Scholarly Communication Report: Final Draft

“FINDINGS
1. Researchers are embracing non-traditional modes of scholarly output. 
2. Researchers are interested in sharing their work more broadly and more meaningfully than they have in the past.
3. Researchers feel a tension between their desire to create and share broadly and the pressures of tenure and promotion.
4. Researchers view the library as a trusted authority with whom they
would like to partner in advocacy and new scholarly production….”

Open+: Versioning Open Social Scholarship

Abstract:  Advocates of the Open Access (OA) movement have been fighting for free and unfettered access to research output since the early 1990s. Open access is a crucial element of a fair, efficient scholarly communication system where all are able to find, interpret, and use the results of publicly-funded research. Universal open access is more possible now than ever before, thanks to networked technologies and the development of open scholarship policies. But what happens after access to research is provided? In this paper I argue that versioning scholarship across varying modes and formats would move scholarly communication from a straightforward open access system to a more engaging environment for multiple communities.

Open and Shut?: eLife and my unanswered questions

“Reporting on the scholarly publishing world can be a frustrating business these days, not just because the business model for journalism has all but collapsed but because scholarly publishers seem to be becoming increasingly reluctant to engage with reporters in a meaningful way, especially where the topic is open access. Their clear preference is to communicate by press release or managed events like webinars.

Until recently, I had assumed that eLife at least was fully committed to openness. In 2016, for instance, it posted details of its publishing costs. But now I am not so sure….”

One Step Closer to the “Paper of the Future” | Research Data Management @Harvard

“As a researcher who is trying to understand the structure of the Milky Way, I often deal with very large astronomical datasets (terabytes of data, representing almost two billion unique stars). Every single dataset we use is publicly available to anyone, but the primary challenge in processing them is just how large they are. Most astronomical data hosting sites provide an option to remotely query sources through their web interface, but it is slow and inefficient for our science….

To circumvent this issue, we download all the catalogs locally to Harvard Odyssey, with each independent survey housed in a separate database. We use a special python-based tool (the “Large-Survey Database”) developed by a former post-doctoral scholar at Harvard, which allows us to perform fast queries of these databases simultaneously using the Odyssey computing cluster….

To extract information from each hdf5 file, we have developed a sophisticated Bayesian analysis pipeline that reads in our curated hdf5 files and outputs best fits for our model parameters (in our case, distances to local star-forming regions near the sun). Led by a graduate student and co-PI on the paper (Joshua Speagle), the python codebase is publicly available on GitHub with full API documentation. In the future, it will be archived with a permanent DOI on Zenodo. Also on GitHub users will find full working examples of the code, demonstrating how users can read in the publicly available data and output the same style of figures seen in the paper. Sample data are provided, and the demo is configured as a jupyter notebook, so interested users can walk through the methodology line-by-line….”

Pioneering ‘live-code’ article allows scientists to play with each other’s results

“The online journal eLife has created its first “computationally reproducible” article, in which figures are integrated with the software, data and computational environment required to produce them.

Readers can change the underlying code and produce modified figures in order to better understand, validate or build on the work. For example, they could rerun the code to see what a figure looks like without outliers, or use a different type of plot to reveal trends more effectively.

Researchers say that the reproducible article, which eLife first published in its conventional format last year1, is a significant step towards a future in which papers are much more than just static pages….”

Pioneering ‘live-code’ article allows scientists to play with each other’s results

“The online journal eLife has created its first “computationally reproducible” article, in which figures are integrated with the software, data and computational environment required to produce them.

Readers can change the underlying code and produce modified figures in order to better understand, validate or build on the work. For example, they could rerun the code to see what a figure looks like without outliers, or use a different type of plot to reveal trends more effectively.

Researchers say that the reproducible article, which eLife first published in its conventional format last year1, is a significant step towards a future in which papers are much more than just static pages….”

By Jupyter–Is This the Future of Open Science? | Linux Journal

In a recent article, I explained why open source is a vital part of open science. As I pointed out, alongside a massive failure on the part of funding bodies to make open source a key aspect of their strategies, there’s also a similar lack of open-source engagement with the needs and challenges of open science. There’s not much that the Free Software world can do to change the priorities of funders. But, a lot can be done on the other side of things by writing good open-source code that supports and enhances open science.

People working in science potentially can benefit from every piece of free software code—the operating systems and apps, and the tools and libraries—so the better those become, the more useful they are for scientists. But there’s one open-source project in particular that already has had a significant impact on how scientists work—Project Jupyter….”

David Worlock | Developing digital strategies for the information marketplace | Supporting the migration of information providers and content players into the networked services world of the future.

The Springer Nature announcement that they were working with ReseachGate on a fair sharing policy has elements that run right through the tracery of fissures . It tells us that commercial players have no commercial reason to do anything but compete , and that Springer Nature , Thieme , CUP and in time others want to be seen as more user supportive in this regard than , others . This is not for me a new form of permitted “syndication “ – simply a gracious concession to license what users were doing anyway and remove some friction. It also says that in the games yet to be played , many people see tracking usage of the traceable communication as an important source of information , and potentially of revenues . The pressures felt by players like Springer Nature and Wiley as they at once try to differentiate themselves from the very clear stance of a market leader like Elsevier while trying to protect their service integrity at the same time are similarly shown in the Projekt DEAL developments . Market leaders get trapped and isolated in market positions they cannot give up , while the rest dissociate and differentiate themselves as best they can , while trying hard not to lose revenue margins in the process . Then sit down and read the reactions to Plan S – Springer Nature were paragons of moderation and reason . The loudest squeals came from those with most to lose – scholarly societies with journal revenue dependence. …

So what can the market leader do about this change as they face increasing user criticism ? The traditional answer always was “ push intransigence as far as it will go , and if those who would change the terms of trade do not come to heel , change your CEO as a way of changing your own policy without losing face “ . It may of course be an entire co-incidence that Elsevier’s CEO Ron Mobed retired last week without prior indication that he was about to go , and has been replaced by a very experienced RELX strategy specialist , Kumsal Bayazit . She is warmly welcomed and deserves a good chance to rethink the strategies that have backed Elsevier into a corner with Projekt DEAL and with the University of California . The people who work at Elsevier are , to my certain knowledge , as dedicated as any group I know to the objectives of their customers and the improvement of scholarly communications : they know that at the end of the dy the customer has the final say . And let’s think about what the power of a market leader now really means : 20 years ago companies like Elsevier demanded that authors surrendered their copyrights on the grounds that only the publisher was powerful enough to protect them , while today no publisher is powerful enough to shutter SciHub….”

The Scientific Paper Is Obsolete. Here’s What’s Next. – The Atlantic

“Perhaps the paper itself is to blame. Scientific methods evolve now at the speed of software; the skill most in demand among physicists, biologists, chemists, geologists, even anthropologists and research psychologists, is facility with programming languages and “data science” packages. And yet the basic means of communicating scientific results hasn’t changed for 400 years. Papers may be posted online, but they’re still text and pictures on a page.

What would you get if you designed the scientific paper from scratch today? …

Software is a dynamic medium; paper isn’t. When you think in those terms it does seem strange that research like Strogatz’s, the study of dynamical systems, is so often being shared on paper …

I spoke to Theodore Gray, who has since left Wolfram Research to become a full-time writer. He said that his work on the notebook was in part motivated by the feeling, well formed already by the early 1990s, “that obviously all scientific communication, all technical papers that involve any sort of data or mathematics or modeling or graphs or plots or anything like that, obviously don’t belong on paper. That was just completely obvious in, let’s say, 1990,” he said. …”