Tavernalc How to transform your OpenOffice Calc into a grid Marek Dopiera Adam Kawa Piotr Krewski Tomek Weksej under the aegis of Jacek Sroka Prof. Jerzy Tyszkiewicz

How to transform your OpenOffice Calc into a grid

Agenda Tavernalc from user's side: Why was there a need for such a tool? What does it offer to the user? Tavernalc from developer's side: Simply - how did we manage to achieve Taverna's functionality using Calc? Our experience learning and using UNO, OpenOffice.org API and tools.

Tavernalc from user's side: Why was there a need for such a tool? What does it offer to the user?

Tavernalc from developer's side: Simply - how did we manage to achieve Taverna's functionality using Calc?

Our experience learning and using UNO, OpenOffice.org API and tools.

Foreword: Experiments in silico Experiments in silico “ in silico” - performed on computer or via computer simulation using remote resources and tools problem - a lot of useless work when constructing complex workflows solution - we need a tool for high-level workflow handling!

Experiments in silico

“ in silico” - performed on computer or via computer simulation

using remote resources and tools

problem - a lot of useless work when constructing complex workflows

solution - we need a tool for high-level workflow handling!

What do we want to integrate? Why Taverna? Powerful tool for managing workflows An effect of cooperation of many institutions such as European Bioinformatics Institute (EBI), Biomoby project, Seqhound, Biomart Processors - most basic entities that process the data Workflow = graph consisting of processors Why OpenOffice.org Calc? Ease of use - the power of Calc's intuitiveness when dealing with such data Many more oportunites: making graphs, applying Calc formulas... An integrated solution

Why Taverna?

Powerful tool for managing workflows

An effect of cooperation of many institutions such as European Bioinformatics Institute (EBI), Biomoby project, Seqhound, Biomart

Processors - most basic entities that process the data

Workflow = graph consisting of processors

Why OpenOffice.org Calc?

Ease of use - the power of Calc's intuitiveness when dealing with such data

Many more oportunites: making graphs, applying Calc formulas...

An integrated solution

Tavernalc from user's side Demonstration Easy interface Calc's standard features (dragging, graphs, formula, etc.) Lazy evaluation Diagrams Content preview

Demonstration

Easy interface

Calc's standard features (dragging, graphs, formula, etc.)

Lazy evaluation

Diagrams

Content preview

Tavernalc from developer's side Main objectives Achieve functionality similar to Taverna's... lazy evaluation iteration workflow diagrams ...in an interface in Calc's style dragging behaviour mapping Taverna's data types to Calc Very important: OpenOffice should do the majority of work - not we!

Main objectives

Achieve functionality similar to Taverna's...

lazy evaluation

iteration

workflow diagrams

...in an interface in Calc's style

dragging behaviour

mapping Taverna's data types to Calc

Very important:

OpenOffice should do the majority of work - not we!

Achieving Taverna's functionality How can we represent a workflow? Problems: It can take a long time until the processor evaluates = we should be able to actualize it's result after time Processor must start evaluating after previous processors have evaluated Solution: Processor output = VolatileResult Can change its value over time Allows addition of listeners which are notified when value changes So... It's simple! When processor produces an output -> change VolatileResult's value!

How can we represent a workflow?

Problems:

It can take a long time until the processor evaluates

= we should be able to actualize it's result after time

Processor must start evaluating after previous processors have evaluated

Solution: Processor output = VolatileResult

Can change its value over time

Allows addition of listeners which are notified when value changes

So...

It's simple! When processor produces an output -> change VolatileResult's value!

Achieving Taverna's functionality What is user intuition of dragging processor cell? Adding new instances of the same processor! Problems: When copying -> new instance should be added When cut&paste -> same instance should be added It should be done by OpenOffice - not us!

What is user intuition of dragging processor cell?

Adding new instances of the same processor!

Problems:

When copying -> new instance should be added

When cut&paste -> same instance should be added

It should be done by OpenOffice - not us!

Achieving Taverna's functionality First idea: Use Calc's relative addressing mechanism! Processor id = cell address Problems with cut&paste Solution: Processor id = cell range address Works fine!

First idea: Use Calc's relative addressing mechanism!

Processor id = cell address

Problems with cut&paste

Solution:

Processor id = cell range address

Works fine!

Achieving Taverna's functionality Mapping Taverna's data types into a Calc Problem: Taverna uses complex, unsupported by Calc's data types Solution: Represent them by using Calc's data types! Examples Lists Images

Mapping Taverna's data types into a Calc

Problem: Taverna uses complex, unsupported by Calc's data types

Solution: Represent them by using Calc's data types!

Examples

Lists

Images

Achieving Taverna's functionality Workflow diagrams Keep minimum amount of data outside the sheet! Using Calc's cell dependencies functionality

Workflow diagrams

Keep minimum amount of data outside the sheet!

Using Calc's cell dependencies functionality

Our experience The tools we used The problems we encountered Our conclusions

The tools we used

The problems we encountered

Our conclusions

The tools we used UNO Java bridge works fine tends to crash the JVM during debugging Netbeans together with OpenOffice plugin a very good helper lacks advanced functionality some bugs

UNO Java bridge

works fine

tends to crash the JVM during debugging

Netbeans together with OpenOffice plugin

a very good helper

lacks advanced functionality

some bugs

The problems we encountered Lacks of documentation not enough samples not many people writing in UNO it's just a matter of time, fortunately :) Lacks of API functionality locking cells getting the address from which a formulae is called slow listeners

Lacks of documentation

not enough samples

not many people writing in UNO

it's just a matter of time, fortunately :)

Lacks of API functionality

locking cells

getting the address from which a formulae is called

slow listeners

Our conclusions A very good integration mechanism (UNO) a powerful OS independent solution A well thought API self explanatory hierarchy A little bit to hard for the masses to start writing plugins over 100 lines of code to produce a simple Calc addin a whole new philosophy to learn to write a plugin (UNO)

A very good integration mechanism (UNO)

a powerful OS independent solution

A well thought API

self explanatory hierarchy

A little bit to hard for the masses to start writing plugins

over 100 lines of code to produce a simple Calc addin

a whole new philosophy to learn to write a plugin (UNO)

Thank You Project's site: http://tavernalc.googlecode.com/ Tavernalc Team Marek Dopiera Adam Kawa Piotr Krewski Tomek Weksej Project Promoters, Motivators and Helpers Jacek Sroka Prof. Jerzy Tyszkiewicz

Project's site:

http://tavernalc.googlecode.com/

Tavernalc Team

Marek Dopiera

Adam Kawa

Piotr Krewski

Tomek Weksej

Project Promoters, Motivators and Helpers

Jacek Sroka

Prof. Jerzy Tyszkiewicz