BioPSE Overview
Overview of the
SCIRun/BioPSE Software
Systems
Hold on to your hats…
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Outline
BioPSE Overview
• Installation
• Documentation Structure and
Layout
• Dataflow Concepts
• Network Design and Conventions
• Modules
• Network Files and Persistent State
• I/O, Bridging, and Thirdparty
• Viewer Interaction
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Installation
BioPSE Overview
• Download from SCI Software website
• http://software.sci.utah.edu (let’s go!)
• Stable (even) vs Development (odd) releases
• SCIRun / Packages / Datasets / Docs
• Install Thirdparty
• configure
• gmake
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Documentation: The Central Source
BioPSE Overview
http://internal.sci.utah.edu/developer/doc/
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Documentation: User Support
On-line Documentation
BioPSE Overview
• Tutorial
• User’s Manual
• FAQ Lists
Printed Documentation
• User’s Manuals
Mailing List 182 registered)
Direct Contact
• Email and Bugzilla
• Phone
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Documentation: Tutorial
BioPSE Overview
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Dataflow
• Dataflow Vocabulary
BioPSE Overview
• Module
• Dataport
• Datapipe
• UI
• Send and Get
• GuiVars
• Scheduler
• Dependencies
• loops: send_intermediate
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Network Design
BioPSE Overview
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Module: Algorithm + UI
• Algorithm
BioPSE Overview
• Function
• Reusability
• User Interface
• Buttons, tabs, slides, text entry, …
• Hidden state
• Module: wrapper
• Infrastructure: setup, shutdown
• Execute
-
1) Why am I being told to execute
2) Get data from ports
3) Update UI variables
4) Invoke algorithm
5) Send data out ports
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Net Files and State
• Net File
BioPSE Overview
• Create modules
• Create datapipes
• Set UI values
• Environment variables to create general
purpose nets
• SCIRUN_DATA
• SCIRUN_DATASET
• Human editable… but be careful!
• Datasets can also be written out and read in…
more on that tomorrow
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I/O, Bridging, and Thirdparty
BioPSE Overview
• Read/Write modules for SCIRun format
• “convert” programs for importing /
exporting external data formats
• Packages = projects
• Internal
• External: bridging
• Store external libraries in Thirdparty
• Independent of SCIRun standards
• Externally maintained
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Viewer Module
• OpenGL
• Scene graph
• Widgets
BioPSE Overview
• See the User’s Guide
for details…
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