Creating BioMoby Workflows
In Taverna
Mark Wilkinson
Edward (Eddie) Kawas
iCAPTURE Centre, St. Paul’s Hospital
Vancouver, BC
Downloading Taverna
• Taverna can be obtained from:
http://taverna.sourceforge.net
• Once at the site, click on Download
• Download the version appropriate for your
operating system.
• Between releases, the Moby functionality may be updated and you
can find instructions on how to acquire those updates from:
http://biomoby.open-bio.org/index.php/moby-clients/taverna_plugin
Running
• For a more comprehensive guide on Running and using
Taverna, please refer to
http://taverna.sourceforge.net/usermanual/manual.html
• Assuming that you have downloaded and unzipped
Taverna, you can run it by double-clicking on runme.bat
(windows) or executing runme.sh (Unix/Linux/OS X)
• Taverna’s splash screen
• Once Taverna has loaded, you will see 3 windows:
– Advanced Model Explorer
– Workflow Diagram
– Available Services
• The Advanced model explorer is Taverna’s primary editor and allows
you to load, save and edit any property of a workflow.
• Workflow diagram contains a read only graphical
representation of your workflow.
• The Available services window lists all of the
services available to a workflow designer.
• Under the node ‘Biomoby @ …’
Moby services and Moby data
types are represented.
• The Object ontology is available
as children of MOBY Objects
node
• Services are sorted by service
provider authority
• If you wish to use registries other than the default one,
you can add a new Moby ‘Scavenger’ by choosing to
‘Add new Biomoby scavenger…’
• Enter the registry’s location and click okay.
Creating Workflows
• I have the workflow saved and would
like to offer it for download.
• We will start by adding the Object ontology node
Object to our workflow.
• The Advanced model explorer
now shows that we have a
processor called Object
– Object has 3 input ports: id,
namespace and article name
– Object has 1 output port:
mobyData
• The Workflow diagram illustrates
our processor
• We can discover services that consume our data type,
context click on ‘Object’ and choose ‘Moby Object
Details’
• A window will pop up that tells you what services Object
feeds into and is produced by
• Expanding the Feeds into node results in a list of service
provider authorities
• Expanding an authority, for example,
bioinfo.icapture.ubc.ca, reveals a list of services
• We will choose to add the service called
‘MOBYSHoundGetGenBankFasta’ to our workflow.
• A look at the state of our current workflow.
• And graphically.
• The service consumes Object, with article name
identifier, and produces FASTA, with article name fasta.
• To discover more services, context click on the service
that outputs the data type that you would like to discover
consuming services for and choose Moby Service
Details.
• The resultant window displays the services inputs and
outputs.
• There are also tool tips that show up when your mouse
hovers over any particular input or output that tells you
what namespaces the data type is valid in
• Context clicking on an output reveals a menu with 3 options.
– A brief search for services that consume our datatype
– A semantic search for services that consume our datatype
– Adding a parser to the workflow that understands our datatype
• The result of choosing to add a parser for FASTA to our workflow.
• The parser allows us to extract:
– The namespace and id from FASTA
– The namespace and id from the child String
– The textual content from the child String
• The result of choosing to conduct a brief search for
services that consume FASTA
• We will add the service getDragonBlastText to our
workflow by choosing ‘Add service -…’ from the context
menu
• The current state of our workflow shown graphically.
• A more complex view of our workflow
• Finding services that consume NCBI_BLAST_Text starts
by viewing the details of the service ‘getDragonBlastText’
• Conduct a brief search
• Add the service ‘parseBlastText’ to our workflow
• Our current workflow
• Workflow inputs are added by context clicking on
Workflow inputs in the Advanced model explorer and
choosing ‘Create New Input…’
• The result from adding 2 inputs:
– Id
– namespace
• The workflow input id will be connected to Object’s input
port ‘id’
• Workflow after connecting the workflow input ‘id’
• The workflow input namespace will connect to Object’s
input port ‘namespace’
• Workflow after connection the workflow inputs.
• Workflow outputs are added by context clicking on
Workflow outputs in the Advanced model explorer and
choosing ‘Create New Output…’
• The result from adding 2 workflow outputs:
– moby_blast_ids
– fasta_out
• The output moby_blast_ids will be connected to
parseBlastText’s output port Object(Collection –’hit_ids’)
• The output fasta_out will be connected to
Parse_Moby_Data_FASTA’s output port fasta_’content’
• To run the workflow, click on ‘Tools and Workflow
Invocation’
• Choose ‘Run workflow’
• A prompt to add values to our 2 workflow inputs
• To add a value to the input ‘id’ click on id from the left
pane and choose ‘New Input’
• Enter 656461 as the id
• Choose namespace from the left and click on ‘New Input’
• Enter NCBI_gi as the value for namespace
• Once you are done, click on ‘Run Workflow’
• Our workflow in action
• Once the workflow is complete, we can examine the
results of our workflow.
• A detailed report is available outlining what happened
when and in what order.
• We can examine the intermediate inputs and output, as
well as visualize our workflow.
• If we choose the Graph tab, our workflow is illustrated.
• Intermediate inputs allow us to examine what a service
has accepted as input
• Similarly, Intermediate outputs allows us to examine the
output from any particular service.
• Without the parser, FASTA is represented as a Moby
message, fully enclosed in its wrapper.
• Non-moby services do not expect this kind of message
• Non-moby services expect the just the sequence
and using the Parse_Moby_Data processor, we
can extract just that
• Moby services can interact with the other services in
Taverna.
• Let’s add a Soaplab service.
• We will choose a
nucleic_restriction
soaplab service called
‘restrict’
• Choose the restrict
service and add it to the
workflow.
• We will connect the output port
fasta_’content’ from the
service
Parse_Moby_Data_FASTA to
the input port
‘sequence_direct_data’ from
the service restrict
• The result of our actions so far.
• We will need to add another workflow
output to capture the output of
restrict.
• Create an output called restrict_out
• Connect the output port ‘outfile’ from the service restrict
to the workflow output restrict_out
• Once the connections
have been made, run the
workflow again using the
same inputs.
• The workflow on the left has some
extra services added to it.
– FASTA2HighestGenericSequenceObject
from the authority
bioinfo.icapture.ubc.ca
– runRepeatMasker
genome.imim.es
from the authority
– A Moby parser for the output
DNASequence from runRepeatMasker.
– A workflow output Masked_Sequence
• Add them to your workflow
• The service runRepeatMasker is configurable, i.e. it
consumes Secondary parameters.
• To edit these parameters, context click on the service
and choose ‘Configure Moby Service’
• The name of the parameter is on the left and the value is
on the right.
• Clicking on the Value will bring up a drop down menu, an
input text field, or any other appropriate field depending
on the parameter.
• The parameter species contains an enumerated list of
possibilities.
• Select human.
• When you have made your selection, you may close the
window.
• Let’s run the workflow
• We will run our workflow with a list
– Click on id in the left pane and then click on New
Input twice
• Enter 656461 and 654321 as the ids
• Enter NCBI_gi as the value for namespace
• Our workflow will now run using each id with the single namespace
• Notice how the workflow is running with iterations. This is
happening because the Enacter is performing a crossproduct on the input
• You can still view intermediate inputs and outputs.
• Using the queryIDs, you can track each invocation of a
moby service through the whole workflow
•
•
Imagine now that you want to run the workflow using a FASTA sequence that you
input yourself (without the gi identifier)
To do this, context click on getDragonBlastText and choose Moby Service Details
–
–
•
Expand the Inputs node and context click on FASTA(‘sequence’)
Choose Add Datatype – FASTA(‘sequence’) to the workflow
A FASTA datatype will be added to the workflow and the appropriate links created
• Notice the datatype FASTA
on the left of the workflow
– Since the datatype FASTA
hasa String, a String was
also added to our workflow
and the appropriate
connection was made
• We will now have to add
another workflow input and
connect it to the String
component of FASTA.
•
A workflow input ‘sequence’ was
added to the workflow and a
connection was made from the
workflow input to the input port ‘value’
of String.
•
We also removed the link between
MOBYSHoundGetGenBankFasta and
getDragonBlastText by context clicking
on the link in the Advanced model
explorers’ Data links and choosing to
remove the link
•
Now when we choose to run our
workflow, we will also have the chance
to enter a FASTA sequence
• Go ahead an enter any FASTA sequence as the input to
the workflow input ‘sequence’
• Run the workflow
•
Any results can be saved by simply choosing to Save to disk
– You will be prompted to enter a directory to save the results.
– Each workflow output will be saved in a folder with the same name as a workflow
output and the contents of the folder will be the results
•
You can also choose Excel, which produces an Excel worksheet with
columns representing the workflow outputs and with rows that represent the
actual data.