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e-InfraMPS2015 is over.

A big thanks to all speakers, discussion leaders, tutorial leaders and participants for making this a successful event.

This workshop brought together scientists sharing their experiences on how to build efficient and sustainable e-infrastructures for massively parallel sequencing data management and storage, as well as setting up and maintaining an associated ecosystem of workflows, pipelines, and bioinformatics software.

Dates: 19-20 January 2015

Location: SciLifeLab , Uppsala, Sweden - Map over Uppsala, Local transportation info

Room: Tripple room (E10 ground floor), Uppsala Biomedical Center (BMC) - Map over BMC, use entrance C11

Workshop registration: WORKSHOP FULLY BOOKED.

Before the workshop: Some tutorials require personal accounts or downloading a virtual machine. Please revise the information in the tutorial section below.

Video recordings: Videos recordings from all talks at the workshop are available in a dedicated youtube channel or linked individual from below.

Workshop program

Day 1
9.30-10.00 Coffee
10.00 Welcome Ola Spjuth, UPPMAX and SciLifeLab, Sweden
 
  Session 1: e-infrastructures for NGS  
10.10 e-Infrastructure for NGS at CRS4 slides, video Luca Pireddu, CRS4, Italy
10.30 e-Infrastructure for NGS- a Swedish perspective [ slides, video] Ola Spjuth, UPPMAX and SciLifeLab, Sweden
10.50 e-Infrastructure for NGS- a Finnish perspective slides, video Aleksi Kallio, CSC - IT Center for Science, Finland
11.10 e-Infrastructure for NGS- a Danish perspective slides, video Thomas Sicheritz-Ponten, Center for Biological Sequence Analysis, Technical University of Denmark
11.30 Local, central or cloud: why we chose to build our e-infrastructure for sequence analysis embedded in the university of Oslo HPC cluster slides, video Lex Nederbragt, University of Oslo, Norway
11.50 BioBankCloud - a platform-as-a-service for biobanking slides, video Gautier Berthou, Swedish Institute for Computer Science (SICS), Sweden
 
  LUNCH
 
  Session 2: NGS pipelines in action
13.00 Greek myth and sequencing: Raw data processing at SNP&SEQ slides, video Johan Dahlberg, National Genomics Infrastructure at SciLifeLab, Sweden
13.20 A pipeline for whole-genome sequencing on Illumina X Ten slides, video Francesco Vezzi, National Genomics Infrastructure at SciLifeLab, Sweden
13.40 Pipelines for genome annotation slides, video Marc Höppner, BILS, Sweden
14.00 Pipelines for PacBio and IonTorrent slides, video Adam Ameur, National Genomics Infrastructure at SciLifeLab, Sweden
14.20 Hadoop pipelines for NGS analysis slides, video Sebastian Schoenherr, Innsbruck Medical University, Austria
 
14.40 COFFEE
 
15.00 State of the art in hardware for analysis of sequence data slides, video1, video2 Kenneth Benedictsson, Life Science Computational Solutions, HP Sweden & Peter Kaee, Go Virtual, Denmark
 
  Session 3: Clinical data management
15.20 Clinical sequencing data management and analysis slides, video Claes Ladenvall, Clinical Sequencing facility, SciLifeLab, Sweden
15.40 Cancelled ClinSeq - clinical sequencing of cancer in Sweden Daniel Klevebring, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Sweden
 
  Knowledge café
16.00-16.45 Round 1
16.45-17.30 Round 2
  Topics Moderator
  1) e-infrastructures planning ahead (triple room) slides Ola Spjuth, UPPMAX and SciLifeLab, Sweden
  2) Cloud and virtualization in NGS (E10:2309 floor 2) slides Aleksi Kallio, CSC - IT Center for Science, Finland
  3) Workflow tools - are they useful? (E10:3309 floor 3) slides
Luca Pireddu, CRS4, Italy
  4) Pipelines in NGS - challenges and opportunities (E10:4308 floor 4) slides Francesco Vezzi, National Genomics Infrastructure at SciLifeLab, Sweden
 
17.30-18.00 Wrap-up of knowledge café, short presentations
 
19 DINNER at Gästrike-Hälsingland Nation (GH)

DAY 2
8.30-9.00 Morning coffee
 
  Session 4: Workflow systems
9.00 SnakeMake slides
Maciej Kańduła, Chair of Bioinformatics Research Group, BOKU University Vienna, Austria
9.20 CloudGene slides, video Lukas Forer, Innsbruck Medical University, Austria
9.40 NGS pipelines with Galaxy slides, video Luca Pireddu, CRS4, Italy
10.00 Pipelining with Luigi slides, video Samuel Lampa, Department of Pharmaceutical Biosciences and BILS, Sweden
 
10.15 Hitachi Object based solutions for genomics slides, video Johan Westin, Hitachi Data Systems
 
10.25 - COFFEE -
 
10.40 Introduction to Piper slides, video Johan Dahlberg, National Genomics Infrastructure at SciLifeLab, Sweden
11.00 Introduction to Bpipe slides, video Marc Höppner, BILS, Sweden
11.20 Introduction to Chipster slides, video Eija Korpelainen, CSC - IT Center for Science, Finland
11.40 Introduction to Nextflow slides, video Pablo Prieto, Barcelona Center for Genomic Regulation (CRG), Spain
 
  - LUNCH -
 
  Session 5: Virtual machines and NGS
13.00 BioImg.org: A catalogue of virtual machine images for the life sciences slides, video Martin Dahlö, UPPMAX and SciLifeLab, Sweden
13.10 Delivering bioinformatics software as virtual machine images slides, video Aleksi Kallio, CSC - IT Center for Science, Finland
13.30 Hadoop-BAM and SeqPig slides, video Keijo Heljanko, Aalto University, Finland
13.45 Mosler: A virtualized e-infrastructure for extra-sensitive data analysis slides, video Jonas Hagberg, BILS, Sweden
14.00 NeIC announcement slides Joel Hedlund, NeIC, Sweden
14.05 Summary and information about tutorials Ola Spjuth
 
14.15 - COFFEE -
 
  Tutorials
14.30

Tutorials round 1

15.30

Tutorials round 2

16.30

Tutorials round 3

 
17.30 WORKSHOP ENDS
 
  Tutorials
  Bpipe Marc Höppner, BILS, Sweden
  Piper/GATK queue Johan Dahlberg, National Genomics Infrastructure at SciLifeLab, Sweden
  NextFlow Pablo Prieto, Centre for Genomic Regulation (CRG), Spain
  RNA-seq data analysis using Chipster Eija Korpelainen, CSC - IT Center for Science, Finland
  CloudGene Sebastian Schoenherr and Lukas Forer, Innsbruck Medical University, Austria
  Luigi Samuel Lampa, Department of Pharmaceutical Biosciences and BILS, Sweden

Accommodation

Participants are required to book and pay for hotels on their own. If you are an invited speaker on SeqAhead COST funding, you will be reimbursed via e-COST system. We have reserved 15 rooms at the newly built Hotel Von Kraemer (walking distance to workshop) at 930 SEK (~100 EUR) per night; enter code WORKSHOP2015 when making reservations.

Organizers

Ola Spjuth and Martin Dahlö, UPPMAX and Science for Life Laboratory, Uppsala University, Sweden

Contact: ola.spjuth(at)farmbio.uu.se

Emergency numbers: +46-70-425 06 28 (Ola) ; +46-70-670 79 55 (Martin)

Funding

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