Recording and Using Provenance in a Protein Compressibility Experiment

1
Recording and Using Provenance in a Protein
Compressibility Experiment

• Paul Groth, Simon Miles, Weijian Fang, Sylvia C.
  Wong,
• Klaus-Peter Zauner and Luc Moreau
• University of Southampton

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Outline

• Biology
• The Workflow
• Use Cases
• Provenance
• Implementation
• Evaluation
• Conclusion

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Biology

• Determine how protein sequences (chains of amino
  acids) fold into a 3D structure?
• Which part of DNA translates into one protein
  sequence?
• Structure of protein sequences may help to answer
  these questions.
• Structure can be quantified by textual
  compressibility.
• Determine the amino acid groupings that maximize
  compressibility?

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The Workflow

• Get Sequences
• Make a Sample
• Recode Sample
• Compress and Measure
• Shuffle the sample
• Compress and Measure each permutation
• Collate all measures
• Produce the average compressibility

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Use Case (1)

• A bioinformatician, A, downloads sequence data of
  microbial proteins from the database RefSeq.
• Runs the compressibility experiment.
• A later performs the same experiment on the same
  sequence data, again downloaded from RefSeq.
• A compares the two experiment results and notices
  a difference.
• A determines whether the difference was caused by
  the algorithms changing

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Use Case (2)

• A bioinformatician performs an experiment on a
  FASTA sequence encoding a protein.
• A reviewer, later determines whether or not the
  sequence was in fact processed by a service that
  meaningfully processes protein sequences only.

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Provenance

• Use cases related to process
• Provenance Definition
• The provenance of a result is the process that
  led to that result.
• This is a conceptual definition.

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Documentation of Process

• Conceive a computer based representation of
  provenance
• We represent the provenance of some data by
  documenting the process that led to the data
• documentation can be complete or partial
• it can be accurate or inaccurate
• it can present conflicting or consensual views of
  the actors involved
• it can provide operational details of execution
  or it can be abstract.

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Heterogeneity

• This is a heterogeneous application
• Has shell scripts, java programs, web services
• Heterogeneity is common in Grid based apps
• LCG Atlas - Athena VDT coexist
• Support for plugging-in different execution
  environments

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Provenance Lifecycle
Record Documentation of Process
Query to retrieve the provenance of a result
Provenance Store
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Use Case 1 Do services differ between
experiments?
Retrieve documentation of experiments

• Service A
• .
• ..

• Service A
• .
• ..
• .

Highlight differences in services between
experiments
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Implementation

• Implemented as a VDT workflow
• Scheduled by Condor
• Each service, script, command records process
  documentation into a provenance store.
• Uses PReServ a web services implementation of a
  provenance store

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PReServ Implementation Diagram
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Evaluation Deployment

• Runs on VMWare
• deployment consistency
• ease of development
• Workflow is executed on one machine
• PReServ runs on another machine

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Recording Performance
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Query Performance
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Conclusion

• Both recording and query times are linear
• 10 overhead for asynchronous recording
• Our provenance concept / system are grounded in a
  number of use cases
• The experiment is ready to be moved to a cluster
  or a grid
• Southampton Cluster
• A Grid
• Will allow us to test scalability

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Contact Info

• Paul Groth
• pg03r_at_ecs.soton.ac.uk
• www.pasoa.org
• use case descriptions
• papers
• PReServ software

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Configuration

• Redhat Linux 9.1 on VMWare on Windows XP
• Pentium P4 2.8 GHZ 1.5 GB RAM
• PReServ on another machine
• Database backend Berkley JDB
• 100 Mb local ethernet