Relevant Papers
First Provenance Challenge
#!/bin/sh
AIR5.2.5/bin/align_warp anatomy1.img reference.img warp1.warp -m 12 -q
AIR5.2.5/bin/align_warp anatomy2.img reference.img warp2.warp -m 12 -q
AIR5.2.5/bin/align_warp anatomy3.img reference.img warp3.warp -m 12 -q
AIR5.2.5/bin/align_warp anatomy4.img reference.img warp4.warp -m 12 -q
AIR5.2.5/bin/reslice warp1.warp resliced1
AIR5.2.5/bin/reslice warp2.warp resliced2
AIR5.2.5/bin/reslice warp3.warp resliced3
AIR5.2.5/bin/reslice warp4.warp resliced4
AIR5.2.5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img
fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm
fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm
fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm
convert atlas-x.pgm atlas-x.gif
convert atlas-y.pgm atlas-y.gif
convert atlas-z.pgm atlas-z.gif
Core provenance queries
Find the process that led to Atlas X Graphic / everything that caused Atlas X Graphic to be as it is. This should tell us the new brain images from which the averaged atlas was generated, the warping performed etc.
Find the process that led to Atlas X Graphic, excluding everything prior to the averaging of images with softmean.
Find the Stage 3, 4 and 5 details of the process that led to Atlas X Graphic.
Find all invocations of procedure align_warp using a twelfth order nonlinear 1365 parameter model (see
model menu describing possible values of parameter “-m 12” of
align_warp) that ran on a Monday.
Find all Atlas Graphic images outputted from workflows where at least one of the input Anatomy Headers had an entry
global maximum=4095
. The contents of a header file can be extracted as text using the
scanheader AIR utility.
Find all output averaged images of softmean (average) procedures, where the warped images taken as input were align_warped using a twelfth order nonlinear 1365 parameter model, i.e. “where softmean was preceded in the workflow, directly or indirectly, by an align_warp procedure with argument -m 12.”
A user has run the workflow twice, in the second instance replacing each procedures (convert) in the final stage with two procedures:
pgmtoppm, then
pnmtojpeg. Find the differences between the two workflow runs. The exact level of detail in the difference that is detected by a system is up to each participant.
A user has annotated some anatomy images with a key-value pair center=UChicago
. Find the outputs of align_warp where the inputs are annotated with center=UChicago
.
A user has annotated some atlas graphics with key-value pair where the key is studyModality
. Find all the graphical atlas sets that have metadata annotation studyModality
with values speech
, visual
or audio
, and return all other annotations to these files.
Second Provenance Challenge
Third Provenance Challenge
Goal
identify weaknesses and strengths of the the OPM specification
encourage the development of concrete bindings for OPM in a variety of languages
determine how well OPM can represent provenance for a variety of technologies (scientific workflow, databases, etc.)
demonstrate that a complex data products provenance can be constructed from provenance documentation produced by multiple combinations of heterogenous applications
Challenge
Generate provenance for the challenge workflow & run queries on it
Export OPM Graphs and import from others
Run queries on imported OPM graph
Fourth Provenance Challenge