Transcript Species Editor

MGX Team
Sadashivudu Basani
Jinny Sebastian
Carlton Vaz
Elizabeth 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
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 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 <filename>.spc.
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
We’re making progress!
* Short stories not what the
customer really wants
* Algorithm seems too
complicated
Questions ?