Tag Archives: github

The price of publishing with GitHub, Figshare, G+, etc

Three years ago I posted The price of publishing with arXiv. If you look at my arXiv articles then you’ll notice that I barely posted on arXiv.org since then. Instead I went into territory which is even less recognized as serious by a big part of academia. I used:

The effects of this choice are put in front of my homepage, so go there to read them. (Besides, it is a good exercise to remember how to click on links and use them, that lost art from the age when internet was free.)

In this post I want to explain what is the price I paid for these choices and what I think now about them.

First, it is a very stressful way of living. I am not joking, as you know stress comes from realizing that there are many choices and one has to choose. Random reward from the social media is addictive. The discovery that there is a way to get out from the situation which keeps us locked into the legacy publishing system (validation). The realization that the problem is not technical but social. A much more cynical view of the undercurrents of the social life of researchers.

The feeling that I can really change the world with my research. The worries that some possible changes might be very dangerous.

The debt I owe concerning the scarcity of my explanations. The effort to show only the aspects I think are relevant, putting aside those who are not. (Btw, if you look at my About page then you’ll read “This blog contains ideas from the future”. It is true because I already pruned the 99% of the paths leading nowhere interesting.)

The desire to go much deeper, the desire to explain once again what and why, to people who seem either lacking long term attention capability or having shallow pet theories.

Is like fishing for Moby Dick.

One of the first articles with means for complete validation by reproducibility

I have not stressed enough this aspect. The article

M. Buliga, Molecular computers

is one of the first articles which comes with complete means of validation by reproducibility.

This means that along with the content of the article, which contains animations and links to demonstrations, comes a github repository with the scripts which can be used to validate (or invalidate, of course) this work.

I can’t show you here how the article looks like, but I can show you a gif created from this  video of a demonstration which appears also in the article (however, with simpler settings, in order to not punish too much the browser).


This is a chemical like computation of the Ackermann(2,2) function.

In itself, is intended to show that if autonomous computing molecules can be created by the means proposed in the article, then impressive feats can be achieved.

This is part of the discussion about peer review and the need to pass to a more evolved way of communicating science.There are several efforts in this direction, like for example PeerJ’s paper-now commented in this post. See also the post Fascinating: micropublications, hypothes.is for more!

Presently one of the most important pieces of this is the peer review, which is the social practice consisting in declarations of one, two, four, etc anonymous professionals that they have checked the work and they consider it valid.

Instead, an ideal should be the article which runs in the browser, i.e. one which comes with means which would allow anybody to validate it up to external resources, like the works by other authors.

(For example, if I write in my article that “According to the work [1]   A is true. Here we prove that B follows from A.” then I should provide means to validate the proof that A implies B, but it would be unrealistical to be ask me to provide means to validate A.)

This is explained in more detail in Reproducibility vs peer review.

Therefore, if you care about evolving the form of the scientific article, then you have a concrete, short example of what can be done in this direction.

Mind that I am stubborn enough to cling to this form of publication, not because I am afraid to submit these beautiful ideas to legacy journals, but because I want to promote new ways of sharing research by using the best content I can make.


PeerJ as a format/paper on Github: PeerJ/paper-now

A simple, interesting, obvious step: PeerJ/paper-now .  That is, or will be soon, exactly what I need for writing a decent article about chemlambda, i.e. one where I can show, in the article, demos with animations like those from the chemlambda pages.

This may be a huge step forward from the discussions about OA because:

  • offers a clear improvement of the article format, allowing it hopefully to merge with  formats like animations, databases, programs which one can execute in the browser.
  • it exports the format of the paper (this is like if latex were a publisher and decides to export the latex programs so that everybody could write a latex article)
  • which has the obvious advantage that one can host on it’s page an article in an uniform format, idea which solves two things at once: (1) how to make an article friendly for future semantic queries (2) where to put the article on the web
  • Github is already the answer and the perpetrator of a silent revolution (is already more than 10 times bigger than arXiv, and git is a model of collaboration tool which is not based on choke points  and centralized thinking), so to export the PeerJ/paper-now to Github is natural and brilliant.


See also The shortest Open Access and New Forms of Publication question


The shortest Open Access and New Forms of Publication question


then wtf is the article good for?

UPDATE: at figshare, they think about that.  Great!

UPDATE 2: for no particular reason, here is an accompanying short video done with the program

UPDATE 3:  See “Publish your computer code: it is good enough” by Nick Barnes, Nature 467, 753 (2010) | doi:10.1038/467753a

“I accept that the necessary and inevitable change I call for cannot be made by scientists alone. Governments, agencies and funding bodies have all called for transparency. To make it happen, they have to be prepared to make the necessary policy changes, and to pay for training, workshops and initiatives. But the most important change must come in the attitude of scientists. If you are still hesitant about releasing your code, then ask yourself this question: does it perform the algorithm you describe in your paper? If it does, your audience will accept it, and maybe feel happier with its own efforts to write programs. If not, well, you should fix that anyway.”


Github laudatio: negative Coase cost

This is a record of a mind changing experience I had with Github, one which will manifest in the months to come. (Well, it’s time to move on, to move further, new experiences await, I like to do this…)

Here is not more than what is in this ephemeral google+ post, but is enough to get the idea.

And it’s controversial, although obvious.

“I  just got hooked by github.io . Has everything, is a dream came true. Publishing? arXiv? pfff…. I know, everybody knows this already, let me enjoy the thought, for the moment. Then it will be some action.

Continuing with github and publishing, this is a worthy subject (although I believe that practically github already dwarfed legacy publishing, academia and arXiv). Here is an excerpt from a post from 2011
“- Publishing is central to Academia, but its publishing system is outclassed by what Open Source software developers have in GitHub

– GitHub’s success is not just about openness, but also a prestige economy that rewards valuable content producers with credit and attention

-Open Science efforts like arXiv and PLoS ONE should follow GitHub’s lead and embrace the social web”

I am aware about the many efforts about publishing via github, I only wonder if that’s not like putting a horse in front of a rocket.

On the other side, there is so much to do, now that I feel I’ve seen rock solid proof that academia, publishing and all that jazz is walking dead, with the last drops of arterial blood splatting around from the headless body. “


Negative Coase cost?