Team:Berkeley Software/LesiaNotebook

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Week of June 8, 2009

Monday was the first day of the SUPERB program. I got introduced to the IGEM team. Doug gave a tutorial on Clotho and on plug ins. Got the Clotho source code from the repository.

""Tuesday"" we had a meeting. I will be working with Adam on the language project. BOL will be a language which is based on the abstract model of parts which form the lowest level of hierarchy and will be the basic data types in this language. Parts can be composed of other parts, but in themselves cannot be decomposed any further into lower level data types. Devices will be at the second level of hierarchy and can consist of multiple devices as well as parts. It will be different from other languages like Antimony, SBML, or BNGL, as BOL will be a structural human readable language not geared towards modeling. BOL has a direct relationship to BOGL parts, the graphical representation and can be used to convert textual designs to graphical representations and vice versa.

""Wednesday"" brainstormed with Adam on the syntax of BOL. It will have defined data structures based on the BOGL symbols like promoter, RFS. Supportive data types will be string, int, composite. Also, an important feature that we would like BOL to have is the ability to create more user defined data types. I created a preliminary data type table on properties, data types, operators. Also started familiarizing myself with GNU Bison, which we will use as our parser for the language.

""Thursday"" continued to work on syntax and to write the code for an available diagram. Researched more on other languages. It seems that BOL will indeed be different from previous languages. The rule based description has been implemented in BNGL, which is a modeling language and concentrates on species, molecules rather than standard parts. We still have to go over the syntax for rules and how we will implement them in BOL. The logical "AND", "OR" and complement operators, as well as <, > seem appropriate for right now.