EMBnet COST.CHARME training school “Big Data for Life Sciences”, 18.-22.9.2017 Uppsala

1. Hands-on sessions 18.-20.9.2017, max 25 participants

(note that every day includes 2 x 30 min coffee breaks and 1 hour lunch break)

Monday 18.9.2017
Local: Hugin and Munin

9-10:00 Erik Bongcam-Rudloff.(SLUBI/SGBC, Swedish University of Agricultural Sciences, Uppsala, Sweden): Opening of the training school an Practicalities explained

Coffee

10-11:30 Lecture

11:30:-13 Lunch

13-17 Jim Dowling: Lecture and hands-on training on Hops Hadoop.
Presentations:
amir_spark_serc.pdf

amir-scala.pdf

genomics-tutorial-uppsala-sep-2017.pdf

Tuesday 19.9.2017
Local: Hugin and Munin

9-10 Gioele La Manno (Karolinska Institute): Introduction to machine learning

Presentation: CourseUppsala.pdf

10-12:30 Marco Capuccini (Uppsala University): Machine learning in Spark hands-on. This is a short introductory lecture and followed by a hands-on.

13:30-16:00 Apurva Nandan (CSC  - IT Center for Science, Finland): Spark SQL. Lecture and Hands On.

16-17:00 Dr Vaughan Wittorff (PetaGene): “PetaSuite: Reducing the size and cost of NGS data storage and transfer”.
Presentation: PetaGene-Wittorff-NGS_compression-Uppsala_Oct2017.pdf

Wednesday 20.9.2017

Local: Hugin and Munin

9-12 Witold Rudnicki (University of Warsaw): Identification of informative variables in highly-multidimensional data  (machine learning hands-on with expression data).
Necessary data for the tutorial:
https://www.dropbox.com/sh/c2nbkpq6z67vtyq/AAA1P2OrpcYxgFtmtv6tksfYa?dl=0

13:00-16:00 Kim Kultima, Payam Emami, Stephanie Herman and Ola Spjuth (Uppsala University): Large-scale medical metabolomics. Two major projects dedicated to this: Caramba.clinic and Phenomenal.

Files will be distributed on USB sticks during the day.

2. Lecture days 21.-22.9.2017, max 120 participants

Thursday 21.9.2017
Local: Audhumbla

9-9:10 Erik Bongcam-Rudloff (SLUBI/SGBC, Swedish University of Agricultural Sciences, Uppsala, Sweden): Welcome by EU COST Action CHARME.

9:10 -9:25 Domenica DÉlia (CNR, Italy, Chairman EMBnet) Welcome by EMBnet

9:25-9:45 Roxana Merino Martinez (Karolinska Institutet): “Tackling the challenges of sharing Biobank data across continents, the B3Africa case”
https://prezi.com/v2ifq1ccptkd/b3africa-general/?utm_campaign=share&utm_medium=copy

9:45-10:00 coffee

10:00-11 Gaurav Kaul (Intel): “Big Data machine learning using Intel Libraries”.

Presentation: SLU_Uppsala.pptx

11-12 Seija Sirkiä (CSC - IT Center for Science, Finland): Running R in parallel: principles and practice. I will introduce some basic concepts of parallel computing as they apply to R. I will then explain how Microsoft Open R (previously Revolution R) and Intel MKL, as well as R packages such as snow, foreach and doParallel work. I will run some live demos to show the effects. http://r.research.att.com/benchmarks/R-benchmark-25.R
Presentation and data: Running R in parallel — principles and practice.pptx

snowforeach.R

12-13 lunch

13-14 Witold Rudnicki (University of Warsaw): Identification of informative variables in highly-multidimensional data

14:00-15:00 Ola Spjuth: Data-intensive bioinformatics on HPC and Cloud (https://pharmb.io/)

https://www.slideshare.net/ospjuth/dataintensive-bioinformatics-on-hpc-and-cloud

15-15:30 coffee

15:30-15:45 Bjorn Lindell (SLU) What to think when planning for Cloud solutions.
Informations:
Amazon Big Data _01192017(1).pdf
analytics_slu.pdf
Clouds_whitelabeled_presentation.pdf
What to think when planning for Cloud solutions.pdf

15:45-16:45 Erik Gullbring (Microsoft) Using clouds in life sciences

16:45-17:15 Panel discussion: “How to harmonise and standardise strategies to handle the Big Data challenge”.

18:00 Ethno- Party, bring food and beverages from your country and mingle!

Friday 22.9.2017
Local: Hörsal W; Hus: Ulls hus E-blocke

9:00-9:30 Anders Herlin (SLU): Precision Livestock Farming, new ways of thinking in research

9:30-10:00 Kim Kultima: Large-scale Medical Metabolomics. Covers two major projects dedicated to this: Caramba.clinic and Phenomenal.

10:00-10:30 Nataša Sladoje (Centre for Image Analysis, Uppsala University): NEUBIAS: Bioimage analysis - Current trends and future directions.

10:30-11:00 coffee

11:00-11:30 Dimitrios P.Vlachakis (Biotech Dept, Agricultural University of Athens, Greece): Pharmacogenomics and big data/large scale genetic analysis

11:30-12:00 Eija Korpelainen (CSC, Finland) "Enabling life scientists to analyze big data".

Auhumla