File Entry: Bonn 2014 Agenda

Agenda “in silico experimentation” course 2014

Please sign up and join the

myExperiment group: Bonn Workshop Sep 2014

http://www.myexperiment.org/groups/1267

Monday 2014-09-01 – Introductions and basics

10:00-10:15 Intro to the workshop – Heiko

10:15-11:00 Introduction to web services, workflows and e-science approaches [0_Bonn_e-science_webservices_workflows.pdf]

11:00-11:30 coffee

11:30-12:00 Finding and using services (BioCatalogue)  [demo]

        Reusing workflows (Sharing your workflows in myExperiment) [demo]

A Practical Introduction to Taverna Workflows

[1_Bonn_Introduction_Tutorial.pdf]

12:00-13:00 Taverna Exercises

        Installing Taverna [T-installing_Taverna.pdf]

        Building a simple workflow [T-Simple_workflow.pdf]

            REST services from BioCatalogue [T-REST_biocatalogue.pdf]

13:00-14:00 Lunch

14:00-15:30 Taverna Exercises (continued)

        Shims [T-Shims_Beanshell.pdf]

Spreadsheet import [T-Spreadsheet import.pdf]

REST Services [T-REST_services.pdf]

        Xpath [T-Xpath.pdf]

15:30   Wrap up of issues and summary of the day - Heiko

Tuesday 2014-09-02 – Workflows in Depth

10:00-11:00 Review of yesterday’s exercises

Asynchronous service pattern [3_asynchronous-services.pdf]

11:00-11:30 Coffee

11:30-13:00 Taverna advanced exercises [T-myExperiment.pdf]

Re-using workflows from myExperiment

Combining workflows from myExperiment

GO associations

Simple text mining

Workflow features [T-Advanced-Taverna.pdf]

List handling

Looping asynchronous services

Looping

Control links

Nested workflows [T-Nested_workflows.pdf]

Retries

Parallel Service Invocation [2_Bonn_myExperiment_Services_iteration_paralell.ppt]        

Taverna Components  [T-Components.pdf]

13:00-14:00 Lunch

14:00-16:00 Taverna advanced exercises (cont)

16:00 Wrap up of issues and summary of the day - Heiko

Wednesday 2014-09-03 – Integrations and Workflows in Practice

10:00–11:00 Taverna Command Line Tool [demo]

Taverna Online & Running Workflows via the Portal  [demo]

           (Workflow with R Script [demo])

External tool  [T-Tool_service.pdf]

11:00-11:30 Coffee

11:30  12:00-13:00 Extra exercises

Taverna Interaction Service [T-Interactions.pdf]

        R scripts [T-RShell.pdf]

        Bio-diversity research example [4_Bonn_BioVel_TavernaTutorial.ppt]

13:00-14:00 Lunch
14:00-14:3014:30-16:00 Finish advanced exercises/Design your own workflow [students]

Thursday 2014-09-04 – RNAseq analysis workflow (Heiko Schoof)

10:00–10:30 Introduction to RNAseq analysis using Cufflinks

10:30-11:00 RNAseq workflow

11:00-13:00 Exercise        

13:00-14:00 Lunch
14:00-16:00 Finish exercises and discussion of results

Friday 2014-09-05 – Final discussion (Martin Hofmann-Apitius)

10:00–12:00 Presentation of workshop results and final discussion