the insight journal
DESCRIPTION
The Insight Journal. Kitware Inc. Credits. Julien Jomier – UNC Caddlab Stephen Aylward – UNC Caddlab Zack Galbreath – Kitware Andy Cedilnik – Kitware Bill Hoffman - Kitware. The Insight Journal. Technical work must be reproducible Papers should be publicly accessible - PowerPoint PPT PresentationTRANSCRIPT
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The Insight Journal
Kitware Inc.
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Credits
Julien Jomier – UNC Caddlab
Stephen Aylward – UNC Caddlab
Zack Galbreath – Kitware
Andy Cedilnik – Kitware
Bill Hoffman - Kitware
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The Insight Journal
Technical work must be reproducible
Papers should be publicly accessible
The Peer-Review process must be open
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Let’s Implement this paper….
Happy Grad Student, unaware
of her destiny
Supervisor
“You just need to implement the code
and try it…”
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Let’s Implement this paper….
Unhappy Grad Student, aware of
her destiny
Six months later…
• Parameters are missing
• Images are not available
• Implementation details are missing
• Abundance of pretty equations
• Abundance of pretty screenshots
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Time to face the
Truth
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Publications are a measure
of scientific productivity
They disseminate knowledge
They allow others to reproduce our results
They are validated by the peer-review process
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Why do we really
want to publish ?
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Because we need
to have publications
in our CV
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We have met the enemy…
and he is us !
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“Publish or Perish”
Who invented this ?
and Why ?
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“Publish or Perish”
Was invented by those who needed to evaluate
researcher’s productivity.
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“Publish or Perish”
Empowers those who read
your CV to grade you by
simply counting lines in the
“Publications” section.
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“Publish or Perish”
The group of best educated
people in the world has been
alienated with a simple trick
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The Scientific Method
Hypothesis
OutcomeExperiment
Galileo Galilei
HypothesisRejection
Confidence
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The Scientific Method
The Logic of Scientific Discovery
by Karl Popper
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Image Processing Method
AlgorithmInput
Image(s)
Parameters
OutputImage(s)
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Insight JournalManager
Author
SubmitsProject
DSpace
StoresProject
AutomaticTesting
Environment
PostsResults
Dashboard
SubmitsEntry
Reviewer
ReviewsProject
Process Flow
SendsCode
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Submission
Code
InputData
JournalRepository
WebSite
ResultsData
Author
BuildMachines
PDF doc
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• Comparison of output images
• Publicly available
• Tests for non-trivial images
• Reviewers and readers can use it as a first view of the paper.
Results Verification
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DSpace
• Open Source
• Developed by MIT & HP
• Persistant URIs
• Prevents data from becoming obsolete
Insight JournalManager
DSpace
StoresProject
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Insight Journal Manager
• Open Access
• Peer Review
• Searchable
Insight JournalManager
Author
ReviewerReviewerReviewerReviewer
Peer-Review is ONLY useful if it enforces reproducibility
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Testing Environment
• Security Issues
• Open source tools
• Dashboard
Insight JournalManager
AutomaticTesting
Environment
Dashboard
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Enjoy the Insight Journal !
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Implementation Details
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Insight Journal Manager
http://insight-journal.org Web interface: PHP/Java/HTML Central place for submissions, reviews,
browsing/searching No delay between submissions & reviews Public reviews
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Issues
Title, comments. Creation/Paper Due/Notification/Publication
dates Tied to a DSpace collection Submission through DSpace + comments
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Adding reviews
Rating Level of Affiliation Expertise Anonymous Review Title Review
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Browsing reviews
No delays Users can post comments Authors can reply to comments PDF can be downloaded
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Scoring
Weighted average of: Sensitivity (STAPLE algorithm) Helpfulness # submissions/max submissions # reviews/max reviews # anonymous reviews
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What’s next?
Moderated submissions SVN repository for code fixing …
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Safe Testing
Virtualization!
Lots of options: User-Mode-Linux, coLinux, VMWare, chroot
Xen: http://www.cl.cam.ac.uk/Research/SRG/netos/xen/
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Tools used in the testing process
Xen Debian CMake Python Dashboards
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Testing Details
two CPUs and two partitions, so two tests can be run simultaneously
VMs can only access their own partition; no network access
Mutexes prevent filesystem corruption Submit test results to dashboard Restore pristine filesystem after every test
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Enjoy the Insight Journal !