SciTran

SciTran

Original author(s)	Robert Dougherty, Gunnar Schaefer, Reno Bowen
Developer(s)	Brian Wandell, Gunnar Schaefer, others
Initial release	January 24, 2012 (2012-01-24) (1.0)
Stable release	2.1.0 (Core)  (March 23, 2018 (2018-03-23)) [±]
Written in	Python
Operating system	Cross-platform (with Vagrant)
Type	Laboratory informatics software
License(s)	MIT License
Website	scitran.github.io

SciTran (Scientific Transparency) is free open-source scientific data management system (SDMS) software. The system is built to process 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."

History

SciTran's predecessor was NIMS, the Neurobiological Image Management System. During the summer of 2009 at the Standford Vision, Imaging Sciences and Technology Activities (VISTA) laboratory, the NIMS project was conceived out of a need "to create an open-source and flexible management prototype system for neurobiological images in order to improve their sharing, storage, mining and analysis between several researchers [sic] groups," as VISTA intern Vincent Simoes put it. Simoes later elaborated on the project:

Nevertheless, the need and the possibility to improve considerably the storage, sharing, mining and analysis of the neuroimaging data still exists and significant improvements will come with the multiplication of system of data management. In this purpose, we would like to create a new data system management called: NIMS: Neurobiological Image Management System, which will be used and shared in a first step by all the laboratories of Stanford University working on the neuroscience, most of them part of the Psychology Department. As last step, the system might be extended to other laboratories. Indeed, we use an open-source approach thanks to a common language (Python) to allow an easy deployment and an easy arrangement in contradiction with current project as CNARI, which use their own language (Swift).

Development on NIMS continued for several years through the Center for Cognitive and Neurobiological Imaging (CNI), with some project direction provided by Dr. Jorge Phillips and CNI head Dr. Brian Wandell. NIMS was eventually made public as open-source code on GitHub on January 24, 2012 and implemented on Stanford's servers that same year. The primary contributors of that first iteration were Robert Dougherty, Gunnar Schaefer, and Reno Bowen. The copyright on NIMS, however, was eventually transferred from those developers to the university itself in September 2014. A few months later, the NIMS project was ceased, with a predecessor project started soon after called SciTran, with original NIMS author Gunnar Schaefer leading the engineering efforts and CNI director Brian Wandell taking on the role of project director.

Though not made entirely clear to the public, the transition from NIMS to SciTran appears to be associated with a new Wandell-led initiative called the Project on Scientific Transparency (PoST). This project had been in development at least as early as the summer of 2013, when Stanford University had posted a job posting for a Python developer, noting:

We have received foundation support for a Project on Scientific Transparency (PoST). The project will extend our existing web-based tools to improve scientific exchange. The first stage of the project is to design and implement web-based tools for sharing data and computational methods for human brain imaging. This project will develop tools to aid in the analysis of magnetic resonance imaging data collected at Stanford's Center for Cognitive and Neurobiological Imaging (CNI). Within the year, we will coordinate this effort with colleagues at several other west coast institutions.

A July 2014 report from the Simons Foundation further confirmed PoST's funding had come from the foundation and laid out future plans for the SciTran software, including the integration of validated computational tools. The first public commits to the new SciTran open-source SDMS went live on GitHub on January 20, 2015.

On September 29, 2015, Flywheel Exchange, LLC announced it would be entering into a partnership with Stanford Center for Cognitive and Neurobiological Imaging director Dr. Brian Wandell to commercialize his radiology and imaging-related scientific data management software. A week later, that software was revealed to be available as a private beta under the name "Flywheel." The software was reported to "offer scientists using functional MRI the tools to effectively capture, store, organize, and share their data." The SciTran free, open-source SDMS application appears to indeed be the base software for the commercial Flywheel SDMS.

Fate

As of February 2020, it's not clear what the ultimate fate of the SciTran project will be. Some of the components of SciTran appear to no longer be developed. The Core component shifted to Flywheel in early 2018, but in the fall of 2019, Flywheel archived the open-source Core repository and ceased working on it. It's possible the Core and Reaper components were absorbed into the still-developed "Flywheel Exchange," but what actually is going on with development remains somewhat confusing. The SciTran page does state: "While SciTran is a set of core open-source components, released under the MIT license, and hosted on GitHub, it is not a complete system. Flywheel has built a comprehensive data management and processing solution..." This lends credence to the idea that the SciTran open-source components have been fully absorbed into Flywheel Exchange and are no longer maintained as separate components.

Features

The features for SciTran include:

• automatic formatting of raw data
• data warehouse
• standardized data file naming
• data import
• user- and group-based access
• advanced query
• data validation and QA
• browser-based interface

Hardware/software requirements

Setup requires Python 2.7 and Git. The software is meant to run off of Linux. If you're not using Linux, you'll need to use Vagrant. Consult the GitHub readme for more information.

Videos, screenshots, and other media

• SciTran documentation

Entities using SciTran

Stanford Center for Cognitive and Neurobiological Imaging

Further reading

• Bowen, Reno (26 August 2012). "NIMS Demo". Vimeo. https://vimeo.com/48271733. 

• Simoes, Vincent (31 August 2009). "NIMS: Neurobiological Image Management System - Improving the storage, sharing, mining and analysis of neuroimaging data using specific data management system" (PDF). Institut Sup´erieur de l’Electronique et du Num´erique. http://nrannou09.googlecode.com/svn/trunk/Latex/report.pdf. 

• Simons Foundation (15 July 2014). "Project on Scientific Transparency". Simons Foundation. https://www.simonsfoundation.org/wp-content/uploads/reports/2014/stories/project-on-scientific-transparency.html. 

• Wandell, B. A.; Rokem, A.; Perry, L. M.; Schaefer, G.; Dougherty, R. F. (2015). "Data management to support reproducible research" (PDF). Stanford University. http://arxiv.org/ftp/arxiv/papers/1502/1502.06900.pdf. 

External links

• Project on Scientific Transparency
• SciTran core, as Flywheel, at Github
• SciTran at Github
• NIMS at GitHub (legacy version of SciTran)
• NIMS at VISTA Lab Wiki