B iological S cripting L anguage

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B iological S cripting L anguage
BSL

• Jared Eng Jay Kota
• Igor Marfin Amna Qaiser

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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

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BSL Functionality

• Specializes in sequence manipulation,
  translation, and analysis
• Methods
• Access
• Search
• Align
• Map
• Translate

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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 /

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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)

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Architecture Overview

• Used ANTLR
• Invoke using java BSL_TreeParser ltfilegt
• Input .bsl file
• Outputs java file and compiles the file

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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

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Testing Plan

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

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Lessons and Future Goals

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