Managing Life Science Information
  NBIC course for Bioinformatics PhD students
                    (and others)


http://...
Factfile

•   Target audience
     – Bioinformatics PhD students
•   Lecturers
     – Ammar Benabdelkader, Peter Boncz, An...
What are key aspects for the Management of
Life Science Information?
• BioAssistants say…
   –   Security
   –   Data comp...
Research cycle




             4
Data flow




        5
Knowledge flow




             6
Motivation

• Life science information is
  – about Life Science
     • meaningless without interpretation
  – complex
   ...
Course credo
Keep your information alive


 Or how to make your information
 understandable and computable




           ...
Day 1 and 2 – information and knowledge

• Knowledge-based information
  management
  – learn about how the Semantic Web
 ...
Day 3 – processing information at large

• Database workhorses
  – learn about how to use relational
    databases for man...
Day 4 - Taverna and web services

• Taverna and web services for
  collaborative data integration
  – get a full tutorial ...
Day 5 - Hands-on Semantic Data integration

• Hands-on Semantic Data
  integration
  – deploy what you have learned on you...
What should the lecturers address?

• BioAssistants say…
  – Organisational issues
  – Reuse
     • Including reuse storag...
What cases would you like to address in the
hands-on sessions?

• BioAssistants say…
  –…




                            ...
Managing Life Science Information
  NBIC course for Bioinformatics PhD students
                    (and others)


http://...
Upcoming SlideShare
Loading in …5
×

Managing Life Science Information (2009)

559 views

Published on

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.

Published in: Education, Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
559
On SlideShare
0
From Embeds
0
Number of Embeds
3
Actions
Shares
0
Downloads
14
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Managing Life Science Information (2009)

  1. 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. 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. 2
  3. 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 3
  4. 4. Research cycle 4
  5. 5. Data flow 5
  6. 6. Knowledge flow 6
  7. 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’ 7
  8. 8. Course credo Keep your information alive Or how to make your information understandable and computable 8
  9. 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 9
  10. 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. 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 11
  12. 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 12
  13. 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 13
  14. 14. What cases would you like to address in the hands-on sessions? • BioAssistants say… –… 14
  15. 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

×