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The Stanford Project on Scientific Transparency (PoST) designed, implemented and contributed the first draft of the scientific transparency data management software. The software works with a MongoDB database, and it comprises a collection of tools to interact with the database (scitran/core), and an AngularJS front end to manage, view, search, annotate, and generally interact with the data.
The scitran code continues to be developed and extended by Flywheel Exchange and the Stanford PoST team in the Wandell lab through a cooperative agreement. The Stanford PoST team has transitioned its main focus from developing the scitran core functions to creating application programs that run by interacting with the scitran platform. The focus of that work is to develop methods that support reproducible methods in neuroscience research.
The scitran software has also been adopted by the Stanford Center for Reproducible Research, led by Professor R. Poldrack and Dr. Chris Filo Gorgolewski. They have supported members of the Wandell lab to make adjustments to the scitran code to support the openFMRI project needs.
Flywheel offers support for installation and maintenance of these tools; such support is beyond the scope of the Wandell lab.
Neuroimaging scientsts may be particularly interested in the scitran client repository. This code coordinates with scitran by allowing users to interact with the scitran database from their own computers. Specifically, the Wandell lab at Stanford has added features to enable users to perform the following functions
- securely obtain an authorization token to read/write from a scitran database
- search the database for collections of files
- download the files for processing, including by reproducible docker containers
- put the results into the database
- store a description of the analysis into the database
These functions are being implemented in both Matlab and Python. They can be run from anywhere on the Internet. In this way, a user can process data stored in a scitran database using their local computational resources. The results and reproducible specification of the analysis can then be placed in the database.
The Wandell lab gratefully acknowledge the Simons Foundation and particularly the Simons Foundation Autism Research Initiative for their support of the [Project on Scientific Transparency] (http://post.stanford.edu).