Per Kraulis, CV Chemical Engineer, KTH Structural Biology Protein NMR & 3D analysis Ph.D. Uppsala...
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Transcript of Per Kraulis, CV Chemical Engineer, KTH Structural Biology Protein NMR & 3D analysis Ph.D. Uppsala...
![Page 1: Per Kraulis, CV Chemical Engineer, KTH Structural Biology Protein NMR & 3D analysis Ph.D. Uppsala Univ Postdoc Cambridge Univ Karolinska Inst Bioinformatics.](https://reader036.fdocuments.net/reader036/viewer/2022082816/56649d8d5503460f94a75a66/html5/thumbnails/1.jpg)
Per Kraulis, CV
Chemical Engineer, KTH
Structural Biology
Protein NMR & 3D analysis
Ph.D. Uppsala Univ Postdoc Cambridge Univ Karolinska Inst
Bioinformatics
Pharmacia Sthlm Bioinfo Center Biovitrum Tartu University SGC
![Page 2: Per Kraulis, CV Chemical Engineer, KTH Structural Biology Protein NMR & 3D analysis Ph.D. Uppsala Univ Postdoc Cambridge Univ Karolinska Inst Bioinformatics.](https://reader036.fdocuments.net/reader036/viewer/2022082816/56649d8d5503460f94a75a66/html5/thumbnails/2.jpg)
More about me...
http://se.linkedin.com/in/perkraulis
http://www.citeulike.org/user/pekrau
http://delicious.com/pekrau
http://www.avatar.se/
![Page 3: Per Kraulis, CV Chemical Engineer, KTH Structural Biology Protein NMR & 3D analysis Ph.D. Uppsala Univ Postdoc Cambridge Univ Karolinska Inst Bioinformatics.](https://reader036.fdocuments.net/reader036/viewer/2022082816/56649d8d5503460f94a75a66/html5/thumbnails/3.jpg)
Systems Architect(Scientific programmer/Systems developer)
Relational database systems
MySQL, Oracle
Other database systems
Gdbm, XML, OODBMS
Software
MolScript ANSIG (protein NMR)
Programming
Python JavaScript (Ajax) C, C++, Simula, Pascal,
Eiffel, Fortran...
![Page 4: Per Kraulis, CV Chemical Engineer, KTH Structural Biology Protein NMR & 3D analysis Ph.D. Uppsala Univ Postdoc Cambridge Univ Karolinska Inst Bioinformatics.](https://reader036.fdocuments.net/reader036/viewer/2022082816/56649d8d5503460f94a75a66/html5/thumbnails/4.jpg)
Task: Software system admin
Setup of common stuff On russola & other “local” servers Tools (executables) Reference databases (Human genome, etc) Documentation
(Help with) sysadmin Disk police Queues?
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Task: LIMS setup
• Geospiza LIMS for Genomics (?)
• Configuration
• Integration with analysis
• Policy for datasets
– Persistent, coherent identifier scheme
– Storage and backup
• ELN issue: Contur, Wiki, Google Wave,...?
![Page 6: Per Kraulis, CV Chemical Engineer, KTH Structural Biology Protein NMR & 3D analysis Ph.D. Uppsala Univ Postdoc Cambridge Univ Karolinska Inst Bioinformatics.](https://reader036.fdocuments.net/reader036/viewer/2022082816/56649d8d5503460f94a75a66/html5/thumbnails/6.jpg)
Task: Analysis Pipeline
Standard analysis for Service-for-fee
Set up analysis modules
Set up self-tests
Visualization tools Explore datasets Identify strange problems
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Task: Workflow system
Current trend in e-Science: Taverna, Galaxy,...
Flownode (under development) Web-integrated (fully, not just client-only) Cloud-computing (Grid) enabled Human interaction (via browser) Programmatic interface
Web Services REST architecture
Implement standard analysis modules