Containers for computational reproducibility

D Moreau, K Wiebels, C Boettiger - Nature Reviews Methods Primers, 2023 - nature.com
The fast-paced development of computational tools has enabled tremendous scientific
progress in recent years. However, this rapid surge of technological capability also comes at …

Issues and recommendations from the OHBM COBIDAS MEEG committee for reproducible EEG and MEG research

C Pernet, MI Garrido, A Gramfort, N Maurits… - Nature …, 2020 - nature.com
Abstract The Organization for Human Brain Mapping (OHBM) has been active in advocating
for the instantiation of best practices in neuroimaging data acquisition, analysis, reporting …

[HTML][HTML] Brian 2, an intuitive and efficient neural simulator

M Stimberg, R Brette, DFM Goodman - elife, 2019 - elifesciences.org
Brian 2 allows scientists to simply and efficiently simulate spiking neural network models.
These models can feature novel dynamical equations, their interactions with the …

[HTML][HTML] Open science challenges, benefits and tips in early career and beyond

C Allen, DMA Mehler - PLoS biology, 2019 - journals.plos.org
The movement towards open science is a consequence of seemingly pervasive failures to
replicate previous research. This transition comes with great benefits but also significant …

Why don't we share data and code? Perceived barriers and benefits to public archiving practices

DGE Gomes, P Pottier… - … of the Royal …, 2022 - royalsocietypublishing.org
The biological sciences community is increasingly recognizing the value of open,
reproducible and transparent research practices for science and society at large. Despite …

Reproducibility in neuroimaging analysis: challenges and solutions

R Botvinik-Nezer, TD Wager - Biological Psychiatry: Cognitive …, 2023 - Elsevier
Recent years have marked a renaissance in efforts to increase research reproducibility in
psychology, neuroscience, and related fields. Reproducibility is the cornerstone of a solid …

[HTML][HTML] NeuroMatic: an integrated open-source software toolkit for acquisition, analysis and simulation of electrophysiological data

JS Rothman, RA Silver - Frontiers in neuroinformatics, 2018 - frontiersin.org
Acquisition, analysis and simulation of electrophysiological properties of the nervous system
require multiple software packages. This makes it difficult to conserve experimental …

Developing image analysis methods for digital pathology

P Bankhead - The Journal of pathology, 2022 - Wiley Online Library
The potential to use quantitative image analysis and artificial intelligence is one of the
driving forces behind digital pathology. However, despite novel image analysis methods for …

Integrated analysis of anatomical and electrophysiological human intracranial data

A Stolk, S Griffin, R Van der Meij, C Dewar, I Saez… - Nature protocols, 2018 - nature.com
Human intracranial electroencephalography (iEEG) recordings provide data with much
greater spatiotemporal precision than is possible from data obtained using scalp EEG …

Knowledge‐based radiation treatment planning: a data‐driven method survey

S Momin, Y Fu, Y Lei, J Roper… - Journal of applied …, 2021 - Wiley Online Library
This paper surveys the data‐driven dose prediction methods investigated for knowledge‐
based planning (KBP) in the last decade. These methods were classified into two major …