APO-SYS Consortium
Apoptosis Systems Biology Applied to Cancer and AIDS
An integrated approach of experimental biology, data mining, mathematical modeling, biostatistics, system engineering and molecular medicine
Workshop
Tuesday June 24 - Friday June 27, 2008
IT Training Room, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton,
Cambridge, UK.
| Organisation: Phil
Jones, EMBL-EBI and
Christophe
Roos, Medicel Oy,
Finland |
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This workshop will run over 4 days. The first two days will explore relevant databases and resources at the EBI with consideration to the mining of these resources and also submission of data to these resources. The second two days will describe the application of the Medicel Integrator Software Platform to the APO-SYS project and provide training in its use. |
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| Registration | ||
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| Confirmed Speakers (in order of appearance): | ||
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| Day 1 / 2: EBI Data Resources |
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| Vicky Schneider, EMBL-EBI | vicky@ebi.ac.uk | |
| Henning Hermjakob, EMBL-EBI | hhe@ebi.ac.uk | |
| Sandra Orchard, EMBL-EBI | orchard@ebi.ac.uk | |
| Helen Parkinson, EMBL-EBI | parkinson@ebi.ac.uk | |
| Philip Jones, EMBL-EBI | pjones@ebi.ac.uk | |
| Bijay Jassal, EMBL-EBI | bj1@ebi.ac.uk | |
| Nicolas Le Novère, EMBL-EBI | lenov@ebi.ac.uk | |
| Susanna-Assunta Sansone, EMBL-EBI | sansone@ebi.ac.uk | |
| Day 3 / 4: The Medicel Integrator Software Platform |
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| Christophe Roos, Medicel Oy, Finland | christophe.roos@medicel.com | |
Schedule
| Tuesday, June 24, 2008 | ||||
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| EBI Resources: Introduction, UniProt, Transcriptomics and Proteomics Data | ||||
| Time | Slides Download | Tutorial Notes | ||
| 09:00 - 09:30 | Registration at EBI Reception | |||
| 09:30 - 09:35 | Administrative Information | Vicky Schneider | ||
| 09:35 - 09:50 | Welcome and Introduction to the APO-SYS Workshop | Henning Hermjakob | Welcome | |
| 09:50 - 10:10 | Introduction to the EBI | Vicky Schneider | EBI-Introduction | |
| 10:10 - 11:00 | The UniProt Database and Aspects of Annotation | Sandra Orchard | UniProt-Power Point | UniProt Tutorials |
| 11:00 - 11:20 | Coffee/tea | |||
| 11:20 - 12:30 | The UniProt Database and Aspects of Annotation (Continued) | Sandra Orchard | (As above) | (As above) |
| 12:30 - 13:30 | Lunch | |||
| 13:30 - 16:00 | Transcriptomics Data: ArrayExpress, MIAME, MAGE-TAB, MAGE-ML and the MGED Ontology | Helen Parkinson | ArrayExpress | Word Doc: MAGE-TAB at ArrayExpress
PDF: ArrayExpress Tutorial PDF: ArrayExpress Atlas for Beginners |
| 16:00 - 16:20 | Coffee/tea | |||
| 16:20 - 18:00 | PRIDE and the HUPO Proteomics Standards Initiative (Mass Spectrometry) | Phil Jones | PSI and PRIDE | Word Doc: PSI and PRIDE Tutorial |
| Wednesday, June 25, 2008 | ||||
| EBI Resources: Molecular Interactions, Pathways, Kinetic Models and 'Omics Data | ||||
| Time | Slides Download | Tutorial Notes | ||
| 09:00 - 11:00 | Molecular Interactions: IntAct and PSI-MI | Sandra Orchard | IntAct | IntAct Tutorial |
| 11:00 - 11:20 | Coffee/tea | |||
| 11:20 - 13:20 | The Reactome Database: A Curated Database of Biological Pathways | Bijay Jassal | Reactome | Reactome-Tutorial |
| 13:20 - 14:20 | Lunch | |||
| 14:20 - 16:20 | The BioModels Database and SBML | Nicolas Le Novère | BioModels |
Exemples:SBML LotkaVoltera |
| 16:20 - 16:40 | Coffee/tea | |||
| 16:40 - 17:10 | A Common Submission Platform for 'Omics Data: ISA-TAB and the BioInvestigation Index Infrastructure | Susanna-Assunta Sansone |
ISA-TAB BioInvestigation Index Infrastructure |
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| 19:00 | Bus shuttle from EBI to Cambridge College | |||
| 20:00 | Dinner at a Cambridge College | |||
| 23:00 | Bus shuttle back to the campus | |||
| Thursday, June 26, 2008 | ||||
| The Medicel Integrator Software Platform day 3: Storing and Documenting Measurements |
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| Time | Slides Download | Tutorial Notes | ||
| 09:00 - 11:00 | General overview of the main APO-SYS working environment on Medicel Integrator: Experiment, Workflow, Query, Pathway applications / the data warehouse. | Christophe Roos | Available at Medicel |
Available at Medicel |
| 11:00 - 11:20 | Coffee/tea | |||
| 11:20 - 12:30 | Import / export of data in tabular format: general issues | Christophe Roos | Available at Medicel |
Available at Medicel |
| 12:30 - 13:30 | Lunch | |||
| 13:30 - 16:00 | Import and annotation of data in tabular format: microarrays, siRNA, interactions, etc. Data management and use of controlled vocabularies. | Christophe Roos | Available at Medicel |
Available at Medicel |
| 16:00 - 16:20 | Coffee/tea | |||
| 16:20 - 17:30 | Experiment (LIMS) application: More on documentation of wet lab procedures | Christophe Roos | Available at Medicel |
Available at Medicel |
| 17:30 - 18:30 | Workflow (tool pipelines) application | Christophe Roos | ||
| Friday, June 27, 2008 | ||||
| The Medicel Integrator
Software Platform day 4: Developing Methodologies and Analysing Data |
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| Time | Slides Download | Tutorial Notes | ||
| 09:00 - 11:00 | More on Experiment, Workflow and Query applications. Data manipulation. | Christophe Roos | Available at Medicel |
Available at Medicel |
| 11:00 - 11:20 | Coffee/tea | |||
| 11:20 - 12:30 | Pathway: creating, navigating, computing | Christophe Roos | Available at Medicel |
Available at Medicel |
| 12:30 - 13:30 | Lunch | |||
| 13:30 - 15:00 | Wrap Up: APO-SYS and Medicel Integrator | Christophe Roos | ||
| 15:00 - 15:20 | Coffee/tea | |||
| 15:20 - 16:00 | Session Close: Panel Discussion | Christophe Roos, Phil Jones | ||
