Tutorial Fraglets : Computing with macromolecules

Fraglets:Computing with MacromoleculesA TutorialBIONETS SP2, Fraglets WorkshopBrussels, January 29-30, 2007Lidia Yamamoto, University of BaselTutorial Overview• Introduction: Original Fraglets, Fraglets in BIONETS• Fraglets Programming Basics: original and new instructions,examples• Programming Methodology: breaking down complexity,backwards derivation• Tools: Automatic code generator (partial), concentration and rateplots, reaction graph• Exercises• Summary and DiscussionLidia Yamamoto, Univ. Basel Fraglets Tutorial, BIONETS SP2, Jan 2007, Brussels 2/45Fraglets: Background• Creation around 2001 by C. Tschudin [AINS’03]– Inspiration: Molecular biology, cell metabolism, chemicalcomputing (Membrane Computing, Gamma, CHAM), multisetrewriting• Goals:– Automated protocol synthesis and evolution– Unified code and data representation (active+passivenetworking)– Efficient packet processing engine: simple instructions withconstant (short!) processing timeLidia Yamamoto, Univ. Basel Fraglets Tutorial, BIONETS SP2, Jan 2007, Brussels 3/45Fraglets: Background• Resulting language:– Fraglet= computation fragment= code= data= packet– Header tag matching, analogous to packet header processing– “Assembly language” of chemical computing:micro-instructions, human-unreadable programs, “write-only”code!Lidia Yamamoto, Univ. Basel Fraglets Tutorial, BIONETS SP2, Jan 2007, Brussels 4/45Fraglets in BIONETS• On-line evolution: start from working ...