Bio PSE Overview of the SCIRunBio PSE Software

Bio. PSE Overview of the SCIRun/Bio. PSE Software Systems Hold on to your hats… NCRR

Outline Bio. PSE 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 NCRR

Installation Bio. PSE 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 NCRR

Documentation: The Central Source Bio. PSE Overview http: //internal. sci. utah. edu/developer/doc/ NCRR

Documentation: User Support On-line Documentation Bio. PSE Overview • Tutorial • User’s Manual • FAQ Lists Printed Documentation • User’s Manuals Mailing List 182 registered) Direct Contact • Email and Bugzilla • Phone NCRR

Documentation: Tutorial Bio. PSE Overview NCRR

Dataflow • Dataflow Vocabulary Bio. PSE Overview • Module • Dataport • Datapipe • UI • Send and Get • Gui. Vars • Scheduler • Dependencies • loops: send_intermediate NCRR

Network Design Bio. PSE Overview NCRR

Module: Algorithm + UI • Algorithm Bio. PSE 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 NCRR

Net Files and State • Net File Bio. PSE Overview • Create modules • Create datapipes • Set UI values • Environment variables to create general purpose nets • SCIRUN_DATASET • Human editable… but be careful! • Datasets can also be written out and read in… more on that tomorrow NCRR

I/O, Bridging, and Thirdparty Bio. PSE 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 NCRR

Viewer Module • Open. GL • Scene graph • Widgets Bio. PSE Overview • See the User’s Guide for details… NCRR