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Team:Berkeley Software/LesiaNotebook/Notes
From 2009.igem.org
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, [http://sbml.org/Main_Page SBML], or [http://bionetgen.org/index.php/Main_Page BNGL], as BOL will be a structural human readable language not geared towards modeling. BOL has a direct relationship to [http://openwetware.org/wiki/Endy:Notebook/BioBrick_Open_Graphical_Language BOGL] symbols, 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 [http://openwetware.org/wiki/Endy:Notebook/BioBrick_Open_Graphical_Language 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 [http://www.gnu.org/software/bison/ 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 [http://bionetgen.org/index.php/Main_Page 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.
Friday created Plugin help file in Clotho. Created plugin xml file generator, which will automatically create a xml file to connect the Plug-in once the information is filled in. Also displays the xml file in the window.
Week of June 15, 2009
Monday had the presentation on Plug-Ins. Got feedback from group and Professor Anderson on the Plug-In xml file generator:
- Have mouse overs on each field that needs to be filled
- Make option to save the xml file under user specified name
- Make restrictions on choice for the interface and package name, since they have to correspond to each other
Started familiarizing myself with [http://www.antlr.org/ ANTLR].
Tuesday had a meeting
