phenomenal getting started with...2018/05/31 · getting started with phenomenal luca pireddu crs4...
TRANSCRIPT
Outline
1. Why might you be interested in PhenoMeNal?2. What is PhenoMeNal3. Cloud basics4. The PhenoMeNal portal5. Creating your own PhenoMeNal Cloud Research
Environments– With live demo!
Why PhenoMeNal?
● Do you have lots of data to analyze?○ Larger datasets and larger studies○ Maybe you workstation is begging you to stop!
● Tired of spending hours installing analysis tools?
● Want a metabolomics-oriented Galaxy or Jupyter installation?
Why PhenoMeNal?
● Do you have lots of data to analyze?○ Larger datasets and larger studies○ Maybe you workstation is begging you to stop!
● Tired of spending hours installing analysis tools?
● Want a metabolomics-oriented Galaxy or Jupyter installation?
PhenoMeNal might be the right tool for you!
PhenoMeNal
PhenoMeNal = Phenome and Metabolome Analysis
● 14 partners● Led by EMBL-EBI● EU H2020 project*
* grant agreement number 654241
PhenoMeNal
Described as: e-infrastructure for metabolomics data processing and analysis pipelines
PhenoMeNal
Described as: e-infrastructure for metabolomics data processing and analysis pipelines
PhenoMeNal
Described as: e-infrastructure for metabolomics data processing and analysis pipelines
PhenoMeNal provides an integrated data analysis platformThe Cloud Research Environment
PhenoMeNal CRE
Data Analysis PlatformsSupports
● Workflows● Interactive
analysis
WorkflowsAlso includes pre-developed workflows, including:● 13C Fluxomics● MetFrag● MS1/MS2 - XCMS - OpenCMS
The Cloud Research Environment
Over 160!● NMR, MS● Data transfer● Add your own
Tools
PhenoMeNal
Described as: e-infrastructure for metabolomics data processing and analysis pipelines
PhenoMeNal
Described as: e-infrastructure for metabolomics data processing and analysis pipelines
PhenoMeNal portal: http://portal.phenomenal-h2020.eu
● Online tool to “install” PhenoMeNal CRE● Use any cloud computing resources available to you● Use it to define your data analysis infrastructure
○ i.e., the CRE will be only accessible with the credentials you set
PhenoMeNal implements simple click-through deployment
Cloud computingInfrastructure
PhenoMeNal
Running CRE
● Given: a cloud computing infrastructure you can use● The portal automatically installs and starts the CRE● Access services via web browser
Cloud Computing 101
What is “the cloud”?
Some Cloud Basics
● The cloud is someone else’s computer● True, but it’s more than that!● Centralizes provisioning of computing power
○ Collect large number of machines in data center○ Optimize energy and maintenance efficiency○ Improve flexibility, reliability, costs
Utility computing
Cloud Basics for Research
What’s in it for you?● Simple and quick set-up of computers● Offload system administration
○ Hardware failures, maintenance, etc.● Pay-as-you-go● Elastic provisioning
○ E.g., temporarily “rent” large number of machines for large study analysis
○ No overcapacity
● Commercial clouds○ Amazon Web Services (AWS)○ Google Cloud Platform (GCP)○ Credit card usually required○ Free starter plans!
● Private cloud: OpenStack○ OpenStack is an open source cloud
software○ Anyone can run it to configure their
cloud○ E.g., if your institute offers a cloud it
probably runs OpenStack
Supported Cloud Providers
PhenoMeNal Portal
● Using the cloud has its own set of complexities○ Provision machines, storage○ Software containers container orchestrators○ Software provisioning○ User management○ ...
● New skill gap!● The PhenoMeNal portal simplifies these things
○ Automation, graphical user interface○ No in-depth cloud infrastructure knowledge
required
PhenoMeNal Portal
So, to take advantage of the portal (and PhenoMeNal)
1. You’ll need to have access a cloud infrastructure
PhenoMeNal Portal
So, to take advantage of the portal (and PhenoMeNal)
1. You’ll need to have access a cloud infrastructure
2. You’ll need to follow my example
We’ll now switch to the live demo:http://portal.phenomenal-h2020.eu
Conclusion
● The cloud can give you:○ Cost efficiency, scalability, flexibility
● PhenoMeNal can use the cloud to give you:○ A ready-to-use data analysis platform○ Metabolomics tools, workflows and interactive
analysis environments○ No more tool installation!
● The PhenoMeNal portal can give you:○ Click-through PhenoMeNal deployment
Coming soon …
A live online training event:
Metabolomics data analysis in the cloud6-8 June 2018
Follow this link for more information:
https://www.ebi.ac.uk/training/events/2018/metabolomics-data-analysis-cloud-live-online-training
Coming soon…
A live online training event:
Metabolomics data analysis in the cloud6-8 June 2018
Follow this link for more information:
https://www.ebi.ac.uk/training/events/2018/metabolomics-data-analysis-cloud-live-online-training
Finally: please tell us what you thought about this session
Thanks for listening!
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