If you want reproducible science, the software needs to be open source
A Github for scientific code doesn't go nearly far enough. The transition from paper journals to electronic publications has only converted dead-paper into "electronic" paper. With some exceptions, e.g. video recordings, animations and supplementary figures/documents/spreadsheets/code, the document that you download from any major science publisher is a PDF that looks almost exactly like the printed publication. Most don't even include links to referenced publications[1]!<p>Today, we know a lot about how to make documents that have complex formatting (think micro formats, links) and even more about making abstract document formats that can be presented and styled in different ways (think XML and stylesheet type separation of data and presentation). Having a standardized scientific publication format (with open-source user or publisher generated extensions as needed) would completely change the way we produce and consume the literature. Imagine the possibilities for meta-analysis!<p>Yes, code should (in most cases) be released together with a paper. But even better would be if the code were released as part of a standardized data format that would allow you to, for instance, selectively download raw data and re-run the computational experiments on your own computer (think: re-running simulations in Mekentosj's Papers as you read the paper).<p>Even simpler (and possibly more useful): provide both low and original (high) resolution versions of figures that can be examined separately from the main document. I can't tell you how many times I've been annoyed by the low quality of the published images and wished I could zoom in to the level of detail I know was in the original image. Even more frustrating: why should I have to take screenshots of images in Preview to add to a figure in my lab meeting. Separate the presentation and the data!<p>[1]although some now include intra-document links from a citation in the text to the reference in the coda