NIMS TODO

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This page contains instructions for testing the NIMS beta site and a list of things to be done for the NIMS database.

Contents

[edit] Accessing the NIMS beta test site

The NIMS beta test is running on the server blue which sits in room 473/475. It's the old Dell hooked up to the old Mac monitor. To access it, you must be on the local (wired) LAN in Jordan Hall. I.e., you can't access it from anywhere else on or off campus, or from anywhere on the SU wireless network. So, find yourself a computer connect to the Jordan Hall wired network and point your browser at port 5000 on blue. If you don't yet have an account, log in as root (password is xyzzy) and use the 'create' menu to create an account for yourself. Once you do this, log out and log back in as yourself.

  • Go to NIMS User Example for a walkthrough of how we expect to use the database when it's finalized.


[edit] NIMS aspects

[edit] Debugging Resources

  1. Data for testing upload - BW linked to his PC, putting the H: drive on his home. He then uploaded a zip file from /biac3/wandell4/data/reading_longitude/dti_adults/ak090724/scannerRaw (DTI). A functional data set is at /biac3/wandell7/data/Words/Retinotopy/amr090806/Raw.

[edit] Input Data Format Specification

As Bob succinctly put it, the database is "not just about adding a little metadata to make our scans searchable. It is about imposing an organization to our data and encouraging careful and consistent annotation so that data are useful beyond an individual's short-term experimental goals. It is about building a database of scans that can be mined by future investigators. And, more mundanely, it is about appeasing the increasingly imposing IRB and NIH requirements to keep organized, secure and complete records of all human subject data, and improving our data archiving system to avoid redundancy and be able to more easily detect (and fix) data corruption."

The quote above lists many aspects of the long term value of the imposed organization, but it is also important to keep in mind that the cost of the imposition is the time burden and mental distraction for the person at the scanner who should be primarily focused on collecting good data and would prefer the most simple, streamlined and secure data delivery system.

This section on format specification will serve as a terse, yet complete, documentation on what organization is imposed. The hope is that the captured thoughts above help to guide the low-level compromise between imposed organization and ease of use.

  • Insert Vincent's graphic on main archive organization
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