees, peer-to-peer networks, analysis of systems and resources, resource sharing, and security, as well as foundational calculi for mobility. The present collection o?ers a rich sample of research results on the above subjects. We acknowledge the Dipartimento di Informatica e Telecomunicazioni of the University of Trento for partially funding the workshop, and the Events and Meetings O?ce of the University of Trento for the valuable collaborat

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.

This book constitutes the refereed proceedings of the International Workshop on Computational Methods in Systems Biology, CMSB 2003, held in Rovereto, Italy, in February 2003. The 11 revised full papers presented together with 2 invited papers, 7 position papers, and 11 abstracts were carefully reviewed and selected from 30 submissions. Among the topics addressed are modeling languages for systems biology, concurrency in biological systems, constraint programming, logical methods in systems biology, formal methods for the analysis of biomolecular systems, quantitative analysis of biomolecular systems, and simulation and modeling techniques for systems biology.

This book explains the state-of-the-art algorithms used to simulate biological dynamics. Each technique is theoretically introduced and applied to a set of modeling cases. 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. An appendix covers the mathematical background, and the authors include further reading sections in each chapter.

This Festschrift volume is published in honor of Pierpaolo Degano on the occasion of his 65th birthday and is the outcome of a colloquium held in Pisa, Italy, in June 2015. Pierpaolo Degano has worked on a large variety of topics including formal program semantics, concurrency theory, systems biology and security. The volume contains 22 refereed papers and one extended abstract, including personal memoirs and regular research papers by close collaborators and friends and a laudatio illustrating his distinguished career and his main scientific contributions. The papers deal with the main research topics explored by Pierpaolo Degano and those still under his investigation.

Technology is taking us to a world where myriads of heavily networked devices interact with the physical world in multiple ways, and at many levels, from the globalInternetdowntomicroandnanodevices. Manyofthesedevicesarehighly mobile and autonomous and must adapt to the surrounding environment in a totally unsupervised way. A fundamental research challenge is the design of robust decentralized c- puting systemsthat arecapableofoperating in changing environmentsandwith noisy input, and yet exhibit the desired behavior and response time, under c- straints such as energy consumption, size, and processing power. These systems should be able to adapt and learn how to react to unforeseen scenarios as well as to display properties comparable to social entities. The observation of nature has brought us many great and unforeseen concepts. Biological systems are able to handle many of these challenges with an elegance and e?ciency far beyond currenthumanartifacts. Basedonthisobservation, bio-inspiredapproacheshave been proposed as a means of handling the complexity of such systems. The goal is to obtain methods to engineer technical systems, which are of a stability and e?ciency comparable to those found in biological entities. This Special Issue on Biological and Biologically-inspired Communication contains the best papers from the Second International Conference on Bio- Inspired Models of Network, Information, and Computing Systems (BIONET- ICS 2007). The BIONETICS conference aims to bring together researchers and scientistsfromseveraldisciplines incomputerscienceandengineeringwhereb- inspired methods are investigated, as well as from bioinformatics, to deepen the information exchange and collaboration among the di?erent communities

Modeling is fast becoming fundamental to understanding the processes that define biological systems. High-throughput technologies are producing increasing quantities of data that require an ever-expanding toolset for their effective analysis and interpretation. Analysis of high-throughput data in the context of a molecular interaction network is particularly informative as it has the potential to reveal the most relevant network modules with respect to a phenotype or biological process of interest.Analysis of Biological Systems collects classical material on analysis, modeling and simulation, thereby acting as a unique point of reference. The joint application of statistical techniques to extract knowledge from big data and map it into mechanistic models is a current challenge of the field, and the reader will learn how to build and use models even if they have no computing or math background. An in-depth analysis of the currently available technologies, and a comparison between them, is also included. Unlike other reference books, this in-depth analysis is extended even to the field of language-based modeling. The overall result is an indispensable, self-contained and systematic approach to a rapidly expanding field of science.