Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Title: Nipype interfaces in CBRAIN      
dateReleased:
10-24-2016
privacy:
not applicable
aggregation:
instance of dataset
dateCreated:
10-19-2016
refinement:
curated
ID:
doi:10.5524/100226
creators:
Glatard, Tristan
Das, Samir
Adalat, Reza
Beck, Natacha
Bernard, Remi
,
Rioux, Pierre
Evans, Alan C
availability:
available
types:
sequence
description:
We aim at the large-scale, automatic sharing of software tools between neuroimaging processing platforms, which will increase the relevance of such platforms by providing them with richer repositories of higher-quality tools. Currently, efforts are hampered by the repetitive porting of the same few tools in different platforms. During the HBM 2015 Hackathon, we worked on the export of software tools from the Nipype workflow engine to the CBRAIN web platform for distributed computing. Nipype includes a large number of tools that would be useful to CBRAIN users.We developed nipype2boutiques a tool to export Nipype interfaces to the “Boutiques” tool description format. Boutiques descriptions are importable by CBRAIN and other platforms (Virtual Imaging Platform and the Pegasus workflow engine). They point to a Docker image containing the implementation of the tool. nipype2boutiques relies on nipype_cmd a tool to run Nipype Interfaces as Linux command lines. nipype2boutiques parses the inputs and outputs of a Nipype interface and extracts their name, type, description and position on the nipype_cmd command line. nipype2boutiques then generates a Boutiques descriptor pointing to a Docker image where the Nipype interface is available. Once a Nipype interface is exported using nipye2boutiques it can be imported to CBRAIN.We prototyped a software tool to export Nipype Interfaces as Boutiques descriptors, which can be imported by CBRAIN and other platforms. Although the solution is still limited to simple interfaces, we believe that it has the potential to enable fully automatic tool sharing between Nipype and CBRAIN. Future extensions of nipype2boutiques will be published in the Nipype Github repository.
accessURL: https://doi.org/10.5524/100226
storedIn:
GigaScience Database
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
GigaDB
homePage: http://gigadb.org/
ID:
SCR:006565
name:
Giga Science Database

Feedback?

If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.