Open is Not Enough. Let's Take the Next Step: An Integrated, Community-Driven Computing Platform for Neuroscience

By Yaroslav O. Halchenko, Michael Hanke. 2012

115 citations recorded by the source corpus.

). However, collecting these resources into a centralized clearing-house addresses only one necessary aspect on the way to a sustainable software ecosystem for neuroscience – availability. Unfortunately it does not ensure ease of deployment, nor does it offer a sustainable model for long-term maintenance.At the same time, the development model of many neuroscience research software projects is broken. Inefficient and opaque procedures combined with a scarce developer workforce result in tools of insuf-ficient quality and robustness that we rely on to conduct our research. Moreover, as the scientists, students, and research groups responsible for these tools move on to new tasks, their software is often left in a state of limbo, with no continued support for bug fixes or sufficiently coordinated main-tenance. Over time, changes in underlying computing environments break the tools completely, and they commonly become abandoned – with costly consequences for the scientists depending upon them.To address this problem, we need to bring our tools further into the open, and consolidate development efforts on an open and community-driven platform – one that is capable of providing easy access, instal-lation, and maintenance for any research software. Such effort will not only help to improve aspects of software engineering, but also meet many unfulfilled require-ments toward the goal of practical

Subfields: Artificial Intelligence, Cognitive Neuroscience, Information Systems and Management

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Artificial Intelligence

1. Christoph Schmidt-Hieber
2. Anders Eklund
3. Satrajit S. Ghosh
4. Russell A. Poldrack
5. Rowan J. Smith
6. Alois Schlögl
7. Mark Jenkinson
8. Guillaume Flandin

In Cognitive Neuroscience

1. Gaël Varoquaux
2. Russell A. Poldrack
3. Tal Yarkoni
4. Anders Eklund
5. Krzysztof J. Gorgolewski
6. Segundo Jose Guzman
7. Alois Schlögl
8. Fidel Alfaro-Almagro

In Information Systems and Management

1. Christoph Schmidt-Hieber
2. Satrajit S. Ghosh
3. Alois Schlögl
4. Segundo Jose Guzman

Citations in the corpus

• Distributed under Creative Commons Cc-by 4.0 Scikit-image: Image Processing in Python (unknown): “2 The package can be installed on all major platforms (e.g., BSD, https://store.continuum.io/cshop/ anaconda 5 https://www.enthought.com/products/ canopy Python(x,y), 6 NeuroDebian (Halchenko & Hanke, 2012) and GNU/Linux distributions 6 https://code.google.com/p/pythonxy such as Ubuntu.”
• BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods (2016, background): “The most notable is the NeuroDebian project [2], which provides Debian and Ubuntu Linux distributions with packages containing many of the popular neuroimaging software tools.”
• Stimfit: quantifying electrophysiological data with Python (2013, methodology): “…(gcc/g ++ ) for GNU/Linux, Mac OS X, the MinGW-cross-compiler environment (MXE, Grabsch, 2013), as well as with Microsoft Visual C ++ 2008 (MSVC2008) (Halchenko and Hanke, 2012), for OS X through the MacPorts repository (https://www . macports . org), and for Windows as a binary installer.”