1. Protein Manipulation Domain Specific Language Lu Sun Shuo Wu

2. Outline Background Development Environment Goals of DSL Grammar model Grammar Editor Code generation Future work and Conclusion

3. Background DSL General-purpose programming language C, Java or Python Domain specific language SQL, HTML, YACC Xtext Define grammar Xtend Language execution

4. Development Environment Operating System: Windows 7 Eclipse Integrated with Xtext JDK 1.7

5. Goals of DSL The PDB(Protein Data Bank) file is used to describe protein structures. An example of PDB files: Only desceibe the name of the atoms as well as their coordinates. ATOM 1 N GLN A 1 12.606 0.298 -13.791 ATOM 2 CA GLN A 1 13.611 1.223 -13.286 ATOM 3 C GLN A 1 14.099 0.753 -11.915 ATOM 4 O GLN A 1 15.229 1.025 -11.507 ATOM 5 CB GLN A 1 13.013 2.631 -13.203 ATOM 6 CG GLN A 1 13.956 3.685 -12.648 ATOM 7 CD GLN A 1 13.321 5.064 -12.624

6. Goals of DSL Our DSL is designed to simplify management and manipulation of the protein description file. expected functionality: import and export protein conformations into or from the DSL program. implement insert and link operations on the protein objects.

7. Grammer - semantic model

8. Grammer

9. //Declaration of protein protein p //import a protein conformation from an external file import 'input.pdb' into p //export a protein conformation into an external file dump 'output.pdb' from p

10. Grammer //link two proteins combine p1 p2 into p //insert a segment into a protein insert p1(12,33) into p2(124,145)

11. Grammer declaration operation *The operations can be in any orders

12. Editor  Eclipse and Xtext automatically generate an editor with code completion and error checking.

13. Editor

14. Code Generation

17. Future Work and Conclusion Grammer Evolution Add iteration to handle the batch task Optimize the structure of the grammer Functionality Evolution Complete the functionalities Manipulate protein structure in other ways Compare a pair of protein’s structure Conclusion Natual language like Easy to use