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Smart manuscripts



In our previous post we described the first (Nature!) publication that used Figlinq for creating interactive, data-connected figures and charts, which were included via a single hyperlink. This is easy, convenient and, importantly, 100% compatible with current academic publishing workflows.

But we can do much better than this.

Enter smart manuscript - an ever-evolving, liquid concept of a manuscript containing more than just text, pictures and videos. While a few individual scientists have been including links to interactive charts in their publications for over half a decade, F1000 Research was perhaps the first academic publisher to embrace this within its workflow. F1000 also enabled readers to control parameters for some of the charts, and even introduced the first living figure, which (still) enables scientists to add new versions of the presented data.

A few years have passed since these pioneering attempts, and with the recent advancements of interconnected digital (web) technology, the potential of smart manuscripts has become essentially limitless. One illuminating illustration of this potential is the Executable Research Article (ERA), introduced by eLife, in collaboration with Stencila. ERA allows inclusion of executable code blocks which can, for instance, ingest source data, process it and spit out a chart or table (but imagine what else it could do, given some extra code!). These blocks can then be examined and re-run, in real-time, by those readers who wish to adjust the analysis steps and/or parameters. Alas, for the time being, the flexibility and scope of ERAs and similar solutions demand some serious effort, as well as programming skills that may be beyond the reach of most scientists.

So, we created our own version of a smart manuscript! We based it on the same Nature paper described in our previous post, but now all 126 panels are embedded directly in the online document, where they can be interacted with, edited, forked, shared, etc. As all Figlinq's charts, they are permanently data-connected. And as we learned to expect, the manuscript behaves well on large as well as small screens, with charts maintaining their interactivity via touch on a mobile device or tablet.

Figlinq's first smart manuscript

Right now, this is just a technology preview - a sneak peek at what's inevitably around the corner. What's next? We're exploring possibilities to provide such next-generation manuscripts at scale (we will likely need help from academic publishers!). We are also reaching out to forward-looking organizations (such as eLife or F1000) to see whether Figlinq's interactive figures can become building blocks for the future smart manuscripts. Please let us know if you have any suggestions and - stay tuned!

First (Nature!) publication using Figlinq



Even though stil in beta phase, Figlinq has been used to create and publish interactive, data-connected figures for a major publication in the high-impact journal Nature. In this paper, Sanne van Neerven and colleagues explore the molecular mechanisms driving initiation of intestinal tumors and discover that lithium chloride - a drug already used for treatment of depression - inhibits the growth of these tumors in mice.

Nature publications tend to be data-heavy beasts, and this one is no different: 14 figures, composed of 126 panels, including 46 images and 117 individual charts, if we count correctly. In this particular case, all original (static) figures were finalized even before Figlinq existed, so the authors recreated all of them using our platform. In the process, the charts became (automatically) linked to the underlying data that can now be accessed via each individual chart. Each chart can also be edited (and data inspected or downloaded) by anyone, with or without Figlinq account. Figlinq's users can, moreover, fork the charts (plus data) and save them to their own workspace for reuse or re-analysis!

Here are two particular charts from this publication: a heatmap with 2 382 data points from Figure 2 and a volcano chart with 17 378 data points from Figure 3.

All interactive figures from this publication - of course permanently connected to the underlying data - are available on Figlinq.

The original paper can be found on Nature's website.

Website is live



We're half-alive! Figlinq's beta website has been launched, with documentation at it's heart. Excellent documentation among the most important goals for our website. We therefore built it on Docusaurus - open source, lightning-fast, fully responsive documentation-centric web creation framework. Coming up soon: web application!

Figlinq is born!



Just before the holiday break, Plotly and Amsterdam UMC have agreed to repurpose Plotly's Chart Studio, a powerful chart creation suite, for charting and (FAIR) publishing of research data! Figlinq will further develop and improve Chart Studio to facilitate data analysis, charting, sharing and publishing in smart, data-connected manuscripts.