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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
The Peer-Review process must be open
Let’s Implement this paper….
Happy Grad Student, unaware
of her destiny
Supervisor
“You just need to implement the code
and try it…”
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
Time to face the
Truth
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
Why do we really
want to publish ?
Because we need
to have publications
in our CV
We have met the enemy…
and he is us !
“Publish or Perish”
Who invented this ?
and Why ?
“Publish or Perish”
Was invented by those who needed to evaluate
researcher’s productivity.
“Publish or Perish”
Empowers those who read
your CV to grade you by
simply counting lines in the
“Publications” section.
“Publish or Perish”
The group of best educated
people in the world has been
alienated with a simple trick
The Scientific Method
Hypothesis
OutcomeExperiment
Galileo Galilei
HypothesisRejection
Confidence
The Scientific Method
The Logic of Scientific Discovery
by Karl Popper
Image Processing Method
AlgorithmInput
Image(s)
Parameters
OutputImage(s)
Insight JournalManager
Author
SubmitsProject
DSpace
StoresProject
AutomaticTesting
Environment
PostsResults
Dashboard
SubmitsEntry
Reviewer
ReviewsProject
Process Flow
SendsCode
Submission
Code
InputData
JournalRepository
WebSite
ResultsData
Author
BuildMachines
PDF doc
• 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
DSpace
• Open Source
• Developed by MIT & HP
• Persistant URIs
• Prevents data from becoming obsolete
Insight JournalManager
DSpace
StoresProject
Insight Journal Manager
• Open Access
• Peer Review
• Searchable
Insight JournalManager
Author
ReviewerReviewerReviewerReviewer
Peer-Review is ONLY useful if it enforces reproducibility
Testing Environment
• Security Issues
• Open source tools
• Dashboard
Insight JournalManager
AutomaticTesting
Environment
Dashboard
Enjoy the Insight Journal !
Implementation Details
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
Issues
Title, comments. Creation/Paper Due/Notification/Publication
dates Tied to a DSpace collection Submission through DSpace + comments
Adding reviews
Rating Level of Affiliation Expertise Anonymous Review Title Review
Browsing reviews
No delays Users can post comments Authors can reply to comments PDF can be downloaded
Scoring
Weighted average of: Sensitivity (STAPLE algorithm) Helpfulness # submissions/max submissions # reviews/max reviews # anonymous reviews
What’s next?
Moderated submissions SVN repository for code fixing …
Safe Testing
Virtualization!
Lots of options: User-Mode-Linux, coLinux, VMWare, chroot
Xen: http://www.cl.cam.ac.uk/Research/SRG/netos/xen/
Tools used in the testing process
Xen Debian CMake Python Dashboards
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
Enjoy the Insight Journal !