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MGX Team

MGX Team. Sadashivudu Basani Jinny Sebastian Carlton Vaz Elizabeth Xu. What is Molecular Genetics eXplorer ?.

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MGX Team

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  1. MGXTeam 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) • 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. MGX Species Editor • 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 theallele actually honors the content restrictions specified. • The Species Editor checks that there is no ambiguity in the list ofcontent restrictions - i.e. that any folded protein matches at most oneallele in shape and content. • For each pair of alleles a phenotype is specified. • Newly created species in file <filename>.spc.

  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 We’re making progress! * Short stories not what the customer really wants * Algorithm seems too complicated

  24. Questions ?

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