e-Science 2014: Computing for Biomedical Research
Have you ever thought that your computer has become too small for your data processing needs?Do you feel overflowed by a tsunami of data?
Do you have the impression that you spend more time arranging computers to run data analysis than actually doing the research that the data is supposed to support in the first place? If this sounds familiar, dont’ worry. You are not alone. Come and join the e-science course, where you can learn how others are addressing the modern challenges of data analysis for biomedical research. NOTE: this course has been completed in 2014. If you are interested in following a future edition of this course, please contact the coordinator. Coordinator:
Silvia Delgado Olabarriaga
Department of Clinical Epidemiology, Biostatistics and Bioinformatics, J1B-206
Tel. +31 (0)20-5664660
Email: s.d.olabarriaga @ amc.uva.nl
https://www.ebioscience.amc.nl See also:
Overview
Computing infrastructures have become an essential ingredient of biomedical sciences. The variety and amount of data has significantly increased, and the typical desktop is not longer sufficient. Large collaborations are necessary to carry out research, involving complex logistics for handling distributed data collection, analysis and management. New approaches (computers, software and methodology) are needed to tackle challenges regarding compute power, storage space, and collaboration. These new approaches enable and enhance science (e-science), and are increasingly used in (AMC) biomedical research. The aim of this course is to bring attention to new approaches that can be used for handling large-scale data in biomedical research, including processing, storage and collaboration. At the end of the course, the participant will (1) be familiar with new concepts and state-of-the-art, (2) understand how these new approaches relate to his/her own research, and (3) be able to apply some of these technologies and tools in practice.Topics
- Basic concepts of research infrastructures and e-science
- Introduction to distributed computing (grids, clouds, clusters)
- Scientific workflow management (concepts and examples)
- Hands-on experience with the AMC e-science platform
Schedule and Location
- 31 March - 4 April 2014, from 1pm to 5pm
- Lecture room: K01-208
- Practice room: L0-211
Program and Contents
Course syllabus- Day 1: Introduction to computing and e-science
- Introduction to the course
- Basics of e-science and e-infrastructures
- Basics of computing and research infrastructures
- Results of the practical exercises: gait virus alert OCT
- Day 2: Visit to the Science Park Amsterdam (SURFsara and e-science center)
- SURFsara e-infrastructure, Jan Bot, SURFsara
- Introduction to the NL e-science center, Rita Azevedo, NL eScience Center
- TraIT project, Rita Azevedo, NL eScience Center
- Biomarker Boosting through eScience infrastructure, Elena Ranguelova, NL eScience Center
- Introduction to the NL e-science center, Maarten van Meersbergen, NL eScience Center
- Day 3: Distributed computing, with practice
- Large scale computing
- DNA data analysis on many infrastructures, Barbera van Schaik, AMC Bioinformatics Laboratory
- Practice: scaling out with distributed computing
- Day 4: Data analysis workflow management, with practice
- Scientific data and workflow management
- Imaging research data management with XNAT, Jordi Huguet, AMC Radiology
- Introduction to WS-PGRADE, Mahdi Jaghoori, AMC KEBB
- Advanced Features in Workflow Development, Mahdi Jaghoori, AMC KEBB
- Practice: Basic usage of WS-PGRADE
- Sample scripts and input files:
- hello-script.sh: Hello-World Script
- hello-script-port.sh: Hello-World with input and output
- paramInputs.zip: Example input for parameter sweep
- main.sh.app.tgz: Contains two scripts, of which "main.sh" is the entry point
- splitLines.sh: splitLines.sh
- merge.sh: merge.sh
- Day 5: Science Gateways, with practice
- Introduction to science gateways
- Science gateways at the AMC
- Practice with the AMC neuroscience gateway
- Advanced topics in e-Science and wrap-up
- Results of the practical exercises: gait virus alert OCT
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