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

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B iological s cripting l anguage

BSL

B iological S cripting L anguage

Jared Eng Jay Kota

Igor Marfin Amna Qaiser


Background overview

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

BSL Functionality

  • Specializes in sequence manipulation, translation, and analysis

  • Methods

    • Access

    • Search

    • Align

    • Map

    • Translate


Sample script

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

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

Architecture Overview

  • Used ANTLR

  • Invoke using java BSL_TreeParser <file>

  • Input: .bsl file

  • Outputs java file and compiles the file


Bsl implementation

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

Testing Plan

  • Phase I

    • BSL Libraries

    • Lexer and Parser (Grammar)

  • Phase II

    • Code Generator

    • Combined Testing


Lessons and future goals

Lessons and Future Goals

  • Start early

  • Keep minutes

  • Stay focused

  • Incorporate more algorithms

  • Access online databases

  • Make millions and retire early


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