October 2012 Evaluation GoNL

People present: Morris Swertz, David van Enckevort, Paul de Bakker, Lennart Karssen, Kai Ye, Tom Visser

E-mail contributions: Hailiang Mei, Jan Bot

Introduction

Action items

Scratch

Technical: File management & replication

• General backup strategy and restore?
• What is where (ToC of files)?
• Is the file in hand the same as in ToC (checksum)?
• What version is this file (e.g. multiple align runs)
• Does the researcher have the file available on site?
• Data freeze: can we mark data sets.
• Data librarian: who is responsible for keeping the lists

(dcache instance writes)

Action items: => create a series of user stories describing => Version individual files, not the whole set because to big (+index, etc) => Have overview of who wants what => Small files we can release as a whole, e.g. SNP releases

Technical: Distribution of the analysis

• Where do you compute what?
• Can we really distribute analyses over multiple sites
• Currently we depend on LISA and UMCG clusters.

=> Make pipelines distributed: deploy pipelines on multiple clusters => Make dependent executable available on other clusters => Make data available on other clusters What pipelines do we want to distribute and why, and what are the barriers???

Technical: QC and tracing of errors

• Robustness of the analysis
• How do we make certain that data analyses are used

=> Action item: clear QC steps but pragmatic. E.g. compare unique aligned reads. => Action item: verification of pipelines accross sites using overlap samples.

Coordination: Communication problems

Organization: which resources are actually available

Science / Roadmap:

• Paper plan
• Get from the steering committee general directions, very broad, what

can / should do next with the data (GoNL flag, or just using)

• Group responsible of rolling roadmap for one year (get from the

steering committee)

• Have more bioinformaticians in the steering committee and recognition of that
• At every SC meeting have one of the subproject report results to SC
• Overview of external GoNL projects
• Very good that we have a SC member (Cisca) on the call all the time.
• The technical people should get appreciation for their scientific

contribution!

• Need experienced person for each working group (SV is okay,

imputation and pheno are a bit light because Yurii left)

• Foreign contributors is nice, but it seems like they take away nice

projects away. Need better communication.

Organization: Roadmap and planning

• Who is responsible for what?
• Decentralized management (we can not boss other locations)

Actions:

• Ask the SC people resources available (do the GoNL members get the

time they need?)

• SV team has too little man power to do the work (largely volunteers,

hard to stimulare people)

Keep:

• Weekly skypes
• Mailing list
• Open communication and low-threshold to find each other
• Sharing of best practices nationally and internationally
• Forming the group
• Access to international collaboration
• Sharing knowledge and code via wiki+svn
• Self-organization in working groups along sensible lines
• Using pragmatic solution and get started