Group: EOS - Keystone Skills in Bioinformatics 13th -14th Feb 2014

Overview

This is a group for all participants of the EOS Keystone Skills in Bioinformatics.

Days 9 -10. Workflows, Taverna and the BioVeL Project.

Timetable:

Thursday, 13th February, 2014

09:30 - 10:00 Introductions. Outline of learning objectives for days 9 & 10

10:00 - 10:30 An introduction to myExperiment.

  • Setting up a myExperiment account

10:30 - 11:15 Demonstration of 2 workflows in the BioVeL portal.

  • Ecological Niche Modelling
  • Fetch GBIF Occurrence Data

11:15 - 11:30 Tea / Coffee break

11.30 - 11:45 ? Setup. F. Quevedo.

11:45 -12:30 An Introduction to Designing and Executing Workflows with Taverna - Part 1

  • Building a simple workflow

12:30 - 13:30 Lunch

13:30 - 15:00 An Introduction to Designing and Executing Workflows with Taverna - Part 2

  • Extending the simple workflow.
  • Inputting data directly, via local files, via URL's
  • Importing and exporting data to / from workflows via spreadsheets

Introductory bioinformatic exercises

15:00 - 15:30 Exploring the Taverna workflow engine.

15:30 - 15:45 Tea / Coffee break

15:45 - 16:30 Working with the BioVeL portal. In this exercise we will upload the workflow we created in the previous exercise and run it on the BioVeL Portal.

 

Friday, 6th December

09:30 - 10:30 Using Rshell in Taverna Workbench tutorial 

10:30 - 11:00 Embedding an R Script in a workflow exercise

11:00 - 11:30 Coffee break and Demonstration. Embedding workflows in your website (Taverna Player) 

11:30 - 12:30 Embedding an R Script in a workflow exercise continued / Bring Your Own R Script (BYOR) 

12:30 - 13:30 Lunch

13:30 - 15:00

15:00 - 15:30 Wrap-up and feedback

Created at: Wednesday 05 February 2014 15:20:10 (UTC)

Feed-icon

News


  1. 3366?size=48x48
    Norman Morrison shared Embedding an R Script in a Workflow Exercise
    This pack has all the files for the problem based learning exercise of embedding an R Script in a workflow
    Thursday 13 February 2014 17:47:42 (UTC)
  2. 3366?size=48x48
    Norman Morrison shared Taverna Tool Service
    Taverna Tool service tutorial pack
    Thursday 13 February 2014 17:41:07 (UTC)
  3. 292?size=48x48
    Tim Booth shared Rserve on Bio-Linux
    The recommended way to run Rserve on Bio-Linux is to install the "r-cran-rserve" package - ie: $ sudo apt-get install r-cran-rserve (Note - this wasn't working on the morning of the 13th but has now been fixed in version 1.7-3-0biolinux2) If you install the library by using install.packages("Rserve") …
    Thursday 13 February 2014 14:56:15 (UTC)
  4. 3366?size=48x48
    Norman Morrison shared An introduction to designing and executing workflows with Taverna Bioinformatics exercises
    This tutorial uses Bioinformatics exercises as an introduction to designing and executing workflows with Taverna.
    Thursday 13 February 2014 08:46:17 (UTC)
  5. 3366?size=48x48
    Norman Morrison shared An introduction to Taverna components
    Tuesday 11 February 2014 16:15:52 (UTC)
  6. 3366?size=48x48
    Norman Morrison shared Working with the BioVeL Portal
    In this exercise we will upload and run a simple workflow that we created in the previous exercises on the BioVeL portal.
    Tuesday 11 February 2014 16:12:36 (UTC)
  7. 3366?size=48x48
    Norman Morrison shared Setup instructions for BioLinux VM
    Version2
    Tuesday 11 February 2014 16:01:51 (UTC)
  8. 3366?size=48x48
    Norman Morrison shared Introduction and learning objectives
    Tuesday 11 February 2014 15:52:31 (UTC)
  9. 3366?size=48x48
    Norman Morrison shared Embedding an R Script in a Workflow Exercise
    This exercise is designed as a problem based learning task to understand how to embed R Scripts in workflows in Taverna.
    Tuesday 11 February 2014 15:42:26 (UTC)
  10. 3366?size=48x48
    Norman Morrison shared mrow workflow
    Thumb
    Tuesday 11 February 2014 15:29:09 (UTC)
  11. 3366?size=48x48
    Norman Morrison shared R Exercise Worm Gen Matrix Data
    Data provided by Daniel Pass, Cardiff University
    Tuesday 11 February 2014 15:28:24 (UTC)

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