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Mon 6 Jan - Tue 7 Jan 2020
09:30, ...

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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Snakemake workshop
PrerequisitesNew

Mon 6 Jan - Tue 7 Jan 2020

Description

Data analyses usually entail the application of many command line tools or scripts to transform, filter, aggregate or plot data and results. With ever increasing amounts of data being collected in science, reproducible and scalable automatic workflow management becomes increasingly important.

The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.

With over 100k downloads on Bioconda, Snakemake is a widely used and accepted standard for reproducible data science that has powered numerous high impact publications.

This 2-day workshop with, at the first day, teach how to use Snakemake for reproducible data analysis. On the second day, we will further discuss advanced topics and everybody is welcome to apply the obtained knowledge for his or her own analysis project while getting help from the organizers.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.

Target audience
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for registered University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here
Prerequisites
  • Basic experience in Python programming
  • The examples presented in this course come from Bioinformatics. However, Snakemake is a general-purpose workflow management system for any discipline.
  • Participants are invited to bring their own data.
Sessions

Number of sessions: 2

# Date Time Venue Trainer
1 Mon 6 Jan 2020   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Johannes Köster
2 Tue 7 Jan 2020   09:30 - 17:00 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Johannes Köster
Topics covered

Bioinformatics

Objectives

After this course you should be able to:

  • create reproducible and scalable data analyses
Aims

During this course you will learn about:

  • the Snakemake workflow definition language
  • how to use Snakemake for reproducible data analysis
  • how to use the execution environment to scale workflows to compute servers and clusters while adapting to hardware specific constraints
  • how to create reproducible analyses that can be adapted to new data with little effort.
Format

Presentations, demonstrations

Timetable

Day 1 Topics
9:30 - 10:00 Presentation: Introduction to Snakemake
10:00 - 12:00 Tutorial: Basic practical session
12:00 - 13:00 Lunch (not provided)
13:00 - 13:30 Presentation: Advanced usage of Snakemake
13:30 - 17:00 Tutorial: Advanced practical session
Day 2
9:30 - 12:00 Snakemake tutorial (cont.)
12:00 - 13:00 Lunch (not provided)
13:30 - 17:30 Bring your own project and implement it in Snakemake while getting advice
Registration fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here
Duration

2

Frequency

Once a year

Related courses
Theme
Specialized Training

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