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Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Overview
Scientific workflows
Characteristics of Scientific Workflow Systems:
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Scientific workflows
workflows needed for different scientific applications and
scientific experiments
designing, automating, controlling and managing the
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Scientific workflows
Workflow - automation of a process during which documents,
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Grid
coordinated use of many heterogeneous and distributed
resources
solving problems in many computing and data intensive
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
process
scientific workflows -modeling large-scale data-intensive
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
OpenMole
parallel execution environments for naturally parallel
processes
advanced numerical experiments on simulation models
distribution of the workflows on multi-core machines,
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Mole components
Tasks
Transitions
Prototypes
Samplings
Environments
Hooks
Sources
In order to be run, a mole must contain at least one task
and a starting task (capsule)
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Mole components
Prototype - a variable that operates in the workflow (must
2- matrix, etc.).
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
dimension one.
Sensitivity task - enables variance-based method
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Mole components
Sampling - can be composed graphically,
many kinds of samplings: complete, shuffle, zip, combine
and domains: range, multiple file, single file, uniform distribution,
logarithmic range domain, etc.
Hook - a Mole listener. It performs a particular action on the
output.
Source - reads data from a CSV file and maps it to
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Taverna
available as a desktop client application (Taverna
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Taverna
support for calling client libraries (in Ruby and Java) and
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Taverna components
Services
WSDL-style Web services (just URL address should be provided)
BioMoby Web services
BioMart Web services
SoapLab Web services
local Java services (Beanshell scripts)
local Java API (API consumer)
R script on an R server (RShell scripts -analyses using the R statistical
package)
Xpath
Oauth services
component services
string constant (for setting a fixed-value input for a service).
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Taverna components
Lists and iterations - Services in Taverna can return single
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
The Workflow
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
The workflow
circle represents a file containing some data
squares a1; a2; a3;.. a64 file actions- merging of files'
contents
choose always 64 combinations of 3 files
two copies of the file list in the directory
each file list is shuffled and the first 4 files of each of the
three file lists are chosen
"folderA" represents the directory where the combinations
are chosen
result of an each action a1; a2; a3;.. a64 is a file saved in a
new directory "folderB
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
The workflow
actions a1; a2; a3;.. a64 are performed in parallel
when three files are created in "folderB", the action b is
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
integer prototype i.
transition between "comb. 3 first and this capsule is an aggregation
executed once in each workflow iteration.
capsule "comb. 3 first" - groovy task, includes a jar file
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
in les by 3 Files".
contents are merged into a new file
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna
systems
Different implementation logic
Taverna offers natural parallelism of processes
in OpenMole the user should explicitly define that
Building Scientific Workflows on the Grid: A Comparison between OpenMole and Taverna