1. MGX Team Sadashivudu Basani Jinny Sebastian Carlton Vaz Elizabeth Xu

2. What is Molecular Genetics eXplorer ? The Molecular Genetics Explorer is a BioQUEST software simulation that integrates genetics, biochemistry, and molecular biology to study a biological phenomenon. It is designed to show students the connections between these three key disciplines of modern molecular genetics. It is based on "Botstein's Triangle“. – quoted in Science 240:1439 (1988)BioQUEST Written by Prof. Brian White (UMB Biology) and Prof. Ethan Bolker (UMB Computer Science)

3. MGX as is…

4. Tools in Molecular Genetics eXplorer Genetics-explains biological phenomena in terms of genes. (e.g. how a flower color is inherited). Biochemistry- explains biological phenomena in terms of proteins. (e.g. how protein sequence in a flower determine protein structure and color). Molecular Biology- explains the relation between genes(DNA) and proteins.

5. Genetics Tool Cross any two organisms Self-cross any two organisms Mutate any organism

6. Biochemistry Tool Examine protein structure and color present in organisms. Compare amino acid sequence that make a protein. Edit/create protein sequence and determine protein structure and color.

7. Molecular Biology Examine pigment protein genes present in organism Design your own genes by editing or entering new DNA sequences. Can save edited DNA as new organism into green house. Compare DNA sequence of 2 pigment protein gene.

8. Overview of the biology

9. MGX Team Approach

10. Team approach towards the goal Steps defined Where are we now ? Where are we heading ?

11. Steps Defined Learn basics of the Biology involved with MGX. Understand the current application. Build UML Diagram. Get the requirements specification. List classes that need refactoring.

12. Learn about current application Functionality, Code and Structure

13. Build UML Diagram Build UML Diagram of the existing MGX application

14. MGX Team Where are we now ?

15. We have … Comprehended MGX source code. Understood that we can use some of the existing algorithms. Completed the UML diagram. Discussed with client the new requirements.

16. MGX Team Where are we heading?

17. We are … Moving close to finalizing the client requirements. Listing out the details of classes to be refactored. UI Design for new MGX tool – Species Editor. Coding and documentation.

18. MGX Species Editor Business Rules

19. Scan set of phenotypes (images) Protein Investigator usage to design template proteins for each allele. Import phenotype images and template proteins for alleles. Define restrictions for alleles. The Species Editor checks that the template protein supplied for the allele actually honors the content restrictions specified. The Species Editor checks that there is no ambiguity in the list of content restrictions - i.e. that any folded protein matches at most one allele in shape and content. For each pair of alleles a phenotype is specified. Newly created species in file.spc. MGX Species Editor

20. Protein Investigator Used to design template proteins for each allele

21. Species Editor Define restrictions for alleles

22. MGX Team What we’ve learned so far ?

23. We have learned … First meeting with customer * Short stories not what the customer really wants * Algorithm seems too complicated We’re making progress!

24. Questions ?