vibbits / gentle-hands-on-python

Course materials for the 'Gentle hands-on introduction to Python programming'.
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Emphasise publishing code (being a good scientific citizen) #93

Open MaybeJustJames opened 2 years ago

MaybeJustJames commented 2 years ago

Ref: https://twitter.com/sTeamTraen/status/1503864395935408128?s=20&t=K5VcFYKXVTL5U6T2h-FAMw https://dx.doi.org/10.1073/pnas.1708290115

When you ask the authors of articles in Science® to share their data, which the journal told you was mandatory when you submitted your article, the response very often boils down to GFY.

There appeared to be some confusion among authors, some of whom seemed unaware of Science's data and code sharing requirement. We can most easily demonstrate this with some anonymised author responses that highlight some of the barriers to sharing they perceived:

When you approach a PI for the source codes and raw data, you better explain who you are, whom you work for, why you need the data and what you are going to do with it.

I have to say that this is a very unusual request without any explanation! Please ask your supervisor to send me an email with a detailed, and I mean detailed, explanation.

The data files remains our property and are not deposited for free access. Please, let me know the purpose you want to get the file and we will see how we can help you.

We do not typically share our internal data or code with people outside our collaboration.

The code we wrote is the accumulated product of years of effort by [redacted] and myself. Also, the data we processed was collected painstakingly over a long period by collaborators, and so we will need to ask permission from them too.

Normally we do not provide this kind of information to people we do not know. It might be that you want to check the data analysis, and that might be of some use to us, but only if you publish your findings while properly referring to us.

Thank you for your interest in our paper. For the [redacted] calculations I used my own code, and there is not public version of this code, which could be downloaded. Since this code is not very user-friendly and is under constant development I prefer not to share this code.

I'm sorry, but our computer code was not written with an eye toward distributing for other people to use. The codes are not documented and we don't have the time or resources to document them. If you have a particular calculation you would like done and it is not a major extension of what we are presently set up to do, we might be able to run the codes for you.

R is a free software package available at www.r-project.org/ I used R for the [redacted] models. As you probably know, [redacted and [redacted] are quite complicated. But I don't have to tell you that given that you are a statistics student! I used Matlab for the geometry.