D2K Web Service Case Studies: Phylomat

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D2K Web Service Case Studies Phylomat
Evolution Highway
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Outline

• Phylomat
• Description
• Architecture
• Itinerary
• Demo
• Evolution Highway
• Description
• Architecture
• Itinerary
• Demo
• D2K Web Service
• Q and A

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Phylomat Description

• Calculates the distribution of a particular
  motif among available (fully sequenced) proteomes
• Extracts motif sequences from full protein
  sequences
• Aligns extracted motif sequences and generates a
  neighbor-joining tree, which can be visualized
  with a supplied applet
• Evolutionary trends resulting from protein
  groups can be inferred from these data and
  hypotheses about the evolutionary origin of the
  motif/domain class can be formulated
• Job runs can be named, saved and rerun in the
  future

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Phylomat (Motif Analysis Tool for Phylogenomics)
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Phylomat Architecture

• User interacts with web browser to specify job
  execution parameters, then submits job to
  Phylomat web application.
• Phylomat web application contacts the D2K Web
  Service via the D2KServiceProxy class, and
  submits job
• Web service brokers job to D2K Server
• Text results are produced by job process
• Phylomat web application checks for job
  completion. Results are collected and displayed
  when job is finished

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Phylomat Itinerary

• Data loaded from central loc.
• Runtime.exec() is used to cluster sequences. Has
  created server dependency
• Tree, Alignments, Sequences, Counts, Summary
  modules all implement
• ncsa.d2k.core.modules.DataProducer
• Data results get saved in web service tier
• Client retrieves results by calling
  getResultModuleData(int jobId, String moduleName)
  on the web service

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Phylomat Demo
DEMO
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Evolution Highway Description

• Loads and visualizes genome data for comparing
  multiple species
• Reference genome data for humans
• Comparative genome data for horses, dogs, cats,
  pig, cattle, rats, mice

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Evolution Highway
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Evolution Highway Architecture

• User interacts with web browser to specify job
  execution parameters, then submits job to
  Evolution Highway servlet.
• Evolution Highway servlet contacts the D2K Web
  Service via the D2KServiceProxy class, and
  submits job
• Web service brokers job to D2K Server
• Visualization result is produced by job.
• Evolution Highway servlet checks for job
  completion. After the job is finished, servlet
  responds with a page containing a shell applet.
• Applet requests back from servlet the
  visualization to display

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Evolution Highway Itinerary

• Data loaded from local file system
• Will be loaded from RDMS soon
• Data is converted to D2K Table instances
• Data is fed into D2K Visualization Object, which
  gets produced as a job result
• Visualization results get saved in web service
  tier
• Client retrieves results by calling
  getResultModuleVisualizations(int jobId, String
  moduleName) on the web service

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Evolution Highway Demo
DEMO
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D2K Web Service Architecture

• Any web enabled client can connect to and use
  the D2K Web Service by sending SOAP messages over
  HTTP.
• Itineraries and modules are stored on the web
  service machine and loaded over the network by
  the D2K Servers.
• Job results are also stored in the web service
  tier.
• Results are returned to clients upon request.
• A relational database is used by the web service
  to lookup accounts, itineraries, servers, and
  jobs. Maintains state.
• Remote D2K Servers handle itinerary processing.
  If possible, modules should load any data from
  remote locations.

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Q and A
Questions?