Introductory Material

This page provides a summary of readings and links that might be of interest to AVISPA members. Return to the AVISPA Website.

• Constraint Programming: Strategic Directions by P. Van Hentenryck and V. Saraswat. A nicely written introduction to CP; some interesting application areas are explained. This paper appeared in the Journal Constraints.
• Constraint Programming: In Pursuit of the Holy Grail by Roman Bartak. See also his Online Guide to Constraints.
• See Barbara Smith's introduction to CP (slides). See also her Talks page for more introductory material.
• Tutorials on Soft Constraints (Slides):
  • Soft constraints: models, algorithms, and applications by P. Meseguer, F. Rossi, T. Schiex. This set of slides was presented in CP 2001. Contains lots of references and concrete eamples. Download it from Rossi's site: part one, part two and part three.
  • Soft Constraint Solving by J. Larrosa and T. Schiex. A tutorial recently presented in CP 06.

• Languages for Concurrency by C. Palamidessi and F. Valencia. This paper is an excellent introduction to concurrency, explaining the main features that models for concurrency usually have. This piece will appear in the Bulletin of EATCS.
• Welcome to the Jungle. A subjective guide to mobile process calculi by Uwe Nestmann. This paper corresponds to a tutorial given at CONCUR 2006, the international conference on concurrency theory.
• A Brief History of Process Algebra by J.C.M. Baeten.
• Modelos para la Computación Móvil by J. F. Díaz and C. Rueda. In this paper three calculi for mobile processes are explained: Milner's Pi, Cardelli and Gordon's Ambient and AVISPA's PiCO. Includes examples. This paper appeared in the Colombian Journal of Computing.
• Notes on Timed CCP by M. Nielsen and F. D. Valencia. This note provides an overview of timed ccp with its basic background and various approaches explored in the literature. Furthermore, the note offers an introduction to the ntcc process calculus.

Papers on bioinformatics, with good (and easy to read) background on molecular biology:

• Recommended !!! Molecular Biology for Computer Scientists by Lawrence Hunter. Chapter 1 of the Book “Artificial Intelligence and Molecular Biology”, freely available from this page
• Bioinformatics—An Introduction for Computer Scientists by Jacques Cohen. This paper appeared in ACM Computing Surveys.

These two papers by Hiroaki Kitano (see this page) are excellent references to understand what biologists want from systems biology. They're not very easy to read, though:

• Systems Biology: A Brief Overview. This paper appeared on Science.
• Computational systems biology. This paper appeared on Nature.

This book provides good background. It's in Javeriana Library (006C646c e1)

• Computational Molecular Biology: An Introduction by R. Backofen and P. Clote.

Papers on biology and process calculi:

• Modelamiento de Sistemas Biológicos Utilizando Cálculos de Procesos (In Spanish) by J. Gutiérrez, J. A. Pérez and C. Rueda. This is an introductory paper to biology and process calculi for biology, with an emphasis on how Concurrent Constraint Programming can help in Biology. This paper appeared in Epiciclos.
• Process Calculi in a Biological Context by D. Prandi and C. Priami and P. Quaglia. This paper appeared in the Concurrency Column of the Bulletin of the EATCS (European Association on Theoretical Computer Science).
• Timed Concurrent Constraint Programming for Analyzing Biological Systems by J. Gutiérrez, J. A. Pérez, C. Rueda and F. Valencia. In this paper it is explained how ntcc fits in the biological context; the calculus is introduced with bio examples and a simple cellular system is modelled and verified.

• Computer aided music harmonization by F. Pachet. A broad overview of the use of constraints for musical harmonization. Includes a brief summary of harmonic rules.
• machine learning of musical style by Dubnov, Assayag et al. This papers introduces statistical models for machine learning of a composer musical style. Once the style is learned, the musician can improvise with a sort of “clone” of himself modeled in the computer.

• A Survey of Authentication Protocol Literature: Version 1.0 by J. Clark and J. Jacob. Excellent, self-contained introduction to authentication and protocols in general.
• Prudent engineering practice for cryptographic protocols by M. Abadi and R. Needham. This paper introduces to basic notions of security and security protocols. It's a good first reading on the subject, as it presents principles for protocol design instead of a particular formalism.
• Security Protocols and their Properties by M. Abadi. Another good introductory paper. Some notions of name-passing calculi are explained in a very gently way.
• A calculus for cryptographic protocols: The spi calculus by M. Abadi and A. Gordon. Everyone interested in formal methods for security should read and understand this paper. Some knowledge on pi and security notions is advisable. This paper appeared in Information and Computation.

• Jefferson D. Bates. Writing with precision: How to write so that you cannot be possible misunderstood. Penguin Books, 2000.
• Lyn Drupé. Bugs in writing: A guide to debugging your prose, Revised Edition. Addyson Wesley Longman, 1998.
• Michel Swan. Practical English Usage, Third Edition. Oxford University Press.

• Process Calculi / Concurrency Theory and their Applications
  • First you might want to read something about Computer Science
  • Calculi for Mobile Processes. Recommended. This is an excellent starting point for newcomers.
  • Wikipedia entries on Process_calculi and Pi-calculus
  • Pi4 Technologies Foundation These guys are interested in applying process algebra and other concurrency formalisms to software development. It seems to be a nice place to learn about real applications of process calculi.
  • Jonathan Bowen's page on Concurrent Systems
  • Theory and Semantics Group at Cambridge
  • Subscribe to the newsletter of the ALP - Association for Logic Programming. Includes articles on the relationship of logic (programming) with concurrency, constraints, verification, and several other areas.
  • Concurrency Group at Stanford
  • Luca Aceto's blogs: Process Algebra Diary and Concurrency Theory
  • Vijay Saraswat's page dedicated to the concurrent constraint programming (ccp) model.
  • Kohei Honda's Selected Bibliography on Mobile Processes
  • SPORE - Security Protocols Open REpository: a very complete reference of security protocols, including description, known attacks and claimed proofs for each of them.
  • Security Protocols Papers and Links This is an excellent site that chronologically lists the most relevant papers on security and protocols <color red> Recommended</color>.
  • Visit the home pages of some experts in formal security: Martin Abadi, Peter Ryan.David Basin

• Constraint Satisfaction
  • The Mozart Programming System
  • The Gecode environment for developing constraint-based systems and applications.
  • Roman Barták's Online Guide to Constraint Programming
  • Wikipedia's entry on Arc_consistency techniques it's very complete
  • Constraint Programming Online, a site maintained by the ACP - Association for Constraint Programming
  • Yahoo! discussion group on constraints
  • Constraint Satisfaction FAQ
  • Interval Arithmetic

• Multimedia Interaction / Music
  • Sibelius Academy
  • Society for Music Theory
  • The OpenMusic web site at IRCAM

(by AVISPA members)

• Concurrency, Time and Constraints: a reduced version of this talk by Frank Valencia (AVISPA Seminar, November 10, 2006)
• Solving Constrained Graph Problems using Reachability Constraints based on Transitive Closure and Dominators: these are slides of the public PhD defense of Luis O. Quesada (November 10, 2006).
• A Gentle Introduction to Languages for Concurrency (AVISPA Seminar, November 3, 2006)
• An Introduction to the REACT Project (In Spanish) This talk was given in the Seminario I course (October 18, 2006).
• Using a Timed Concurrent Constraint Process Calculus for Modeling and Verifying Biological Systems This talk was given in MeCBIC'06, Venice, Italia.
• SeminarioI-2007 This talk (in Spanish) was given to the course Seminario I, at Universidad Javeriana-Cali (February 2007).
• NTTC and the http://cic.puj.edu.co/~ggutierrez/lect/slides
• NTTC Applications
• Interview with a musician about music improvisation