SciTran

From LIMSWiki
Jump to navigationJump to search
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)[1]
Stable release

2.1.0 (Core)  (March 23, 2018; 4 years ago (2018-03-23))

[±]
Written in Python
Operating system Cross-platform (with Vagrant)
Type Laboratory informatics software
License(s) MIT License
Website scitran.github.io
github.com/scitran

SciTran (Scientific Transparency) is free open-source application programming interface (formerly described as a scientific data management system [SDMS][2]) that "delivers efficient and robust organization, archiving, and sharing of scientific data.[3] The system was originally built to process neuroimaging data, with a goal to be "a system that is flexible enough to accommodate all types of scientific data – from paper-and-pencil tests to genomics data."[2] The API has since been utilized in commercial endeavors such as those by Flywheel Exchange, LLC.

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,"[4] as VISTA intern Vincent Simoes put it. Simoes later elaborated on the project[4]:

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.[5][4] NIMS was eventually made public as open-source code on GitHub on January 24, 2012[1] and implemented on Stanford's servers that same year. The primary contributors of that first iteration were Robert Dougherty, Gunnar Schaefer, and Reno Bowen.[6] The copyright on NIMS, however, was eventually transferred from those developers to the university itself in September 2014.[7] A few months later, the NIMS project was ceased[8], 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.[9]

Though not made entirely clear to the public, the transition from NIMS to SciTran appears to have been associated with a new Wandell-led initiative called the Project on Scientific Transparency (PoST).[10][11] 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[12]:

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.[10] The first public commits to the new SciTran open-source SDMS went live on GitHub on January 20, 2015.[13]

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.[14] 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."[15]

Fate

According to the SciTran GitHub page, a number of key takeaways are made clear[3]:

  • In its current iteration, SciTran is a open-source application programming interface (API), and the commercial organization FlyWheel is developing and maintaining it (though it hasn't been updated on GitHub since March 2018[16]).
  • SciTran "is not a complete system" but rather "a set of core open-source components."
  • Flywheel has taken those components and built a commercial data management platform with them.
  • VISTA continues to use the SciTran API to develop its own scientific applications for neuroscience.

Features

The SciTran API includes three components[3]:

  • Core, containing a RESTful HTTP API, written in Python and backed by MongoDB
  • Reaper, containing instrument integration tools, with a focus on DICOM
  • Apps, containing an number of applications for image conversion, metadata extraction, etc.

Hardware/software requirements

Setup requires Python 2.x and Git. The software is meant to run off of Linux. If you're not using Linux, you'll need to use Vagrant.

Videos, screenshots, and other media

Documentation for the Core API can be found on GitHub at https://scitran.github.io/core/branches/<branchname> and https://scitran.github.io/core/tags/<tagname>.

Entities using SciTran

Stanford Center for Cognitive and Neurobiological Imaging; Standford Vision, Imaging Sciences and Technology Activities Lab

Further reading

External links

References

  1. 1.0 1.1 "NIMS - Initial Commit". GitHub. 24 January 2012. https://github.com/cni/nims/commit/082d64c6a4ef0304f0c7cbe4cd41cc4e07c65665. Retrieved 04 November 2015. 
  2. 2.0 2.1 "Scientific Transparency". Stanford University. Archived from the original on 13 February 2016. https://web.archive.org/web/20160213115752/https://scitran.github.io/. Retrieved 30 July 2022. 
  3. 3.0 3.1 3.2 "Scientific Transparency". Stanford University. https://scitran.github.io/. Retrieved 30 July 2022. 
  4. 4.0 4.1 4.2 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. Archived from the original on 04 November 2015. https://web.archive.org/web/20151104202814/http://nrannou09.googlecode.com/svn/trunk/Latex/report.pdf. Retrieved 30 July 2022. 
  5. Phillips, Jorge (30 September 2010). "NIMS Contract". VISTA Lab Wiki. Stanford University. http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/NIMS_Contract. Retrieved 30 July 2022. 
  6. "About NIMS". Stanford University. https://cni.stanford.edu/nims/about. Retrieved 30 July 2022. 
  7. "NIMS - Prep for deployment". GitHub. 3 September 2014. https://github.com/cni/nims/commit/3f0abdc823df6d3dcbdf30daa52ef66fce8b4dbb. Retrieved 30 July 2022. 
  8. "NIMS - Add pointer to @scitran". GitHub. 21 November 2014. https://github.com/cni/nims/commit/eae03cc8762352b030257a04a06905f5028a0c54. Retrieved 30 July 2022. 
  9. "The CNI Team". Center for Cognitive and Neurobiological Imaging. Stanford University. Archived from the original on 19 March 2016. https://web.archive.org/web/20160319211108/http://cni.stanford.edu/cni-team/. Retrieved 30 July 2022. 
  10. 10.0 10.1 "Project on Scientific Transparency". Simons Foundation. 15 July 2014. Archived from the original on 19 September 2015. https://web.archive.org/web/20150919124305/https://www.simonsfoundation.org/wp-content/uploads/reports/2014/stories/project-on-scientific-transparency.html. Retrieved 30 July 2022. 
  11. "Project on Scientific Transparency". Stanford University. Archived from the original on 27 October 2015. https://web.archive.org/web/20151027083539/https://post.stanford.edu/. Retrieved 30 July 2022. 
  12. Stanford University (18 July 2013). "Python Developer". HigherEd Jobs. Internet Employment Linkage, Inc. Archived from the original on 04 November 2015. https://web.archive.org/web/20151104223014/https://www.higheredjobs.com/details.cfm?JobCode=175777356. Retrieved 04 November 2015. 
  13. "SciTran - Initial Commit". GitHub. 20 January 2015. https://github.com/scitran/scitran/commit/ee9f3c0d8e06c19c087d93a73e9e792d87fa639d. Retrieved 04 November 2015.  Template:Dead url
  14. "Flywheel Partners with Dr. Brian Wandell". PR Newswire. PR Newswire Association, LLC. 29 September 2015. https://www.prnewswire.com/news-releases/flywheel-partners-with-dr-brian-wandell-300150255.html. Retrieved 30 July 2022. 
  15. "Flywheel Launches Private Beta Phase of its Data Management Platform". PR Newswire. PR Newswire Association, LLC. 7 October 2015. https://www.prnewswire.com/news-releases/flywheel-launches-private-beta-phase-of-its-data-management-platform-300155073.html. Retrieved 30 July 2022. 
  16. Stanford University (30 March 2018). "scitran/core". GitHub. https://github.com/scitran/core. Retrieved 30 July 2022.