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Showing posts from December, 2017

2017: Research Summary

Even though the passing of the year is more or less an arbitrary date it's a good opportunity to give a status update on various activities and projects I have been involved in this year. Here's a brief summary of 2017.
Brain Imaging Data Structure (BIDS) Since the BIDS Specification version 1.0.0 and the accompanying Nature Scientific Data paper were published last year we have been focusing on three things: stability, sustainable growth, and the software ecosystem.
Stability meant that we had to be very careful not to break backward compatibility even though many great ideas for BIDS 2.0 have been submitted. It also means that we focused on reaching out to new communities: I gave BIDS tutorials in London, Oxford, Birmingham, Glasgow and Chapel Hill this year and Dora Hermes published the BIDS Starter Kit (a super handy resource with tutorials and code snippets). 
Sustainable growth translated into adopting a system of BIDS Extension Proposals (BEPs) and providing a BIDS Cont…

To pin or not to pin dependencies: reproducible vs. reusable software

We recently had a very interesting conversation in our lab about how to describe software dependencies (libraries one needs to install) for a software project in the context of research. One camp was proposing explicitly listing which version of a dependency is required (a scheme also referred to "pinning") and the other camp was more in favor of either not specifying version at all or specifying the minimal required version. Luckily both camps agreed on the importance of specifying dependencies, but what's the big deal about pinning vs not pinning?

Advantages of pinning dependencies When you pin a dependency (for example by saying "numpy==1.1.3") you explicitly point to a version of a library that a) you know works with your script b) was used to generate the result you present in your paper. This is very useful for people trying to replicate your results using your code as well as yourself attempting to revisit a project that was put aside for a while (for e…