Github for science? Shouldn’t we perhaps build TCP/IP first?

It’s one of those throw away lines, “Before we can talk about a github for science we really need to sort out a TCP/IP for science”, that’s geeky, sharp, a bit needly and goes down a treat on Twitter. But there is a serious point behind it. And its not intended to be dismissive of the ideas that are swirling around about scholarly communication at the moment either. So it seems worth exploring in a bit more detail.

The line is stolen almost wholesale from John Wilbanks who used it (I think) in the talk he gave at a Science Commons meetup in Redmond a few years back. At the time I think we were awash in “Facebooks for Science” so that was the target but the sentiment holds. As once was the case with Facebook and now is for Github, or Wikipedia, or StackOverflow, the possibilities opened up by these new services and technologies to support a much more efficient and effective research process look amazing. And they are. But you’ve got to be a little careful about taking the analogy too far.

If you look at what these services provide, particularly those that are focused on coding, they deliver commentary and documentation, nearly always in the form of text about code – which is also basically text. The web is very good at transferring text, and code, and data. The stack that delivers this is built on a set of standards, with each layer building on the layer beneath it. StackOverflow and Github are built on a set of services, that in turn sit on top of the web standards of http, which in turn are built on network standards like TCP/IP that control the actual transfer of bits and bytes.

The fundamental stuff of these coding sites and Wikipedia is text, and text is really well supported by the stack of web technologies. Open Source approaches to software development didn’t just develop because of the web, they developed the web so its not surprising that they fit well together. They grew up together and nurtured each other. But the bottom line is that the stack is optimized to transfer the grains of material, text and code, that make up the core of these services.

When we look at research we can see that when we dig down to the granular level it isn’t just made up of text. Sure most research could be represented as text but we don’t have the standardized forms to do this. We don’t have standard granules of research that we can transfer from place to place. This is because its complicated to transfer the stuff of research. I picked on TCP/IP specifically because it is the transfer protocol that supports moving bits and bytes from one place to another. What we need are protocols that support moving the substance of a piece of my research from one place to another.

Work on Research Objects [see also this paper], intended to be self-contained but useable pieces of research is a step in this direction, as are the developing set of workflow tools, that will ultimately allow us to describe and share the process by which we’ve transformed at least some parts of the research process into others. Laboratory recording systems will help us to capture and workflow-ify records of the physical parts of the research process. But until we can agree how to transfer these in a standardized fashion then I think it is premature to talk about Githubs for research.

Now there is a flip side to this, which is that where there are such services that do support the transfer of pieces of the research process we absolutely should be  experimenting with them. But in most cases the type-case itself will do the job. Github is great for sharing research code and some people are doing terrific things with data there as well. But if it does the job for those kinds of things why do we need one for researchers? The scale that the consumer web brings, and the exposure to a much bigger community, is a powerful counter argument to building things ‘just for researchers’. To justify a service focused on a small community you need to have very strong engagement or very specific needs. By the time that a mainstream service has mindshare and researchers are using it, your chances of pulling them away to a new service just for them are very small.

So yes, we should be inspired by the possibilities that these new services open up, and we should absolutely build and experiment but while we are at it can we also focus on the lower levels of the stack?They aren’t as sexy and they probably won’t make anyone rich, but we’ve got to get serious about the underlying mechanisms that will transfer our research in comprehensible packages from one place to another.

We have to think carefully about capturing the context of research and presenting that to the next user. Github works in large part because the people using it know how to use code, can recognize specific languages, and know how to drive it. It’s actually pretty poor for the user who just wants to do something – we’ve had to build up another set of services at different levels, the Python Package Index, tools for making and distributing executables, that help provide the context required for different types of user. This is going to be much, much harder, for all the different types of use we might want to put research to.

But if we can get this right – if we can standardize transfer protocols and build in the context of the research into those ‘packets’ that lets people use it then what we have seen on the wider web will happen naturally. As we build the stack up these services that seem so hard to build at the moment will become as easy today as throwing up a blog, downloading a rubygem, or firing up a machine instance. If we can achieve that then we’ll have much more than a github for research, we’ll have a whole web for research.

There’s nothing new here that wasn’t written some time ago by John Wilbanks and others but it seemed worth repeating. In particular I recommend these posts [1, 2] from John.