MIAMExpress development and local installation

DESPRAD Meeting,November 2002

Mohammad shojatalab

shoja@ebi.ac.uk

Talk structure

• History

• Underlying concepts

• Design & Development

• Current status

• Local Installation

• Future

History (March 2001 ~ present)

• Need for a submission tool for ArrayExpress

• Obviously It should be a web base tool

• It was supposed to be quick and dirty prototype

• Start about May 2001

Underlying concepts

• Based on MIAME concepts and questionnaire

• Submission of Experiment, Arrays, Protocols

• Avoiding free text as much as possible

• Using controlled vocabulary

Login

Pending/New Experiment

Sample1 Sample2 Sample3 Samplen Sample protocol

Hybridisations Hyb protocol

Array1 Array2 Array3 Arrayn Scanning protocol

Data1 Data2 Data3 Datan Image analysis protocol

Combined Experiment Data Transformation protocol

Submit Final free text comment

Extracts 1…nExtracts 1…n Extracts 1…n Extracts 1…n

E1 E2 En E1 E2 En E1 E2 En E1 E2 En

Extraction protocol

Design considerations

• Complex submission structure

• Long submission time (may be weeks)

• So it needs a database

• It meant to be fast, Open source and free

• Usable as a Lab Notebook

• Free database management system

• Web based submissions

• MAGE-ML file as output

Technologies & Tools

• Using MySQL DBMS for its database

• Using Perl CGI technology

• Using DBI, DBD::MySQL to interact with db

• Using javascript

• CVS as source code repository to keep track of changes and also incorporate changes made by other developers in to all developers working copy.

MIAMExpress GUI,MAGExpress,…

Biology Layer

Data accesdat

a

Physical data layer (Database, files,…)

Biology;MIAME Layer

Data access functions

Development

• Started at May 2001

• Simple data model; around 30 tables

• Avoiding hard code in program

• Debug tools to assist developer

• Log functionality which write down user’s activities in a file to assist developer to find out what is wrong if an controlled error happened.

• Readable and maintainable code

Impact on data access layer and APIs

New Requirement

Requirement Analysis

Impact analysis

Essential information for development

Impact on data model

Impact on UI Impact on MAGExpress

Development

Test

DevelopmentNew Release

New ReleaseBeta version

Requirement Analysis Impact

Analysis

Development

Test

Steady state

MIAMExpress development states

Apache HTTP

TestProduction

Apache HTTP

Developers

CVSCVS

Infrastructure

Submissions Types

• Array submission: Array Description File (Excel sheet, tab delimited files)

• Experiment submission

• experiment design,samples,extractions,labelled extracts,protocols (Web based forms)

• Hybridization data files (Excel sheet, tab delimited files)

• combined data file (Excel sheet, tab delimited files)

MAGE-ML Creation; MAGExpress module

• MAGEstk: A set of APIs which are created from OM and are able to read MAGE-ML file and create object structure and vice versa

• To create MAGE-ML file from MIAMExpress we have to know which piece of data fits where in the model

• that means we need map MIAMExpress Data model(schema) to MAGE-OM

• Still we have problem because MAGE classes are quite abstract in terms of working with physical data

MAGE-ML Creation (2)

• To have a object oriented design we need to have a new set of classes which are derived from MAGE classes but are MIAMExpress specific

• Objects which are instantiated from these new set of classes know how get their attributes from MIAMExpress database

• Also they are inheriting all of the properties of their parents

MAGE-ML Creation; Example

• biosrc instantiated from original BioSource class

• mx_biosrc instantiated from MXBioSource class

• MXBioSource class is inherited from original BioSource class

• biosrc.go&Load_your_data -> ERROR!!!

• mx_biosrc.go&Load_your_data -> you have a loaded object from MIAMExpress

• Encapsulation of dirty works inside the object

How go&Load_your_data works?

• By calling our one or a sequence of appropriate biology(MIAME) APIs.

Note that the method name in all Classes is the same but behaviour is context sensitive which is hard coded inside;

For example ; for BioSource we say;

mx_biosrc. go&Load_your_data;

And also for labelled extract;

Mx_label. go&Load_your_data and all others the like.

How we create MAGE-ML file

• We Create the top level object; experiment

• experiment.go&create_all_your_associations; which creates whole object structure

• experiment.go&Load_your_data; which load data to whole structure

• write MAGE-MLby starting from experiment top level object

Incorporating data into MAGE-ML

• BioAssay Data, Derived BioAssay Data

• Problem with different data formats; Generic, GenePix, Genesping,…

• So we have to have plugins in MIAMExpress for each of these formats.

• Retrieving the following info from data files: Quantitation types, Features, Reporters, Composite Sequences

Problem with new releases

• Usually new releases means new schema as well.

• that means we have to change the data access layer.

• that means we have to change our mapping model which map MIAMExpress schema to MAGE model.

• that means we have to migrate the existing data.

• that introduce data migration module; dmm

• dmm is have to be provided with new release

Missing bits behind the scene

• We are using MySQL which at least at the moment doesn’t support constraints and foreign keys, sub queries.

• They have promised to to solve these in their next releases soon.

• Persistent connection with database.

• Having an automated schema MAGE mapping.

Current status

• Release 1.0 is ready soon (Dec 2002)

• With this we get the experiment submissions, and create the MAGE-ML file

• get the Array submissions and create the MAGE-ML file

Local Installation

• Installation of most stable release of MySQL

• Installing Apache HTTP server

• Perl core modules and some other from CPAN

• Xerces-C and Xerces-Perl modules

• Create MIAMExpress database and load seed data

• Change database entry in a constant module

• Change data of the system option table

-machine name; on which MySql is running

-Database name ,Address of database configuration file

-Path of the data files,Path of the application

-Main URL, CGI URL, Path of log files,…

Future

• MIAMExpress 1.x/2.0 ??

• Graphical representation of experiment structure.

• Organism specific

• Integrated with Curation tool ??

• be able to work with a full MAGE-ML file?

• cover all missing pieces behind the scene

• http://www.ebi.ac.uk/miamexpress

URL

• European Union for funding (TEMBLOR).

• MIAMExpress developers: Niran,Sergio

• Helen Parkinson and others database curators in Microarray Group in EBI.

• Ugis Sarkans, Alvis Brazma

• All people involved in MAGEstk collaborative effort.

Acknowledgement

Questions