3. Mission
Establish 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
4. Built a portal by combining
pre-existing building blocks
Communication platform
Ticketing/Service platform
Workflow platform
5. 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
6. 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 ...
7. 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
8. For bioinformaticians - developers:
Version Control System
Version Control System
Revision 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 !
12. CloudBioLinux (http://cloudbiolinux.org/
quickly build-your-own suite/ready to roll
graphical and command line acces
CloudMan (http://usecloudman.org/)
create a scalable and shareable processing platform
orchestrates 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
13. Next Steps
Planning 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
