European Lisp Symposium

- 2008, Talence
(and online)
The conference is over!

Highlights

  • The Right Mix: Common Lisp in Bioinformatics, Systems Biology and in the Larger Semantic Network World

    • photo Marco Antoniotti Marco Antoniotti Universita Milano Bicocca (COMMITTEE SPEAKER) Italy

    Working with CL nowadays is a choice based on a long programming experience (and/or lazyness and or/inertia). Many times this choice is hard because of a number of entrenched limitations of the CL (or simply Lispy) world: lack of many agreed upon, modern and portable extensions, and lack of new programmers being the most visible. Yet, this talk will argue that the situation has improved and that CL is even more "the right mix" for many researchers in the sciences, and, in particular, in the fields I have been working for a few years. For CL, being the right mix comes from the strenghts of the standard and of the nature itself of the language. The ability to build code with more than decent numerical performance and the ability to morph in any (declarative) DSL are the key characteristics that make CL the right tool for many of the sciences. Bioinformatics and Systems Biology are two relatively broad terms that serve to describe a number of system and algorithmic solutions to problems stemming from the needs of biologists and clinicians. Very roughly speaking, these terms cover the range from "sequence analysis" (DNA, RNA, and protein) to statistical interpretation of "high throughput experiments" (micro-array and new ion-trap protein studies), to model simulation and testing of metabolic, regulatory and signaling pathways. The numerical capabilities of CL do fit well with these problems. On the other end, these problems require the support of many data manipulation, sharing and, above all, description systems that nowadays are continuously crystallized in different "ontologies" and "controlled vocabularies" which are then rendered in XML/RDF. CL systems for solving such "representation" task predate all of these efforts and it should come to no surprise that Lisp-based systems provide a very good platform to build more expressive DSL's capable of improving the inference capabilities of the tools needed by biologists and physicians. At this point in time, the "basic library" situation for CL is good enough to support its use in the field. CLSQL and XML parsing libraries are the basis for such use. Numerical libraries abound, as well as web development frameworks. Writing inference engines and DSL's has never been a problem for CL programmers and researchers. It is therefore a well founded conclusion that CL is a "well mixed solution" for Bioinformatics and Systems Biology, life, universe and everything else. It just needs to be put together. Marco Antoniotti is an Associate Professor at the Dipartimento di Informatica Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Italy. His interests concentrate in the field of Computational and Systems Biology. He is the author or co-author of several papers and software systems - SHIFT from UC Berkeley, Jester from PARADES, Simpathica and GOALIE from NYU - and co-authored three patents in the field of Genomics Optical Mapping. He received his PhD from New York University in 1995.

Location

photo LaBRI Université Bordeaux https://www.labri.fr/ (CONFERENCE) 351 Cours de la Libération 33400 Talence France

Hotels

Organization

Programme Chair

  • photo Pascal Costanza Pascal Costanza Vrije Universiteit Brussel (PROGRAMME-CHAIR) Belgium

Organizing Chair

Committee

  • photo António Leitão António Leitão Technical University of Lisbon (COMMITTEE SPEAKER) Portugal
  • photo Christophe Rhodes Christophe Rhodes Goldsmiths University of London (COMMITTEE SPEAKER) United Kingdom
  • photo Didier Verna Didier Verna https://www.didierverna.info EPITA / LRE (ORGANIZING-CHAIR COMMITTEE SPEAKER) France
  • photo Durand Irène Durand Anne Irène Université Bordeaux (COMMITTEE) France
  • photo Erick Gallesio Erick Gallesio Université de Nice / Sophia Antipolis (COMMITTEE) France
  • photo Henry Lieberman Henry Lieberman MIT (COMMITTEE) USA
  • photo Jeffrey Siskind Jeffrey Mark Siskind Purdue University (COMMITTEE) USA
  • photo Jerry Boetje Jerry Boetje College of Charlston (COMMITTEE) USA
  • photo Kent Pitman Kent Pitman PTC (COMMITTEE) USA
  • photo Marc Feeley Marc Feeley Université de Montréal (COMMITTEE) Canada
  • photo Marco Antoniotti Marco Antoniotti Universita Milano Bicocca (COMMITTEE SPEAKER) Italy
  • photo Marie Beurton-Aimar Marie Beurton-Aimar Université Bordeaux (COMMITTEE) France
  • photo Nicolas Neuss Nicolas Neuss Universität Karlsruhe (COMMITTEE) Germany
  • photo Rainer Joswig Rainer Joswig Independent Consultant (COMMITTEE) Germany
  • photo Ralf Möller Ralf Möller Hamburg University of Technology (COMMITTEE) Germany
  • photo Scott McKay Scott McKay ITA Software (COMMITTEE) USA
  • photo Theo D'Hondt Theo D'Hondt Vrije Universiteit Brussel (COMMITTEE) Belgium

Programme

Times are local to the conference. You can download the programme in iCalendar format here.

  1. May 22nd

  2. Registration

  3. Welcome Message

  4. Writers' Workshop I

  5. Writers' Workshop II

  6. Coffee

  7. Writers' Workshop III

  8. Writers' Workshop IV

  9. Lunch

  10. Writers' Workshop V

  11. Writers' Workshop VI

  12. Writers' Workshop VII

  13. Coffee

  15. Reception at City Hall

  17. May 23rd

  18. Registration

  19. Welcome Message

  20. The Right Mix: Common Lisp in Bioinformatics, Systems Biology and in the Larger Semantic Network World

    • Marco Antoniotti

  21. Coffee

  22. Context-Oriented Programming with the Ambient Object System

    • Sebastián González
    • Kim Mens
    • Alfredo Cádiz

  23. Reasoning about qualitative temporal information with S-words and S-languages

    • Irène Durand
    • Sylviane Schwer

  24. Lunch

  25. Binary Methods Programming: the Clos Perspective

    • Didier Verna

  26. Custom Specializers in Object-Oriented Lisp

    • Jim Newton
    • Christophe Rhodes

  27. UCL-GLORP - An ORM for Common Lisp

    • António Leitão

  28. Coffee

  29. An Implementation of CLIM Presentation Types

    • Timothy Moore

  30. Visual Programming in PWGL

    • Mikael Laurson
    • Mika Kuuskankare

  31. Conference End

  33. Conference Dinner

Proceedings

You can find the proceedings in PDF form here:

../static/proceedings/2008.pdf

Please wait...