Introduction of NBIC's information management course for Bioinformatics PhD students, presented at the BioAssist programmers face to face meeting, Friday April 17, 2009. The programmers were asked to give feedback, which has been incorporated.

1. Managing Life Science Information
NBIC course for Bioinformatics PhD students
(and others)
http://www.nbic.nl/biowise/school/EduProg/InfoMan09/
http://tinyurl.com/BioWiseInformationManagement

2. Factfile
• Target audience
– Bioinformatics PhD students
• Lecturers
– Ammar Benabdelkader, Peter Boncz, Andrew Gibson, Frank van
Harmelen, Iwan Herman, M. Scott Marshall, Barend
Mons, Marco Roos, Morris Swertz, Katy Wolstencroft
• Coordinators
– M. Scott Marshall, Marco Roos
• Date
– 25-29 May 2009
• Location
– Informatics Institute, F0.09, Science Park Amsterdam, the
Netherlands
• Limitations
– For participants without their own laptop with wifi we have
limited hands-on facilities.
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3. What are key aspects for the Management of
Life Science Information?
• BioAssistants say…
– Security
– Data compatibility
– Data versioning
– Data
– Information life cycle management
– Dissemination of data to other scientists
– Transport and size
– Data provenance
– Usability
– Searchability
– Life science
– Tools
– Management
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4. Research cycle
4

5. Data flow
5

6. Knowledge flow
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7. Motivation
• Life science information is
– about Life Science
• meaningless without interpretation
– complex
• Biology is complex
– scattered
• Many experiments with limited scope
– often dead and buried in
'data graveyards‘
• >1000 databases: ‘cottage industry’
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8. Course credo
Keep your information alive
Or how to make your information
understandable and computable
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9. Day 1 and 2 – information and knowledge
• Knowledge-based information
management
– learn about how the Semantic Web
languages and tools can be used to
manage biological data
– learn what OWL and RDF mean and why
they exist
– acquire hands-on experience with these
languages and tools
– learn about sharing knowledge and
community-based science
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10. Day 3 – processing information at large
• Database workhorses
– learn about how to use relational
databases for managing heterogeneous
and distributed data
– learn how laboratory information can be
realistically managed, example:
MolGenis
– get hands-on experience with
postgreSQL/mySQL and MolGenis
10

11. Day 4 - Taverna and web services
• Taverna and web services for
collaborative data integration
– get a full tutorial on applying Taverna to
implement data integration pipelines
– get hands-on experience with Taverna
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12. Day 5 - Hands-on Semantic Data integration
• Hands-on Semantic Data
integration
– deploy what you have learned on your
own application or on an example case,
with experts present
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13. What should the lecturers address?
• BioAssistants say…
– Organisational issues
– Reuse
• Including reuse storage facilities
– Types of usage of data/information
• When to use what?
– Who is doing what?
– Web2.0
– Reproducibility
• Example myExperiment
• Provenance
• Social aspects
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14. What cases would you like to address in the
hands-on sessions?
• BioAssistants say…
–…
14

15. Managing Life Science Information
NBIC course for Bioinformatics PhD students
(and others)
http://www.nbic.nl/biowise/school/EduProg/InfoMan09/
http://tinyurl.com/BioWiseInformationManagement