MGX Team

Sadashivudu Basani Jinny Sebastian

Carlton VazElizabeth Xu

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)

MGX as is…

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.

Genetics Tool

Cross any two organisms

Self-cross any two organisms

Mutate any organism

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.

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.

Overview of the biology

MGX Team Approach

Team approach towards the goal

Steps defined

Where are we now ?

Where are we heading ?

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.

Learn about current application

Functionality, Code and Structure

Build UML Diagram

Build UML Diagram of the existing MGX application

MGX Team

Where are we now ?

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.

MGX Team

Where are we heading?

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.

MGX Species Editor

Business Rules

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.

MGX Species Editor

Protein Investigator

Used to design template proteins for each allele

ALA ALA ALA ALA LYS GLY VAL TYR TRP PHE PRO ILE ILE ILE CYS THR THR THR THR

Species Editor Define restrictions for alleles

MGX Team

What we’ve learned so far ?

We have learned …

First meeting with customer

* Short stories not what the customer really wants

* Algorithm seems too complicated

We’re making progress!

Questions ?