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We present the Canadian Open Neuroscience Platform (CONP) portal to answer the research community's need for flexible data sharing resources and provide advanced tools for search and processing infrastructure capacity. This portal differs from previous data sharing projects as it integrates datasets originating from a number of already existing platforms or databases through DataLad, a file level data integrity and access layer. The portal is also an entry point for searching and accessing a large number of standardized and containerized software and links to a computing infrastructure. It leverages community standards to help document and facilitate reuse of both datasets and tools, and already shows a growing community adoption giving access to more than 60 neuroscience datasets and over 70 tools. The CONP portal demonstrates the feasibility and offers a model of a distributed data and tool management system across 17 institutions throughout Canada., (© 2023. The Author(s).)

Neuroimaging stands to benefit from emerging ultrahigh-resolution 3D histological atlases of the human brain; the first of which is 'BigBrain'. Here, we review recent methodological advances for the integration of BigBrain with multi-modal neuroimaging and introduce a toolbox, 'BigBrainWarp', that combines these developments. The aim of BigBrainWarp is to simplify workflows and support the adoption of best practices. This is accomplished with a simple wrapper function that allows users to easily map data between BigBrain and standard MRI spaces. The function automatically pulls specialised transformation procedures, based on ongoing research from a wide collaborative network of researchers. Additionally, the toolbox improves accessibility of histological information through dissemination of ready-to-use cytoarchitectural features. Finally, we demonstrate the utility of BigBrainWarp with three tutorials and discuss the potential of the toolbox to support multi-scale investigations of brain organisation., Competing Interests: CP, JR, LL, CL, TG, KW, JD, SV, LC, AK, KA, AE, TD, BB none, PT None, (© 2021, Paquola et al.)

Background: Software containers greatly facilitate the deployment and reproducibility of scientific data analyses in various platforms. However, container images often contain outdated or unnecessary software packages, which increases the number of security vulnerabilities in the images, widens the attack surface in the container host, and creates substantial security risks for computing infrastructures at large. This article presents a vulnerability analysis of container images for scientific data analysis. We compare results obtained with 4 vulnerability scanners, focusing on the use case of neuroscience data analysis, and quantifying the effect of image update and minification on the number of vulnerabilities., Results: We find that container images used for neuroscience data analysis contain hundreds of vulnerabilities, that software updates remove roughly two-thirds of these vulnerabilities, and that removing unused packages is also effective., Conclusions: We provide recommendations on how to build container images with fewer vulnerabilities., (© The Author(s) 2021. Published by Oxford University Press GigaScience.)

We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science.

This paper presents the Virtual Imaging Platform (VIP), a platform accessible at http://vip.creatis.insa-lyon.fr to facilitate the sharing of object models and medical image simulators, and to provide access to distributed computing and storage resources. A complete overview is presented, describing the ontologies designed to share models in a common repository, the workflow template used to integrate simulators, and the tools and strategies used to exploit computing and storage resources. Simulation results obtained in four image modalities and with different models show that VIP is versatile and robust enough to support large simulations. The platform currently has 200 registered users who consumed 33 years of CPU time in 2011.

Grids offer powerful infrastructures and promising concepts for the development and deployment of advanced applications in medical research and healthcare. The construction of HealthGrids in practice, however, is challenging due to reasons of scientific, technical, and cultural nature, among them the large gap between communities that develop and use the technology. Whereas grid developments focus mostly on functionality, usability issues are also very important to enable the potential of grids to be fully exploited by those who could mostly benefit from it, the end-users. In this paper we make a retrospective of our efforts to develop the Virtual Lab for functional Magnetic Resonance Imaging (fMRI). This project aims at providing for the end-users a grid-based system to facilitate research and clinical usage of fMRI data for study of brain activation. We present the evolution of this project in three phases coined "low hanging fruit", "trying out" and "end-user ready", and the lessons learnt in each one. The evolution of the software architecture, which had a large impact on the user front-end, is discussed in more detail. The current architecture facilitates the construction of front-ends that enable users to access the grid infrastructure from a single user-friendly GUI. All (local and grid) resources are accessed directly by the users from a virtual desktop implemented by the Virtual Resource Browser (VBrowser).