Open-source software for studying neural codes

TL;DR

This paper reviews open-source software tools for analyzing neural data, emphasizing their benefits for the scientific community and providing a directory of relevant packages.

Contribution

It introduces the concept of open-source software in neural coding research and compiles a directory of freely available tools for the community.

Findings

Open-source tools are valuable for neural data analysis.

Many open-source packages are available for studying neural codes.

Open-source software promotes transparency and collaboration.

Abstract

In this chapter we first outline some of the popular computing environments used for analysing neural data, followed by a brief discussion of 'software carpentry', basic tools and skills from software engineering that can be of great use to computational scientists. We then introduce the concept of open-source software and explain some of its potential benefits for the academic community before giving a brief directory of some freely available open source software packages that address various aspects of the study of neural codes. While there are many commercial offerings that provide similar functionality, we concentrate here on open source packages, which in addition to being available free of charge, also have the source code available for study and modification.