European Lisp Symposium

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The conference is over!

Highlights

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

    • 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 (CONFERENCE)
351 Cours de la Libération
Talence 33400 France

Hotels

Organization

Programme Chair

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

Committee

  • António Leitão António Leitão Technical University of Lisbon (COMMITTEE SPEAKER) Portugal
  • Christophe Rhodes Christophe Rhodes Goldsmiths University of London (COMMITTEE SPEAKER) United Kingdom
  • Didier Verna Didier Verna http://www.european-lisp-symposium.org EPITA (ADMINISTRATOR COMMITTEE SPEAKER) France
  • Durand Irène Durand Anne Irène Université Bordeaux (COMMITTEE) France
  • Erick Gallesio Erick Gallesio Université de Nice / Sophia Antipolis (COMMITTEE) France
  • Henry Lieberman Henry Lieberman MIT (COMMITTEE) USA
  • Jeffrey Siskind Jeffrey Mark Siskind Purdue University (COMMITTEE) USA
  • Jerry Boetje Jerry Boetje College of Charlston (COMMITTEE) USA
  • Kent Pitman Kent Pitman PTC (COMMITTEE) USA
  • Marc Feeley Marc Feeley Université de Montréal (COMMITTEE) Canada
  • Marco Antoniotti Marco Antoniotti Universita Milano Bicocca (COMMITTEE SPEAKER) Italy
  • Marie Beurton-Aimar Marie Beurton-Aimar Université Bordeaux (COMMITTEE) France
  • Nicolas Neuss Nicolas Neuss Universität Karlsruhe (COMMITTEE) Germany
  • Rainer Joswig Rainer Joswig Independent Consultant (COMMITTEE) Germany
  • Ralf Möller Ralf Möller Hamburg University of Technology (COMMITTEE) Germany
  • Scott McKay Scott McKay ITA Software (COMMITTEE) USA
  • 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

  14. Reception at City Hall

  15. May 23rd

  16. Registration

  17. Welcome Message

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

    • Marco Antoniotti
  19. Coffee

  20. Context-Oriented Programming with the Ambient Object System

    • Sebastián González
    • Kim Mens
    • Alfredo Cádiz
  21. Reasoning about qualitative temporal information with S-words and S-languages

    • Irène Durand
    • Sylviane Schwer
  22. Lunch

  23. Binary Methods Programming: the Clos Perspective

    • Didier Verna
  24. Custom Specializers in Object-Oriented Lisp

    • Jim Newton
    • Christophe Rhodes
  25. UCL-GLORP - An ORM for Common Lisp

    • António Leitão
  26. Coffee

  27. An Implementation of CLIM Presentation Types

    • Timothy Moore
  28. Visual Programming in PWGL

    • Mikael Laurson
    • Mika Kuuskankare
  29. Conference End

  30. Conference Dinner

Proceedings

You can find the proceedings in PDF form here:

../static/proceedings/2008.pdf