This reads like an ad for Mathematica
You didn't read very carefully then.
Redesigning the Scientific Paper
11–20 of 110 posts
Re: Redesigning the Scientific Paper
#12We need GitHub for science. But that's not enough. It needs to be combined with a mechanism for peer-review and publishing that funding agencies will find acceptable--that's the key.
There are academics interested in building journals on top of the arXiv. It's an idea that's been kicking around for a while. In math, Tim Gowers is one of the people who has been pushing for something like this.
If your background is in not-academia, you may well be forgiven for looking at the scene and seeing no progress. However, academia is more slow-moving and conservative in some aspects than other places. This is not a bad thing; not everyone has to move fast and break things. But at academia's normal pace, things are going pretty fast.
Re: Redesigning the Scientific Paper
#13We need GitHub for science. But that's not enough. It needs to be combined with a mechanism for peer-review and publishing that funding agencies will find acceptable--that's the key.
It's not only about funding agencies, though. Researchers need to be trained in the use of a GitHub like system - as a former graduate student, I knew NO ONE using Github. Furthermore, after working in scientific publishing where it was MS Office or bust, I doubt you will convince Elsevier and the publishing giants that GitHub for Science is the way to go. How do these huge companies make money if scientists are shar…
I doubt you will convince Elsevier and the publishing giants
Who says we need to convince them? How about we leave them behind? They are rentiers, gatekeeping society's access to publicly funded scientific knowledge. I can't think of a reason why society should allow this hostage situation to continue.
Re: Redesigning the Scientific Paper
#14This reads like an ad for Mathematica
At first then it talks about Wolfram's idiosyncracies - it is quite a rambling article, though there is a long bit about IPython/Jupyter.
Re: Redesigning the Scientific Paper
#15We need GitHub for science. But that's not enough. It needs to be combined with a mechanism for peer-review and publishing that funding agencies will find acceptable--that's the key.
> We need GitHub for science
http://www.gitxiv.com/page/about
> It needs to be combined with a mechanism for peer-review and publishing...
Maybe an "interpretation" mechanism, similar to the Distill[1] project is doing, can serve two purposes at once: review and digestion.
Re: Redesigning the Scientific Paper
#16Average clickbait
Maybe look a bit closer? I slog through "average clickbait" for hours a day in the hope of sparing this community of it, and can assure you that is far from the case.
Re: Redesigning the Scientific Paper
#17> These programs tend to be both so sloppily written and so central to the results that it’s contributed to a replication crisis, or put another way, a failure of the paper to perform its most basic task: to report what you’ve actually discovered, clearly enough that someone else can discover it for themselves. This is the crux of the of the problem IMHO - at least for the fields I study (AI/ML). Replicating the resu…
>"Honestly, I'd much rather have your actual code and data that you used to get your results than read through the research paper if I had to choose (assuming the paper is not pure theory) - but instead there is a disproportionate focus on paper quality over "project quality" at least IMHO."
I think at first new students know this wrong but then get dragged into the circular logic of:
it is standard in the field -> it is ok -> it is standard in the field
Re: Redesigning the Scientific Paper
#18We need GitHub for science. But that's not enough. It needs to be combined with a mechanism for peer-review and publishing that funding agencies will find acceptable--that's the key.
Some scientists are using github as github for science, including development done in the open. For instance, this is just one particle physics project I happen to be aware of https://github.com/DisplacedHiggs
Open development is a policy for these projects and part of the grant stipulations.
Of course, data sets are more closely guarded initially until the groups that created them can publish. After that, though, CERN /LHC has done a decent job of making data publicly available from my understanding (not as someone directly involved).
I would be interested to hear more from scientists involved in projects doing open science.
Re: Redesigning the Scientific Paper
#19as a practical matter, papers will remain relevant as long as they are the metric by which grant applications and tenure decisions are made. as a philosophical matter, for computation heavy fields, i would love to see literate programming tools become de rigeur in the peer-reviewed distribution of results. In some fields (AI) this basically happens already — the blog post with code snippets and a link to arxiv at the…
Papers (and PDFs) are relevant because they are easy to organize and archive, essentially in perpetuity. Source code is too, so nothing wrong with a "Github for Science". Notebooks, blogs, or interactive dashboards, on the other hand, are an amazing tool both for research and for communication, but they are far more ephemeral than a paper. They need a large overhead to keep them running that cannot be sustained over decades or centuries. Typically, you'll have lots of trouble re-running a 5 year old notebook. That's not to say they're useless, e.g. as supplementary material (quite the opposite). They're just not going to replace papers anytime soon.
Re: Redesigning the Scientific Paper
#20We need GitHub for science. But that's not enough. It needs to be combined with a mechanism for peer-review and publishing that funding agencies will find acceptable--that's the key.
I assume you don't just means using Github for version control of scientific papers, because that sounds pretty pointless to me.
As far as tracking incremental improvements over time goes, I think it'll be hard to do better than our current method of including references to papers. It's impossible to track ideas the same way tracking code works (which itself is limited for similar reasons).
It would be nice if you could reference papers in a way that immediately allowed you to access them. And the technology to do so is there, but has limited use if papers aren't freely accessible from the internet.
But, given that the system of papers with references is essentially a DAG, I imagine someone will attempt to 'solve' the problem with blockchains before you can say 'initial coin offering'.