SciTran - Revision history

Shawndouglas: Updated due to website changes

2022-07-30T20:18:32Z

Updated due to website changes

Shawndouglas: /* History */ Added more

2020-02-05T18:38:31Z

History: Added more

← Older revision		Revision as of 18:38, 5 February 2020
Line 38:		Line 38:

	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.<ref name="PRFETeamUp">{{cite web \|url=http://www.prnewswire.com/news-releases/flywheel-partners-with-dr-brian-wandell-300150255.html \|title=Flywheel Partners with Dr. Brian Wandell \|work=PR Newswire \|publisher=PR Newswire Association, LLC \|date=29 September 2015 \|accessdate=03 November 2015}}</ref> 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."<ref name="PRFEFly">{{cite web \|url=http://www.prnewswire.com/news-releases/flywheel-launches-private-beta-phase-of-its-data-management-platform-300155073.html \|title=Flywheel Launches Private Beta Phase of its Data Management Platform \|work=PR Newswire \|publisher=PR Newswire Association, LLC \|date=07 October 2015 \|accessdate=03 November 2015}}</ref> The SciTran free, open-source SDMS application appears to indeed be the base software for the commercial Flywheel SDMS.<ref name="STGit">{{cite web \|url=https://github.com/scitran/scitran \|title=SciTran – Scientific Data Management \|publisher=GitHub \|accessdate=04 November 2015}}</ref><ref name="STHome" />		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.<ref name="PRFETeamUp">{{cite web \|url=http://www.prnewswire.com/news-releases/flywheel-partners-with-dr-brian-wandell-300150255.html \|title=Flywheel Partners with Dr. Brian Wandell \|work=PR Newswire \|publisher=PR Newswire Association, LLC \|date=29 September 2015 \|accessdate=03 November 2015}}</ref> 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."<ref name="PRFEFly">{{cite web \|url=http://www.prnewswire.com/news-releases/flywheel-launches-private-beta-phase-of-its-data-management-platform-300155073.html \|title=Flywheel Launches Private Beta Phase of its Data Management Platform \|work=PR Newswire \|publisher=PR Newswire Association, LLC \|date=07 October 2015 \|accessdate=03 November 2015}}</ref> The SciTran free, open-source SDMS application appears to indeed be the base software for the commercial Flywheel SDMS.<ref name="STGit">{{cite web \|url=https://github.com/scitran/scitran \|title=SciTran – Scientific Data Management \|publisher=GitHub \|accessdate=04 November 2015}}</ref><ref name="STHome" />

			===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..."<ref name="SciTranGH">{{cite web \|url=https://scitran.github.io/ \|title=Scientific Transparency \|work=Github \|accessdate=05 February 2020}}</ref> 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==		==Features==

Shawndouglas: Link

2020-02-05T18:20:45Z

Link

← Older revision		Revision as of 18:20, 5 February 2020
Line 77:		Line 77:

	* [https://post.stanford.edu/ Project on Scientific Transparency]		* [https://post.stanford.edu/ Project on Scientific Transparency]
			* [https://github.com/flywheel-io/core SciTran core, as Flywheel, at Github]
	* [https://github.com/scitran/scitran SciTran at Github]		* [https://github.com/scitran/scitran SciTran at Github]
	* [https://github.com/cni/nims NIMS at GitHub] (legacy version of SciTran)		* [https://github.com/cni/nims NIMS at GitHub] (legacy version of SciTran)

Shawndouglas: /* History */ Comma

2015-11-04T23:05:15Z

History: Comma

← Older revision		Revision as of 23:05, 4 November 2015
Line 25:		Line 25:

	==History==		==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,"<ref name="SimoesNIMS">{{cite web \|url=http://nrannou09.googlecode.com/svn/trunk/Latex/report.pdf \|format=PDF \|title=NIMS: Neurobiological Image Management System - Improving the storage, sharing, mining and analysis of neuroimaging data using specific data management system \|author=Simoes, Vincent \|publisher=Institut Sup´erieur de l’Electronique et du Num´erique \|date=31 August 2009 \|accessdate=04 November 2015}}</ref> as VISTA intern Vincent Simoes put it. Simoes later elaborated on the project<ref name="SimoesNIMS" />:		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,"<ref name="SimoesNIMS">{{cite web \|url=http://nrannou09.googlecode.com/svn/trunk/Latex/report.pdf \|format=PDF \|title=NIMS: Neurobiological Image Management System - Improving the storage, sharing, mining and analysis of neuroimaging data using specific data management system \|author=Simoes, Vincent \|publisher=Institut Sup´erieur de l’Electronique et du Num´erique \|date=31 August 2009 \|accessdate=04 November 2015}}</ref> as VISTA intern Vincent Simoes put it. Simoes later elaborated on the project<ref name="SimoesNIMS" />:

	<blockquote>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).</blockquote>		<blockquote>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).</blockquote>

Shawndouglas: Created as needed.

2015-11-04T23:04:41Z

Created as needed.

New page

{{Infobox software
| name = SciTran
| title = '''SciTran'''
| logo =
| screenshot = 
| caption =
| collapsible =
| author = Robert Dougherty, Gunnar Schaefer, Reno Bowen
| developer = Brian Wandell, Gunnar Schaefer, others
| released = {{Start date|2012|01|24}} (1.0)<ref name="NIMSStartGit">{{cite web |url=https://github.com/cni/nims/commit/082d64c6a4ef0304f0c7cbe4cd41cc4e07c65665 |title=NIMS - Initial Commit |publisher=GitHub |date=24 January 2012 |accessdate=04 November 2015}}</ref>
| discontinued =
| frequently updated = yes
| programming language = Python
| operating system = Cross-platform (with Vagrant)
| platform =
| size =
| language =
| status =
| genre = [[Laboratory informatics]] software
| license = MIT License
| website = [https://scitran.github.io/ 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."<ref name="STHome">{{cite web |url=https://scitran.github.io/ |title=Scientific Transparency |publisher=Stanford University |accessdate=04 November 2015}}</ref>

==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,"<ref name="SimoesNIMS">{{cite web |url=http://nrannou09.googlecode.com/svn/trunk/Latex/report.pdf |format=PDF |title=NIMS: Neurobiological Image Management System - Improving the storage, sharing, mining and analysis of neuroimaging data using specific data management system |author=Simoes, Vincent |publisher=Institut Sup´erieur de l’Electronique et du Num´erique |date=31 August 2009 |accessdate=04 November 2015}}</ref> as VISTA intern Vincent Simoes put it. Simoes later elaborated on the project<ref name="SimoesNIMS" />:

<blockquote>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).</blockquote>

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.<ref name="NIMSContract">{{cite web |url=http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/NIMS_Contract |title=NIMS Contract |author=Phillips, Jorge |work=VISTA Lab Wiki |publisher=Stanford University |date=30 September 2010 |accessdate=04 November 2015}}</ref><ref name="SimoesNIMS" /> NIMS was eventually made public as open-source code on GitHub on January 24, 2012<ref name="NIMSStartGit" /> and implemented on Stanford's servers that same year. The primary contributors of that first iteration were Robert Dougherty, Gunnar Schaefer, and Reno Bowen.<ref name="NIMSAboutStan">{{cite web |url=https://cni.stanford.edu/nims/about |title=About NIMS |publisher=Stanford University |accessdate=04 November 2015}}</ref> The copyright on NIMS, however, was eventually transferred from those developers to the university itself in September 2014.<ref name="NIMSCopyGit">{{cite web |url=https://github.com/cni/nims/commit/3f0abdc823df6d3dcbdf30daa52ef66fce8b4dbb |title=NIMS - Prep for deployment |publisher=GitHub |date=03 September 2014 |accessdate=04 November 2015}}</ref> A few months later, the NIMS project was ceased<ref name="NIMSCeaseGit">{{cite web |url=https://github.com/cni/nims/commit/eae03cc8762352b030257a04a06905f5028a0c54 |title=NIMS - Add pointer to @scitran |publisher=GitHub |date=21 November 2014 |accessdate=04 November 2015}}</ref>, 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.<ref name="CNITeam">{{cite web |url=http://cni.stanford.edu/cni-team/ |title=The CNI Team |work=Center for Cognitive and Neurobiological Imaging |publisher=Stanford University |accessdate=04 November 2015}}</ref>

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).<ref name="SFPoST">{{cite web |url=https://www.simonsfoundation.org/wp-content/uploads/reports/2014/stories/project-on-scientific-transparency.html |title=Project on Scientific Transparency |publisher=Simons Foundation |date=15 July 2014 |accessdate=04 November 2015}}</ref><ref name="PoSTHome">{{cite web |url=https://post.stanford.edu/ |title=Project on Scientific Transparency |publisher=Stanford University |accessdate=04 November 2015}}</ref> 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<ref name="StanPostArch">{{cite web |url=https://www.higheredjobs.com/details.cfm?JobCode=175777356 |archiveurl=https://web.archive.org/web/20151104223014/https://www.higheredjobs.com/details.cfm?JobCode=175777356 |title=Python Developer |author=Stanford University |work=HigherEd Jobs |publisher=Internet Employment Linkage, Inc |date=18 July 2013 |accessdate=04 November 2015 |archivedate=04 November 2015}}</ref>:

<blockquote>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.</blockquote>

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.<ref name="SFPoST" /> The first public commits to the new SciTran open-source SDMS went live on GitHub on January 20, 2015.<ref name="STStartGit">{{cite web |url=https://github.com/scitran/scitran/commit/ee9f3c0d8e06c19c087d93a73e9e792d87fa639d |title=SciTran - Initial Commit |publisher=GitHub |date=20 January 2015 |accessdate=04 November 2015}}</ref>

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.<ref name="PRFETeamUp">{{cite web |url=http://www.prnewswire.com/news-releases/flywheel-partners-with-dr-brian-wandell-300150255.html |title=Flywheel Partners with Dr. Brian Wandell |work=PR Newswire |publisher=PR Newswire Association, LLC |date=29 September 2015 |accessdate=03 November 2015}}</ref> 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."<ref name="PRFEFly">{{cite web |url=http://www.prnewswire.com/news-releases/flywheel-launches-private-beta-phase-of-its-data-management-platform-300155073.html |title=Flywheel Launches Private Beta Phase of its Data Management Platform |work=PR Newswire |publisher=PR Newswire Association, LLC |date=07 October 2015 |accessdate=03 November 2015}}</ref> The SciTran free, open-source SDMS application appears to indeed be the base software for the commercial Flywheel SDMS.<ref name="STGit">{{cite web |url=https://github.com/scitran/scitran |title=SciTran – Scientific Data Management |publisher=GitHub |accessdate=04 November 2015}}</ref><ref name="STHome" />

==Features==

The features for SciTran include<ref name="STHome" />:

* 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 [https://github.com/scitran/scitran/blob/master/README.md the GitHub readme] for more information.

==Videos, screenshots, and other media==

* [http://scitran.github.io/docs/ SciTran documentation]

==Entities using SciTran==

Stanford Center for Cognitive and Neurobiological Imaging

==Further reading==

* {{cite web |url=https://vimeo.com/48271733 |title=NIMS Demo |author=Bowen, Reno |publisher=Vimeo |date=26 August 2012}}

* {{cite web |url=http://nrannou09.googlecode.com/svn/trunk/Latex/report.pdf |format=PDF |title=NIMS: Neurobiological Image Management System - Improving the storage, sharing, mining and analysis of neuroimaging data using specific data management system |author=Simoes, Vincent |publisher=Institut Sup´erieur de l’Electronique et du Num´erique |date=31 August 2009}}

* {{cite web |url=https://www.simonsfoundation.org/wp-content/uploads/reports/2014/stories/project-on-scientific-transparency.html |title=Project on Scientific Transparency |author=Simons Foundation |publisher=Simons Foundation |date=15 July 2014}}

* {{cite web |url=http://arxiv.org/ftp/arxiv/papers/1502/1502.06900.pdf |format=PDF |title=Data management to support reproducible research |author=Wandell, B. A.; Rokem, A.; Perry, L. M.; Schaefer, G.; Dougherty, R. F. |publisher=Stanford University |date=2015}}

==External links==

* [https://post.stanford.edu/ Project on Scientific Transparency]
* [https://github.com/scitran/scitran SciTran at Github]
* [https://github.com/cni/nims NIMS at GitHub] (legacy version of SciTran)
* [http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/NIMS NIMS at VISTA Lab Wiki]

==References==
<references />


[[Category:Laboratory informatics software (open source)]]
[[Category:Scientific data management systems (open source)]]