Scientific Transparency

Saving Science – Starting with Neuroscience

Scientific Transparency (SciTran) is a software project that has grown out of the Project on Scientific Transparency at Stanford University. At the heart of SciTran is a scientific data management system – SDM – designed to enable and foster reproducible research.

SciTran SDM delivers efficient and robust archiving, organization, and sharing of scientific data. We have developed the system around neuroimaging data, but our goal is to build a system that is flexible enough to accommodate all types of scientific data – from paper-and-pencil tests to genomics data. SDM will also allow for the sharing of data and computations between remote sites.

SciTran is open-source software, released under the MIT license. Our code is hosted on GitHub. Feel free to try it out or to contribute.

Commercial support for SciTran SDM is available through our partners at .

features

Features

The focus of SciTran is the development of a scientific data management system – SDM. Below we describe some of the features of SDM that make it different from many other data management solutions available.

Data Integrity   Raw data from the MRI scanner are automatically formatted and stored in SDM - no user action is needed. This ensures data integrity and eliminates the possibility of data loss.
Archiving   Centralized data backup is greatly simplified because all the data are in a single location rather than distributed amongst many sites. Individual labs need not arrange separate backup protocols. This supports data integrity.
Retrieval   At the end of a measurement session, users download their data from a web-page. To find your lab’s data, simply log in to the SDM database and you will see all data that is open to your lab.
Organization   Files and experiments are stored using a standard naming convention that helps lab members keep track of their experiments.
Uploading   Data can be added to SDM by using a simple web-interface or by placing files in an identified directory. In this way older datasets or datasets collected at another institution can be brought into SDM.
Sharing and Rights Management   By default, only the PI's group has access to the data. Using a simple web-interface, however, the PI can grant access to other individuals or groups. Access can be granted to entire projects or to individual datasets. The PI has the option to make the data publicly available.
Search and Discovery   The SDM database can be searched in many ways, such as by investigator, subject type, data type, and so forth. When potentially useful data are discovered from another lab, it is simple to request the PI for access.
Quality Assurance   Data entered into SDM are routinely analyzed to identify instrument and data quality. These are run in the background, without user intervention. The results are summarized both for the MRI Center staff and for the users.
Transparency   SciTran is open-source software, released under the MIT license. Our code is hosted on GitHub. You can also access our technical documentation on our GitHub Site.
technology

Technology

team

Team

Brian Wandell
Project Lead
Gunnar Schaefer
Software Engineering Lead
Michael Perry
Project Manager
Renzo Frigato
Software Engineer
Ariel Rokem
Data Scientist
Robert Dougherty
Scientific Advisor
funding

Funding Sources