B iological S cripting L anguage Jared Eng Jay Kota Igor Marfin Amna Qaiser Jared Eng Jay Kota Igor Marfin Amna Qaiser BSL

Background / Overview Sequence handling  DNA, RNA, amino acid etc…  Nucleotides A, C, G, T, U, F, L, S, Y, C, etc …  Sizeable number  Massive amounts

BSL Functionality Specializes in sequence manipulation, translation, and analysis Methods  Access  Search  Align  Map  Translate

Sample Script /* Here is a test script */ start method int TestMethod (Sequence a, Sequence b) Print: a, “myfile.txt”; return 0; end method; new Sequence dnaSeq1 type DNA = “AGGGAACCTT”; new Sequence dnaSeq2 type DNA = “AGGAACTC”; new int dnaSum; dnaSum = TestMethod: dnaSeq1, dnaSeq2; Print: dnaSum; /* End script */

Syntax and Semantics Primitives and BSL objects (int vs Sequence)  Sequence has “type” associated with it Properties: length, type, value Method calls: Align: Sequence, Sequence; User defined methods (Overloading)

Architecture Overview  Used ANTLR  Invoke using java BSL_TreeParser  Input:.bsl file  Outputs java file and compiles the file

BSL Implementation  Method symbol tables  Java Classes handle method calls  Align is taken care of by Aligner  Uses Smith-Waterman Algorithm  Approach to implementation  Modularity allowed for faster coding time  Easier testing

Testing Plan Phase I  BSL Libraries  Lexer and Parser (Grammar) Phase II  Code Generator  Combined Testing

Lessons and Future Goals Start early Keep minutes Stay focused Incorporate more algorithms Access online databases Make millions and retire early