new: "Ten simple rules for creating reusable pathway models for computational analysis and visualization"

Figure 3 of the article (CC-BY).

Our scientific knowledge dissemination system is broken. Scholars have devices a system where knowledge is encrypted in PDF and HTML and ReadCube, many of these have been deliberately obfuscated to make text and data mining hard. After all, as some claim, without prestige and high stakes, no quality science. Utter bollocks, of course. So, we're wasting enormous amounts of research money in the process. Welcome to the market economy. Fortunately, there is a growing generation of scholars that actually see beyond nonsense like impact factors and encrypted prestige journals, a generation that does value knowledge dissemination.

So, many people are often silently working on better knowledge dissemination approaches. Me included. After all, you cannot do machine learning, theory building and testing, etc, without data. But we must go to a reality where data goes into proper places, unencrypted, not hidden in silly PDFs or ReadCubes. Scientific knowledge is not a bedtime story (tho, they do make excellent bedtime stories). Sure, the narrative is important, but not so important that data, models, etc, should not be shared.

Just like a picture says a thousand words, a proper FAIR and Open data file does so too.

But since adequate education at universities is generally missing, people are writing guidance. Minimal reporting standards, define file formats, etc, etc. We just published one too: "Ten simple rules for creating reusable pathway models for computational analysis and visualization". Pathway diagrams is one powerful way to tell a narrative about your knowledge, but without the need to encrypt this into a PDF that is very costly to reuse. Pathway diagrams are not take advantage of the power of visual representation of biology, the underlying mechanism of publishing platforms like WikiPathways, Reactome, and KEGG ensure the embedded biology can be understood by computers too. The FAIR and Open approach ensures swift dissemination of new biological insights.

This new paper explains how you can take advantage of this to make your new biological insights spread much faster and further in our fast growing knowledge about biology. Have fun reading, and please do not hesitate to contact me or any of the other authors if you have additional questions.