May, 2016 |

31/05/201610/05/2023

50th publication in RIO Journal: Report of the first FORCE11 Scholarly Commons workshop

What if scholars, librarians, archivists, publishers and funders could restart scholarly communication all over? This was the slogan of the first FORCE11 Scholarly Commons Working Group (SCWG) workshop, which took place in February. Advocating for an open, sustainable, fair and creditable future that is technology- and business-enabled, not -led, FORCE11’s SCWG committee published a Workshop Report in the open access journal Research Ideas and Outcomes (RIO), becoming the anniversary 50th publication in the innovative research publishing platform.

The community of FORCE11, comprising scholars, librarians, archivists, publishers and research funders from around the globe, was born at the FORC Workshop held in Dagstuhl, Germany in August 2011. Ever since, the community have been working and striving together towards a change in modern scholarly communication through the effective use of information technology. Their aim has always been to facilitate the change to improved knowledge creation and sharing.

In 2016, the Scholarly Commons Working group within FORCE11 conducts two workshops in order to find the answers to the question how scholarly communication would have looked now, had it not been for the 350 years of traditional practices. They also focus on the implications of modern technology and modes of communications that could help bring the right change about.

“Too often, scholars are unaware of the origins of current practices and accept the status quo because ‘that’s how it’s done’,” the authors point out. “But what if we could start over? What if we had computers, Internet, search engines and social media, but no legacy of journals, articles, books, review systems etc.?”

The first workshop, held between 25th and 27th February in Madrid, Spain, was titled “What if we could start over?”. The second one is planned for later this year under the slogan “Putting the pieces together.”

During the three-day workshop, the fifty participants, representing experts, early career researchers and new voices from across disciplines and countries, engaged in various activities. In order to”diverge and then converge”, the participants were encouraged through a number of enjoyable tasks to freely think outside the box, assuming that the current system of scholarly communication, based on a paper-based reward system, never existed.

“Given today’s technology and the amount of money currently in the system, how would you design a system of scholarly communications (“The Scholarly Commons”), the goal of which is to maximize the accessibility and impact of scholarly works,” they were asked. “By putting us in an alternate reality with a clear charge, we sidestepped issues that often engulf such discussions: why do we publish and who do we publish for.”

At the end of the workshop, the group’s principles were ordered under five subheadings, namely:

Open and sustainable
Fair
Credit for all endeavors
Technology- and business-enabled, not -led
Governance and funding

The attendees’ ideas, visions and suggested principles were also captured in a live and interactive visualization, consisting of the participants’ virtual post-it notes, also available through Trello.

In the spirit of the workshop itself, the report is now formally published in the form of a new scholarly communication artifact. Workshop Report is only one of the various innovative research publication types, provided by the open access journal Research Ideas and Outcomes(RIO), whose aim is to acknowledge and disseminate all quality and valuable research outputs from across all stages of the research cycle.

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Original source:

Kramer B, Bosman J, Ignac M, Kral C, Kalleinen T, Koskinen P, Bruno I, Buckland A, Callaghan S, Champieux R, Chapman C, Hagstrom S, Martone M, Murphy F, O’Donnell D (2016) Defining the Scholarly Commons – Reimagining Research Communication. Report of Force11 SCWG Workshop, Madrid, Spain, February 25-27, 2016. Research Ideas and Outcomes 2: e9340. doi: 10.3897/rio.2.e9340

31/05/201610/05/2023

RIO celebrates its 50th publication

We are pleased to announce that RIO published its 50th article!

The milestone paper “Defining the Scholarly Commons – Reimagining Research Communication. Report of Force11 SCWG Workshop, Madrid, Spain, February 25-27, 2016” is a Workshop Report by Bianca Kramer et al., one among many showcasing RIO’s innovative publication types in use. To date, the journal has published outputs in various innovative categories (see chart), including Research Ideas, Workshop Reports, Data Management Plans, Research Posters, Conference Abstracts and PhD Project plans. We are especially proud to host Grant Proposals from a wide variety of funding initiatives worldwide.

See a more detailed breakdown of RIO’s publications in the pie chart above.

17/05/201610/05/2023

Open Science environment Unicorn allows researchers and decision makers to work together

Given that the most important societal needs require multidisciplinary collaboration between researchers and decision makers, a suitable environment has to be provided in the first place. A proposal, prepared by a Finnish consortium and published in the open access journal Research Ideas and Outcomes, suggests a new, open virtual work and modeling platform to support evidence-based decision making in a number of areas, while also abiding by the principles of openness, criticism and reuse.

The Finnish consortium, led by Prof. Pekka Neittaanmäki, University of Jyväskylä, and bringing together Timo Huttula and Janne Ropponen, Finnish Environment Institute, Juha Karvanen and Tero Tuovinen, University of Jyväskylä, Tom Frisk, Pirkanmaa Centre for Economic Development, Transport and the Environment, Jouni Tuomisto, National Institute for Health and Welfare, and Antti Simola, VATT Institute for Economic Research, acknowledge that, “it is not enough that experts push data to politicians.”

“There must be practices for mutual communication: experts must answer policy questions in a defendable and useful way; decision makers must more clearly explain their views using evidence; and there must be ICT tools to support this exchange,” the authors explain. “The focus is on end-users.”

Unicorn is to combine shared practices, tools, data, working environments and concerted actions in order to aggregate open information from multiple databases, and create tools for efficient policy studies.

The consortium have already developed and tested prototypes of such practices and tools in several projects, and insist that they are now ready to apply their experience and knowledge on a larger scale. They are also certain that open data and models are deservedly the “mega trend” nowadays.

“Unicorn directs this trend to paths that are the most beneficial for societal decision making by providing quick, reliable and efficient decision support,” they say.

“Significant saving of resources will be manifested with improved data collection, analyses and modeling. Also, the quality and amount of assessments that can be done to support work.”

“The major challenges related to evidence-based decision making actually are about changing the practices of researchers and decision makers,” according to the authors. Therefore, they see their project as a demonstration of the needed shifts.

Although the approach is applicable in all areas, the researchers are to initially implement them in environment, human health, and regional economy, “as they are complex and challenging enough to offer a good test bed for general development.”

Having already been submitted to the Strategic Funds of Academy of Finland in 2015, the Unicorn environment proposal has been rejected due to overambitiousness and low commercial potential. However, the authors are confident that the Unicorn environment along with its growing community of developers can, in fact, meet a great success. They are currently looking for further funding suggestions and forming new consortiums.

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Original source:

Neittaanmäki P, Huttula T, Karvanen J, Frisk T, Tuomisto J, Simola A, Tuovinen T, Ropponen J (2016) Unicorn-Open science for assessing environmental state, human health and regional economy. Research Ideas and Outcomes 2: e9232. doi: 10.3897/rio.2.e9232

12/05/201610/05/2023

Open neuroscience: Collaborative Neuroimaging Lab finalist for the Open Science Prize

Despite the abundance of digital neuroimaging data, shared thanks to all funding, data collection, and processing efforts, but also the goodwill of thousands of participants, its analysis is still falling behind. As a result, the insight into both mental disorders and cognition is compromised.

The Open Neuroimaging Laboratory framework, promises a collaborative and transparent platform to optimise both the quantity and quality of this invaluable brain data, ultimately gaining a greater insight into both mental disorders and cognition.

The project was submitted for the Open Science Prize competition by Katja Heuer, Max Planck Institute for Human Cognitive and Brain Sciences, Germany, Dr Satrajit S. Ghosh, Massachusetts Institute of Technology (MIT), USA, Amy Robinson Sterling, EyeWire, USA, and Dr Roberto Toro, Institut Pasteur, France. Amongst 96 submissions from all around the globe, it was chosen as one of six teams to compete in the second and final phase of the Prize.

Simply having access and being able to download brain magnetic resonance imaging (MRI) data is not enough to reap all potential benefits. In order for it to be turned into insight and knowledge, it needs to also be queried, pre-processed and analysed, which requires a substantial amount of human curation, visual quality assessment and manual editing. With research being rather patchy, a lot of efforts are currently redundant and unreliable.

On the other hand, the Open Neuroimaging Laboratory aims to aggregate annotated brain imaging data from across various resources, thus improving its searchability and potential for reuse. It is to also develop a tool that will facilitate and encourage the creation of distributed teams of researchers to collaborate together in the analysis of this open data in real time.

“Our project will help transform the massive amount of static brain MRI data readily available online into living matter for collaborative analysis,” explain the researchers.

“We will allow a larger number of researchers to have access to this data by lowering the barriers that prevent their analysis: no data will have to be downloaded or stored, no software will have to be installed, and it will be possible to recruit a large, distributed, group of collaborators online.”

“By working together in a distributed and collaborative way, sharing our work and our analyses, we should improve transparency, statistical power and reproducibility,” they elaborate. “Our aim is to provide to everyone the means to share effort, learn from each other, and improve quality of and trust in scientific output.”

Having already developed a functional prototype of the BrainBox web application, which provides an interactive online space for collaborative data analyses and discussions, the team will now turn it into a first version with an improved user experience, stability and documentation. Planned for the Open Science Prize Phase 2 are furthering the type of analyses and exploring the development of interfaces for database-wise statistical analyses.

In the spirit of the competition, the scientists have decided to release their code open source on GitHub to facilitate bug fixes, extension and maintainability.

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Original source:

Heuer K, Ghosh S, Robinson Sterling A, Toro R (2016) Open Neuroimaging Laboratory.Research Ideas and Outcomes 2: e9113. doi: 10.3897/rio.2.e9113

03/05/201610/05/2023

Influence of religion and predestination on evolution and scientific thinking

Generally seen as antithetical to one another, evolution and religion can hardly fit in a scientific discourse simultaneously. However, biologist Dr Aldemaro Romero Jr., Baruch College, USA, devotes his latest research article, now published in the open access Research Ideas and Outcomes (RIO), to observing the influences a few major religions have had on evolutionists and their scientific thinking over the centuries.

Inspired by the lack of pigmentation and/or eyes in some cave organisms, he focuses on biospeleology to challenge the notions of predetermination and linearity. Although the author makes it clear that fellow scientists do not claim their findings based on religion, he notes that “words matter and that words can hide a lot of the philosophical baggage that sooner or later may influence their ultimate conclusion”.

Using examples from across the centuries, Dr Aldemaro Romero Jr. goes back to the times long before Charles Darwin had started compiling his prominent “The Origin of Species” and then turns once again to his evolutionist successors. Thus, he explores the link between the notion of predestination, underlying in various religions and nations, and the evolutionary theories.

The author notices that despite conclusions that evolution is not a linear process, biologists have never stopped seeing and contemplating “preadaptations” and “regressive evolution”, when speculating on phenomena such as the lack of eyes in some exclusively cave-dwelling animals. Such choice of words can be easily traced back to assumptions of linearity and, therefore, predestination, common for various religions.

FALCON STATE, VENEZUELA - Aldemaro Romero Jr., Executive Director, BIOMA, during cave exploration in Paraguana in 1988. — FALCON STATE, VENEZUELA – Aldemaro Romero Jr., Executive Director, BIOMA, during cave exploration in Paraguana in 1988.

“Since the advent of Modern Synthesis we have a pretty consistent set of evidence that evolution is not linear, that there is not such a thing as direction for evolutionary processes, and that nothing is predetermined since natural selection, the main evolutionary mechanism, is a process that is not moved by any mystical force, nor directs beings toward a particular end,” points out Dr Aldemaro Romero Jr..

“Therefore, I hope this paper serves as a warning to scientists that no matter what reductionist view they have in the way they practice their research, if they do not understand the historical roots and the philosophical framework of their research, they are doomed at presenting only a very partial (and many times biased) view of nature,” he concludes.

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Original source:

Romero Jr. A (2016) The influence of religion on science: the case of the idea of predestination in biospeleology. Research Ideas and Outcomes 2: e9015. doi: 10.3897/rio.2.e9015