december 2012 drylab
TRANSCRIPT
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Molecular Profiling
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Personal Genomics
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MissionEstablish a dry lab that empowers both researcher and clinicians with state-of-the-art bioinformatics solutions in order to enable translational medicine today
ADAM = A DryLab AMsterdam
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Built a portal by combining pre-existing building blocks
Communication platform
Ticketing/Service platform
Workflow platform
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Creating syngery by combining building blocks
Communication platform based on wordpress
Manage contacts, calendars, events
Share educational resources
Proactive use of social media by integration RSS, Twitter
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Creating syngery by combining building blocks
Ticketing platform based on Mantis
Establish a wiki type internal knowledge base
Make inventory of existing competences
Leverage/manage expectations, response times
Match expertises, prioritize most important recurring problem, distinguish urgent from important problems ...
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Creating syngery by combining building blocks
Workflow platform based on Galaxy
Reuse, leverage other systems ... ensure CVS - concurrent versioning system (for the bioinformaticians) ... ensure education towards researchers
USE CASES (running project, miRNA, CRC integration work, H2G2, cervix ... other TRAIT examples)
Aim for re-use-ability of pipelines
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For bioinformaticians - developers: Version Control System
Version Control SystemRevision control is any practice that tracks and provides control over changes to source code (inclusing scripting, statistical pipelines).
It has become increasingly common for a single snippet of code to be edited by a team, the members of which may be geographically dispersed and may pursue different interests.
Sophisticated revision control that tracks and accounts for ownership of changes to documents and code may be extremely helpful or even necessary in such situations.
Essential for consolidation !
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implementation
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Galaxy
CloudMan
BioCloudCentral
CloudBioLinux
implementation
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CloudBioLinux (http://cloudbiolinux.org/quickly build-your-own suite/ready to rollgraphical and command line acces
CloudMan (http://usecloudman.org/)create a scalable and shareable processing platformorchestrates the steps required to provision and manage compute clusters on a cloud infrastructure, all through a web browser. In minutes, you can use a vanilla SGE cluster or a complete bioinformatics analysis environment.
Galaxy (http://usegalaxy.org)do exploratory analysis
BioCloudCentral (http://biocloudcentral.org)get started easily
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Next StepsPlanning phase
Circulate internal within pathology PIL
Get feedback, remarks, setup implementation meeting (hardware, location)
Define KPI (key performance indicators)
Implemention phase
Deploy ADAM: Wordpress, mantis, galaxy
USE CASES
Evaluate using KPI