using the lifeportal - universitetet i oslo · using the lifeportal katerina michalickova, nikolay...
TRANSCRIPT
![Page 1: Using the Lifeportal - Universitetet i oslo · Using the Lifeportal Katerina Michalickova, Nikolay Vazov The Research Computing Services, USIT November 15, 2013 . Lifeportal The Lifeportal](https://reader034.vdocuments.us/reader034/viewer/2022042219/5ec5b7ee1f459c34c15fd71c/html5/thumbnails/1.jpg)
Using the Lifeportal
Katerina Michalickova, Nikolay Vazov
The Research Computing Services, USIT
November 15, 2013
![Page 2: Using the Lifeportal - Universitetet i oslo · Using the Lifeportal Katerina Michalickova, Nikolay Vazov The Research Computing Services, USIT November 15, 2013 . Lifeportal The Lifeportal](https://reader034.vdocuments.us/reader034/viewer/2022042219/5ec5b7ee1f459c34c15fd71c/html5/thumbnails/2.jpg)
Lifeportal
The Lifeportal at UiO is a portal service to ease the access to high performance computing resources for researchers.
https://lifeportal.uio.no
![Page 3: Using the Lifeportal - Universitetet i oslo · Using the Lifeportal Katerina Michalickova, Nikolay Vazov The Research Computing Services, USIT November 15, 2013 . Lifeportal The Lifeportal](https://reader034.vdocuments.us/reader034/viewer/2022042219/5ec5b7ee1f459c34c15fd71c/html5/thumbnails/3.jpg)
Topics
• login and user management • Galaxy framework • UiO changes to Galaxy • using Lifeportal
– tools – histories – sharing histories – slurm and Abel – upload a file – run an application
• from Bioportal to Lifeportal • future developments • questions, questions, questions
![Page 4: Using the Lifeportal - Universitetet i oslo · Using the Lifeportal Katerina Michalickova, Nikolay Vazov The Research Computing Services, USIT November 15, 2013 . Lifeportal The Lifeportal](https://reader034.vdocuments.us/reader034/viewer/2022042219/5ec5b7ee1f459c34c15fd71c/html5/thumbnails/4.jpg)
Login and user/project management
• live demo
![Page 5: Using the Lifeportal - Universitetet i oslo · Using the Lifeportal Katerina Michalickova, Nikolay Vazov The Research Computing Services, USIT November 15, 2013 . Lifeportal The Lifeportal](https://reader034.vdocuments.us/reader034/viewer/2022042219/5ec5b7ee1f459c34c15fd71c/html5/thumbnails/5.jpg)
Galaxy project Galaxy is "an open, web-based platform for performing accessible, reproducible, and transparent genomic science."
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.
![Page 6: Using the Lifeportal - Universitetet i oslo · Using the Lifeportal Katerina Michalickova, Nikolay Vazov The Research Computing Services, USIT November 15, 2013 . Lifeportal The Lifeportal](https://reader034.vdocuments.us/reader034/viewer/2022042219/5ec5b7ee1f459c34c15fd71c/html5/thumbnails/6.jpg)
Galaxy framework
Galaxy server
rweb server
database
applications
data
Nekrutenko lab in the Center for Comparative Genomics and Bioinformatics at Penn State and the Taylor lab at Emory University
user authenticat
ion
![Page 7: Using the Lifeportal - Universitetet i oslo · Using the Lifeportal Katerina Michalickova, Nikolay Vazov The Research Computing Services, USIT November 15, 2013 . Lifeportal The Lifeportal](https://reader034.vdocuments.us/reader034/viewer/2022042219/5ec5b7ee1f459c34c15fd71c/html5/thumbnails/7.jpg)
Galaxy/Lifeportal at UiO
Galaxy server
Apache web server
proxy
USIT database hotel
applications on Abel
data on Abel file system
FEIDE user authentic.
DRMAA
accounting
![Page 8: Using the Lifeportal - Universitetet i oslo · Using the Lifeportal Katerina Michalickova, Nikolay Vazov The Research Computing Services, USIT November 15, 2013 . Lifeportal The Lifeportal](https://reader034.vdocuments.us/reader034/viewer/2022042219/5ec5b7ee1f459c34c15fd71c/html5/thumbnails/8.jpg)
The Lifeportal – physical configuration
External authentication (FEIDE)
Locally registered users
Apache proxy
Paster (WSGI)
1. accounting DB
2. user DB
node node node
node node node
Abel cluster
SSL connection
Interface between
Galaxy and SLURM – DRMAA
job scheduler - SLURM
VIR
TU
AL M
AC
HIN
E (th
e g
ala
xy s
erv
er)
database hotel
FhGFS partitions mounted on the VM
GOLD
accounting system checking/updating
job accounting module
![Page 9: Using the Lifeportal - Universitetet i oslo · Using the Lifeportal Katerina Michalickova, Nikolay Vazov The Research Computing Services, USIT November 15, 2013 . Lifeportal The Lifeportal](https://reader034.vdocuments.us/reader034/viewer/2022042219/5ec5b7ee1f459c34c15fd71c/html5/thumbnails/9.jpg)
Using Lifeportal
• live demo
– Apps
– History
– Datasets
– Sharing histories
– Uploading files
– Running an app
– Job params
![Page 10: Using the Lifeportal - Universitetet i oslo · Using the Lifeportal Katerina Michalickova, Nikolay Vazov The Research Computing Services, USIT November 15, 2013 . Lifeportal The Lifeportal](https://reader034.vdocuments.us/reader034/viewer/2022042219/5ec5b7ee1f459c34c15fd71c/html5/thumbnails/10.jpg)
Bioportal
![Page 11: Using the Lifeportal - Universitetet i oslo · Using the Lifeportal Katerina Michalickova, Nikolay Vazov The Research Computing Services, USIT November 15, 2013 . Lifeportal The Lifeportal](https://reader034.vdocuments.us/reader034/viewer/2022042219/5ec5b7ee1f459c34c15fd71c/html5/thumbnails/11.jpg)
Phylogeny apps in the Lifeportal
• Live demo
![Page 12: Using the Lifeportal - Universitetet i oslo · Using the Lifeportal Katerina Michalickova, Nikolay Vazov The Research Computing Services, USIT November 15, 2013 . Lifeportal The Lifeportal](https://reader034.vdocuments.us/reader034/viewer/2022042219/5ec5b7ee1f459c34c15fd71c/html5/thumbnails/12.jpg)
Future developments
• work flows and SLURM
• large files upload
• tuning SLURM parameters to help users
• more tools (emphasis on next generation sequencing)
![Page 13: Using the Lifeportal - Universitetet i oslo · Using the Lifeportal Katerina Michalickova, Nikolay Vazov The Research Computing Services, USIT November 15, 2013 . Lifeportal The Lifeportal](https://reader034.vdocuments.us/reader034/viewer/2022042219/5ec5b7ee1f459c34c15fd71c/html5/thumbnails/13.jpg)
Resources
• Lifeportal help [email protected]
• UiO documentation - http://www.uio.no/english/services/it/research/hpc/lifeportal/
• Galaxy project - http://galaxyproject.org/
• Galaxy wiki - http://wiki.galaxyproject.org/
• Galaxy tutorials - http://wiki.galaxyproject.org/Learn
![Page 14: Using the Lifeportal - Universitetet i oslo · Using the Lifeportal Katerina Michalickova, Nikolay Vazov The Research Computing Services, USIT November 15, 2013 . Lifeportal The Lifeportal](https://reader034.vdocuments.us/reader034/viewer/2022042219/5ec5b7ee1f459c34c15fd71c/html5/thumbnails/14.jpg)
The Lifeportal team
• Developers – Nikolay Vazov (Galaxy framework,user management, user support) – Katerina Michalickova (tool integration, user support) – Georgios Magklaras (Galaxy EMBnet at UiO) – Bjørn-Helge Mevik (Abel job management) – Thierry Toutain (applications on Abel)
• Project leaders – Hans Eide – Gard Thomassen
• Galaxy steering group – Kamran Shalchian-Tabrizi – Eivind Hovig – Hans A. Eide – Nils Christophersen
• Collaborations – ELIXIR Norway