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Domain-oriented services and resources
of Polish Infrastructure for Supporting
Computational Science in the European
Research Space – PLGrid Plus
Domain-oriented services and resources
of Polish Infrastructure for Supporting
Computational Science in the European
Research Space – PLGrid Plus
EUROPEAN UNION
EUROPEAN REGIONAL
DEVELOPMENT FUND
INNOVATIVE ECONOMY NATIONAL COHESION STRATEGY
Genomic Data Analysis Services Available for PL-Grid Users
Clinical Genomic Analysis (CGA) Workshop
EUROPEAN UNION
EUROPEAN REGIONAL
DEVELOPMENT FUND
INNOVATIVE ECONOMY NATIONAL COHESION STRATEGY
2
Academic Computer Centre Cyfronet AGH
• Established in 1973 (40 years of experience)
• Main mission: to provide network, computational power and data storage capabilities for Polish science
• ~374 TFlops (145@top500), 2.5 PB (disks) and 3.5 PB (tapes)
• Regular and bigmem nodes, vSMP, GPGPU, FPGA, MPI over Infiniband
• Details: http://kdm.cyfronet.pl/
PL-Grid Infrastructure for Polish science
• Five computing centers with Cyfronet as the consortium leader
• Total: ~588 TFlops and ~5.6 PB (disks) • Planned for 1Q2015: >900 TFlops, 8 PB
• Available free of charge to all Polish scientists and their foreign collaborators
• Details: http://www.plgrid.pl
ACC Cyfronet AGH and
PL-Grid Infrastructure
EUROPEAN UNION
EUROPEAN REGIONAL
DEVELOPMENT FUND
INNOVATIVE ECONOMY NATIONAL COHESION STRATEGY
3
Register at https://portal.plgrid.pl
User verification process based on Polish OPI number
Assistants and foreigners are confirmed by Polish PIs
Variety of basic and higher level services available after login
Local SSH access, cloud computing, middlewares
Considerable library of installed applications
GATK, MACS, SAMTools, Picard, TopHat, Bowtie, (p)BWA,
R/Bioconductor, AutoDock/AutoGrid, BLAST, Clustal, CPMD,
Gromacs, NAMD, Matlab, Mathematica …
Free to compile and install own applications using the shell login
Possibility to use own commercial licenses on HPC resources
Questions: https://helpdesk.plgrid.pl or [email protected]
Using PL-Grid Infrastructure
EUROPEAN UNION
EUROPEAN REGIONAL
DEVELOPMENT FUND
INNOVATIVE ECONOMY NATIONAL COHESION STRATEGY
4
Preparation of specific computing environments, i.e., solutions, services and extended infrastructure tailored to the needs of different groups of scientists (2012-2014)
Life Science among 13 domains of science
LS Domain Leader: Kraków LifeScience Klaster
Tasks:
Analysis of user needs
Development of services
Procurement and deployment of applications on HPC res.
Continuous assistance for the Life Science community
PLGrid PLUS: Domain-oriented
Services, Resources and Tools
EUROPEAN UNION
EUROPEAN REGIONAL
DEVELOPMENT FUND
INNOVATIVE ECONOMY NATIONAL COHESION STRATEGY
5
https://lifescience.plgrid.pl/ For people who perform biological investigations using DNA microarrays
Goal: help to analyze gene expression information and correlate it with other clinical data
In development since 1Q2013, first version deployed
Analyses available now: normalization, clustering, SAM, T-test, GO-based enrichment, ANNs, PCA, panel filtering
Integromics analyses in preparation
CCA, PLS (gene expression and lipidomics)
Roleswitch, TargetScore (gene expression and miRNA)
Supported models: Affymetrix, Agilent (support for others is possible in case of demand)
DNA Microarray Integromics
Analysis Platform (1/2)
EUROPEAN UNION
EUROPEAN REGIONAL
DEVELOPMENT FUND
INNOVATIVE ECONOMY NATIONAL COHESION STRATEGY
6
Notable features Integration with EBI ArrayExpress (import, MIAME)
Sharing experiments with others
Importing own data for further analysis
Supported languages: PL, EN
Manual: https://docs.cyfronet.pl/x/JpaZ
Cooperation Jagiellonian University Medical Collage, Kraków
Medical University of Silesia, Katowice
Institute of Oncology, Gliwice
DNA Microarray Integromics
Analysis Platform (2/2)
EUROPEAN UNION
EUROPEAN REGIONAL
DEVELOPMENT FUND
INNOVATIVE ECONOMY NATIONAL COHESION STRATEGY
7
https://galaxy.plgrid.pl/ ”Galaxy is an open, web-based platform for data intensive
biomedical research.”
Goal: deploy high-performance, high-throughput NGS data
analysis solution on top of HPC resources for PL-Grid users
Needs a lot of adjustments and in-house add-on development
Work started 12.2013, first version planned ~08.2014
Planned integrated tools (list not closed): GATK, SAMtools,
Bowtie, TopHat, BWA, bedtools, Cufflinks, Picard,
SnpEff/SnpSift, Flexbar, FastQC, MACS
References: human, mouse, domestic animals
Targeted platforms: Illumina *Seq, Roche 454, Ion Proton
Galaxy NGS Server (1/2)
EUROPEAN UNION
EUROPEAN REGIONAL
DEVELOPMENT FUND
INNOVATIVE ECONOMY NATIONAL COHESION STRATEGY
8 Galaxy NGS Server (2/2)
Notable features Full integration with Zeus cluster and large disk arrays
PBS and MQ system for effective job queuing and management
Secured environment (open for all PL-Grid users, not ”public”)
All major Galaxy features (history, sharing, viewers) enabled
Well documented workflows designed by NGS experts Basics (alignment and quality control, trimming, filtering)
DNA-Seq, RNA-Seq, variant calling, SNP calling, methylation, exome analysis with annotations
Manual: https://docs.cyfronet.pl/x/voas (available when service goes production)
Cooperation Institute of Pharmacology, Polish Academy of Sciences, Kraków
Jagiellonian University Medical Collage, Kraków
National Research Institute of Animal Production, Kraków-Balice
EUROPEAN UNION
EUROPEAN REGIONAL
DEVELOPMENT FUND
INNOVATIVE ECONOMY NATIONAL COHESION STRATEGY
9 Agilent GeneSpring GX
RDP: genespring.plgrid.pl
Used with Windows Remote Desktop
Integrated with the DNA Integromics Platform for uniform microarray files management
5-year, single-seat license for all registered Polish scientists
Manual: https://docs.cyfronet.pl/x/JIq1
EUROPEAN UNION
EUROPEAN REGIONAL
DEVELOPMENT FUND
INNOVATIVE ECONOMY NATIONAL COHESION STRATEGY
10 PLGData – Simple Service to
Manage Files on Clusters
https://data.plgrid.pl/ Simple file and folder management
upload, delete, download, rename, change rights
Integrated with Cyfronet’s Zeus cluster, accessible for all users
Uses GridFTP and HTTPS protocols for secure data transfer
Access to group storage for team/project collaboration
Manual: https://docs.cyfronet.pl/x/64es
EUROPEAN UNION
EUROPEAN REGIONAL
DEVELOPMENT FUND
INNOVATIVE ECONOMY NATIONAL COHESION STRATEGY
11
These resources, services and tools (and much more) are available after registering to PL-Grid
https://portal.plgrid.pl/
PL-Grid User Manual https://docs.plgrid.pl/podrecznik_uzytkownika (PL)
https://docs.plgrid.pl/display/PLGDoc/User+manual (EN)
Questions, problems, requests about PL-Grid https://helpdesk.plgrid.pl or [email protected]
Contact for LifeScience domain services [email protected]
Collaborative effort Academic Computer Centre Cyfronet AGH, Kraków (project leader)
Kraków LifeScience Klaster (Life Science domain services leader)
10 expert institutes/laboratories from Małopolska and Śląsk
Links, Contact, Partners
