Upload
bowen
View
53
Download
0
Tags:
Embed Size (px)
DESCRIPTION
DSL for Pedigree Rearrangements. CSI5112 Software Engineering Team: Andrei Anisenia Margi Fumtiwala. Agenda. DSL overview Goals of DSL Tool support for the DSL DSL creation technology Sample usage Foreseen impact of language evolution Potential for analysis - PowerPoint PPT Presentation
Citation preview
DSL for Pedigree RearrangementsCSI5112 Software Engineering
Team: Andrei Anisenia Margi Fumtiwala
AgendaDSL overviewGoals of DSL Tool support for the DSLDSL creation technology Sample usageForeseen impact of language evolution Potential for analysis Conclusions
DSL OverviewDomain Specific Language (DSL) is a specific
language being used to solve problems in a particular domainIt is not intended to work outside that domainContains very specific goals in design and
implementation
DSL for Pedigree Rearrangements Genetic analysis of biological data is one of the most
important research directions in modern bioinformatics
The data to be analyzed is supplied in different textual formats by hospitals/researchers and may be analyzed by different bioinformatics tools
Our focus is on the type of genetic data called pedigree data presented in so-called PEDFILES
Typical pedigree data is presented by the family structureIncludes persons and child-parents relations between the
persons
A simple pedigree exampleGraphical representation of the pedigree data
Textual representation of the pedigree data - PEDFILES
Each line represents Pedigree data and Biological data for a specific person
Why do we need a graphical tool?Usual work flow of a bio informaticians involve extensive editing
of PEDFILEs Initial PEDFILEs received from hospitals may include too big
pedigrees or too much biological data in order to be analyzed by existing software
This problem requires splitting PEDFILEs into smaller sub pedigrees or/and removal of different persons from a pedigree in order to make it analyzable
The rearrangement of a pedigree requires multiple point changes within pedigree data It is not feasible
Bio informaticians thus need some visual graphical environment for presentation and rearrangement of pedigrees
Scope of tool support for the DSLProvides visual graphical environment for
presentation and rearrangement of pedigreesProvides the possibility to save the
constructed and rearranged pedigrees to textual PEDFILEs
DSL creation technology
Overview of the approachMeta-model: Construction and development of objects,
relations, constraints and actions for modelling a predefined class of problems.
In the case of Pedigree Rearrangements problem the meta-model is defined as the set of the following:Objects:
Person – represents single person in a pedigree. Holds the following data: name (unique within a pedigree), person's sex and biological data
Pedigree – a set of persons and relations among them. Pedigree has unique id (Pedigree ID)
Relations: Person has a father Person has a mother Pedigree consists of persons
ConstraintsPerson can have maximum one father and
one motherPerson can be associated to exactly one
pedigreePerson can not be connected to persons in
another pedigreeAdding a new relation of type child-parents
shouldn't create directed cycles in a pedigreeIn simple words, circular relationships can not
exist between persons, ex: mother can not be a child....
Pedigree Rearrangements Model
Example – input PEDFILEPed1 grandfather1 0 0 1 1 2 1 1 2 2 1 2 3Ped1 grandmother1 0 0 2 1 1 1 2 3 4 2 12 3 5Ped1 grandfather2 0 0 1 1 2 3 2 2 2 2 2 2 2 2Ped1 grandmother2 0 0 2 4 4 4 4 423 2 3 2 4Ped1 grandfather3 0 0 1 1 2 1 2 4 5 6 3 2Ped1 father grandfather1 grandmother1 1 12 1 3 4 56 4 3 56 7 8Ped1 mother grandfather2 grandmother2 2 1 2 4 5 6 3 4 2 45 32Ped1 stranger grandfather3 grandmother2 1 2 3 4 5 1 3 4 6 7 8
56Ped1 mother2 grandfather3 grandmother2 2 1 2 3 4 6 4 5 6 7 8Ped1 child1 father mother 1 1 2 1 2 1 2 1 2 1 2 Ped1 child2 stranger mother2 2 1 2 34 54 6 7 8
Example - editor view of the input pedigree
Example – editor view of the output pedigree
Example – output PEDFILEPed1 grandfather1 0 0 1 1 2 1 1 2 2 1 2 3Ped1 grandmother1 0 0 2 1 1 1 2 3 4 2 12 3 5Ped1 grandfather2 0 0 1 1 2 3 2 2 2 2 2 2 2 2Ped1 grandmother2 0 0 2 4 4 4 4 423 2 3 2 4Ped1 father grandfather1 grandmother1 1 12 1 3 4 56 4 3 56 7 8Ped1 mother grandfather2 grandmother2 2 1 2 4 5 6 3 4 2 45 32Ped1 child1 father mother 1 1 2 1 2 1 2 1 2 1 2 Ped2 grandfather3 0 0 1 1 2 1 2 4 5 6 3 2Ped2 grandmother2 0 0 2 4 4 4 4 423 2 3 2 4Ped2 stranger grandfather3 grandmother2 1 2 3 4 5 1 3 4 6 7 8
56Ped2 mother2 grandfather3 grandmother2 2 1 2 3 4 6 4 5 6 7 8Ped2 child2 stranger mother2 2 1 2 34 54 6 7 8
Model-to-text (M2T) transformation technique used
The Model to Text (M2T) transformations focus on the generation of textual artifacts from models
New PEDFILEs are generated using XpandXpand is a language specialized on code
(text) generation based on EMF modelsProvides OCL-like expressions (semantics)
with Java-like syntax
Language evolution – GUI adjustmentsDifferent shapes and/or colors for person
items according to person sexesPersons dropped onto the pedigree “canvas”
instead of being linked to it by arrowsThese require minor changes in GMF
components Considered for the upcoming release on the
18th of April
Language evolution – functionality extensions
Pedigree layout is the crucial parameter in visual analysis of pedigree structure
Different auto-layout algorithms should provide different views of a pedigree structure
It takes a lot of time to build a pedigree from a given PEDFILE manually
Automatic construction of a pedigree by only browsing a PEDFILE would be helpful
These are hard to implement in existing DSL Toolkit and require extensions to the framework
Potential for analysis – Bayesian networks
These statistical networks are used to analyze biological data stored in pedigrees
They are provided as input to different statistical bioinformatics software (Superlink, Gene hunter, Allegro etc.)
BNs are graphs with specific properties, constructed using pedigree structure and biological data
BNs are much more complex to construct than pedigrees (more nodes, more links)
Potential for analysis – Bayesian networks, example pedigree
Potential for analysis – Bayesian networks, example network
Potential for analysis – Bayesian networks, transformation
BNs are presented in structured textual files, just as PEDFILEs
Define meta-model for BayesianNetworkDefine model-to-model (M2M) transformation
from Pedigree Model to Bayesian Network model
Define model-to-text (M2T) transformation for Bayesian Network
Run BN analysis software and find disease gene locations!
ConclusionsOur tool provides support for graphical
representation of biological instancesExisting DSL creation tools do not provide
full coverage for all DSL editor needsData to be manipulated is very complex,
therefore automation of transformations between different models becomes essential
Software Engineering should enhance the ongoing research in biology, otherwise it is not feasible due to exponentially growing amount of biological data