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 Genomic Data Analysis Services Available for PL-Grid Users Clinical Genomic Analysis (CGA) Workshop
ACC Cyfronet AGH and PL-Grid Infrastructure 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
Using PL-Grid Infrastructure 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 helpdesk@plgrid.pl
PLGrid PLUS: Domain-oriented Services, Resources and Tools 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
DNA Microarray Integromics Analysis Platform (1/2) 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 (2/2) 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
Galaxy NGS Server (1/2) 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 (2/2) 8 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
Agilent GeneSpring GX 9 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
PLGData Simple Service to Manage Files on Clusters 10 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
Links, Contact, Partners 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 helpdesk@plgrid.pl Contact for LifeScience domain services plgrid@lifescience.pl 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