My grid
Sponsored Links
This presentation is the property of its rightful owner.
1 / 23

my Grid PowerPoint PPT Presentation


  • 106 Views
  • Uploaded on
  • Presentation posted in: General

my Grid. Personalised extensible environments for data-intensive in silico experiments in biology http://www.mygrid.org.uk Professor Carole Goble, University of Manchester,UK carole@cs.man.ac.uk. my Grid. EPSRC funded pilot project Generic middleware within application setting

Download Presentation

my Grid

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


myGrid

Personalised

extensible environments for

data-intensive

in silico experiments in biology

http://www.mygrid.org.uk

Professor Carole Goble,

University of Manchester,UK

carole@cs.man.ac.uk


myGrid

  • EPSRC funded pilot project

  • Generic middleware within application setting

  • 36 monthhttp://www.mygrid.org.uk

IBM


In silico experimentation

  • Discovery, interoperation, fusion, sharing

  • Process is as important as outcome

  • Science is dynamic – change happens

  • Scientific discovery is personal & global

  • Ad-hoc solutions, people-powered


myGrid resources

Question:

Nucleotide binding protein in mouse

Answer:

P12345 in Swiss-Prot is an ATPase

Terri Attwood is an expert on this

Jackson labs have a database but you need to register

A paper has just been published in Proteins by the Stanford lab on this.


Grid viewpoints

What is it?

Where is it?

How to get it?

When did it happen?

Who knows it?

Why does it?

What are you doing?

interrogation

results

private

New Biology

workflows

public

Governance

& Control

Technology Grid

Access Grid


myGrid e-Science objectives

Active support of scientific practice in biology

  • Straightforward discovery, interoperation, sharing

    • information AND processes AND best practice

  • Improving quality of both experiments and data

    • provenance through information <-> process linkage

    • propagating change

  • Individual creativity & collaborative working

    • personalisation

      Cottage Industry to an Industrial Scale


myGrid operational environment

Open Source

Open-Bio Foundation, Bio*

Consortium

Expertise

View propagation,

reasoning, workflow …

(DeFacto) Standards

OMG LSR, I3C, MGED, Gene Ontology

Semantic Web

RDF, RDFS, DAML+OIL

Bioinformatics integration platforms

DAS,OpenBSA, ISYS, OpenMMS, Kleisli, Ensembl, AppLab,

SRS, BioNavigator, DiscoveryLink, GX, OPM, TAMBIS

Web Services

XML, SOAP, WSDL, UDDI

Distributed Computing Environments

CORBA, RMI, Jini, JXTA, DCOM

GRID

Globus/SRB/Condor


Applications

Toolkits

Context mgt

Process mgt

Data mgt

Communication fabric

myGrid Stack

Approach

Metadata

Personalisation

Interoperation layer


Context mgt

Process mgt

Data mgt

1. Resource management

2. Middleware technologies incl. Globus

3. Incorporating existing resources

Applications

Toolkits

Metadata

Personalisation

Interoperation layer

Communication fabric


1. Integration & distributed queries 2. View management3. Personal repositories

Applications

Toolkits

Metadata

Personalisation

Interoperation layer

Context mgt

Process mgt

Data mgt

Communication fabric


1. Process description & storage

2. Process enactment

3. Process personalisation

Applications

Toolkits

Metadata

Personalisation

Interoperation layer

Context mgt

Process mgt

Data mgt

Communication fabric


  • Security & Confidentiality & Trust

  • Provenance & Attribution

  • Versioning

Applications

Toolkits

Metadata

Personalisation

Interoperation layer

Context mgt

Process mgt

Data mgt

Communication fabric


Context mgt

Process mgt

Data mgt

1. Ontology languages & services

2. Resource service descriptions

3. Annotation with metadata

Applications

Toolkits

Metadata

Personalisation

Interoperation layer

Communication fabric


Context mgt

Process mgt

Data mgt

1. Agent based communication abstraction

2. Software engineering paradigm for extensible distributed services

3. Foundation for architectural evolution

Applications

Toolkits

Metadata

Personalisation

Interoperation layer

Communication fabric


Context mgt

Process mgt

Data mgt

  • Personal data repositories

  • Personal processes

  • Models of sharing

Applications

Toolkits

Metadata

Personalisation

Interoperation layer

Communication fabric


Context mgt

Process mgt

Data mgt

1. User interfaces & visualisation

2. Collaboration environments

3. Environment development

4. User-centred application development

Applications

Toolkits

Metadata

Personalisation

Interoperation layer

Communication fabric


Context mgt

Process mgt

Data mgt

1. Specialist process: information extraction

Applications

Toolkits

Metadata

Personalisation

Interoperation layer

Communication fabric


myGrid outcomes

  • e-Scientists

    • Environment built on toolkits for service access, personalisation & community

    • Gene function expression analysis using S. cerevisiae

    • Annotation workbench for the PRINTS pattern database

  • Developers

    • myGrid-in-a-Box developers kit

    • Re-purposing DAS, AppLab and OpenBSA …

    • Integrating ISYS & GlaxoSmithKline platforms


myGrid generic technologies

  • Database access from the Grid

  • Process enactment on the Grid

  • Personalisation services

  • Metadata services

  • Laying the foundations for Agent Services

  • Ontologies, Protocols & APIs

    Grid+ Services+ Semantic Web


Interoperability, higher level ontologies, reasoning,

discovery, Reasoning services, Discovery services

Fulfillment

Grid

Scientific Problems

Knowledge

Knowledge / capability

Processes

Information

Value chain

Semantics / process

Jobs and Data

Data

Data / applications

Raw Resources

"Reproduced by permission of the IT Innovation Centre,

University of Southampton."http://www.it-innovation.soton.ac.uk


myGrid phased development

6 months

  • Versions of myGrid

  • Varying degrees of functionality

Pre-prototype

12 months

Architecture

Simple services

24 months

Early toolkit trials

33 months

Extended services

Application trials

Developers toolkit

Release


myGrid

Personalised

extensible environments for

data-intensive

in silico experiments in biology

http://www.mygrid.org.uk

Professor Carole Goble,

University of Manchester,UK


  • Presented at the BiGUM1: Biological Grid Users Meeting 1

  • NeSC, Glasgow, Scotland

  • October 30th 2001

  • http://www.nesc.ac.uk/esi/progs/bigum1.html


  • Login