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20/01/201610/05/2023

BioUnify COST Grant proposal brings EU biodiversity scientists and their data together

Mobilisation, coordination and cooperation are among the pillars of the Unifying European Biodiversity Informatics (BioUnify) project, described in a Grant proposal, submitted to the COST Association and published in the open-access journal Research Ideas and Outcomes (RIO). Both short-and long-term plans are clearly set to bring together the biodiversity informatics community and simultaneously synthesise the available data from across the relevant disciplines. The outcomes are to eventually translate into efficient global biodiversity policy.

While structuring, aggregating, linking and processing the constantly increasing biodiversity data efficiently is a globally recognised issue, many isolated research groups are working on their own. The large international team of scientists, led by Dr. Dimitrios Koureas, Natural History Museum, London, address the problem by providing a detailed plan, which builds on experience and available data to create a new platform, promoting cooperation across disciplines and expertise.

The proposed COST Action is probably the first to be fully published in the context of Open Science practices. It promises to aid biodiversity research through improving the access and reproducibility of data, mobilised from both natural history collections as well as remote sources from across Europe; bringing together the outcomes of ongoing separate biodiversity projects; transferring skills and technical awareness between researchers and information technologists, and formulating long-term goals in order to ensure that the European biodiversity informatics are aligned with the global ones.

While the common approaches used to achieve scientific dialogue rely mainly on scientific publications and conferences, the authors accept that such practice is time-consuming, while not necessarily focused on specific and urgent technical or societal issues. Therefore, in their present proposal the scientists list a summary of the activities to be undertaken by the project’s initial network of supporters. They include among others 30 Short Term Scientific Missions, 8 Training schools, 6 Joined Student Supervisions, 10 Consolidated Reports/Task-specific documents as well as a website.

“Agile and effective communication between people, at the level (across scientific domains and communities) and timeframe needed to address explicit societal challenges, demands a highly focused network of people and activities,” the researchers explain. “A network that will enable researchers to jointly shape research goals and adjust methodologies for delivering results in scope and on time.”

Having been marked by three external reviewers, the proposal eventually received an average mark of 29.33/40, which fell just a step short of being selected for funding by the COST Association. However, in their present publication, the scientists list the key points from the received feedback, and discuss them.

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Original source:

Koureas D, Hardisty A, Vos R, Agosti D, Arvanitidis C, Bogatencov P, Buttigieg P, de Jong Y, Horvath F, Gkoutos G, Groom Q, Kliment T, Kõljalg U, Manakos I, Marcer A, Marhold K, Morse D, Mergen P, Penev L, Pettersson L, Svenning J, van de Putte A, Smith V (2016) Unifying European Biodiversity Informatics (BioUnify). Research Ideas and Outcomes 2: e7787. doi:10.3897/rio.2.e7787

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Image credit: NASA. http://www.nasa.gov/mission_pages/NPP/news/vegetation.html

License: Public Domain

12/01/201610/05/2023

PhD Project Plan published to invite community feedback early on

Development and implementation of novel methods for publication, visualisation and dissemination of the constantly growing biodiversity and genomic bioinformatic data are the main objective of the first PhD Project Plan available from the open-access Research Ideas and Outcomes journal, a journal created to publish the outputs of the whole research cycle. Founded on the principles of open science, the project addresses digitally born scholarly papers and digitised data, aiming to make them more accessible and citable, and the results more reproducible.

The gradual realisation of the project, inspired by the Open Biodiversity Knowledge Management System, begins with the publishing of data in semantically enriched publications, and is completed when this data is properly linked to the Web of data, also known as the Semantic Web, ensuring its re-usability and citability. PhD student Viktor Senderov and advisor Prof. Lyubomir Penev, both affiliated with Pensoft Publishers and the Bulgarian Academy of Sciences, believe that this is the way the entire scientific data life-cycle should opera.

A fundamental part of the project is the so-called Enhanced Publication (EP), which unlike a conventional academic paper enables the user to easily access the data contained within a publication, while providing various dynamic features. For instance, there are interlinked external resources or tools that gather information on certain objects or data elements in real time. Most importantly, an EP is an object-based artifact that is highly interactive and machine-readable.

The project’s idea is that all of the featured objects should be exportable and citable. The authors of the project plan give examples with the biodiversity-themed journals ZooKeys, PhytoKeys, and the Biodiversity Data Journal, which have already adopted some of the features of an EP.

The plan also includes development of visualisations of genomic and other biodiversity-related data. This is planned to be executed within the BIG4 consortium, where Viktor Senderov is a trainee. Both data from BIG4’s expeditions and from museum collections are to be utilised for the purposes of the project.

“As part of the scientific and methodological results, we expect to develop new approaches, methods and formats for data publishing, and for publishing in biodiversity science,” explain the scientists. “We also expect to develop novel methods for exchange between publications and external data repositories, and to illustrate the aforementioned methods by means of examples using data gathered in the consortium.”

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Original source:

Senderov V, Penev L (2016) The Open Biodiversity Knowledge Management System in Scholarly Publishing. Research Ideas and Outcomes 2: e7757. doi: 10.3897/rio.2.e7757

Additional information:

The work has been supported by the ITN Horizon 2020 project BIG4 (Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow’s researchers and entrepreneurs), under Marie Sklodovska-Curie grant agreement No. 542241.

06/01/201610/05/2023

Mental synthesis experiment could teach us more about our imagination

While there is general consensus that the ability to imagine a never-before-seen object or concept is a unique and distinctive human trait, there is little that we know about the neurological mechanism behind it. Neuroscientist Dr. Andrey Vyshedskiy proposes a straightforward experiment that could test whether the ability to imagine a novel object involves the synchronization of groups of neurons, known as neuronal ensembles. Since the process involves mentally combining familiar images, scenes or concepts, Dr. Vyshedskiy proposes calling this process ‘mental synthesis.’ His research idea is published in the open-access Research Idea and Outcomes (RIO) Journal.

In the past scientists have managed to isolate and record from individual neurons that fire only when a particular object (e.g. an apple) is shown or imagined. Now, Dr. Andrey Vyshedskiy, Boston University, USA, and Rita Dunn, ImagiRation, USA, suggest an experiment that utilizes currently available methods for isolating so-called “object neurons” in the human brain.

Dr. Vyshedskiy proposes extending this experimental paradigm by isolating any two object neurons and monitoring their neuronal activity when these two objects are imagined together for the very first time. If two object neurons that fire only when a particular object is imagined can be identified, then the current experiment would seek to measure the firing activity when these two objects are imagined together. For example, an apple on top of a dolphin.

According to this Mental Synthesis Theory, the subject’s brain will trigger an increased firing rate in both object neurons and, more importantly, a synchronization of their activities would occur. “Understanding the basis of mental synthesis can shed light on the evolution of the brain in general and on the evolution of language in particular,” the authors point out.

“Since researchers can often identify several object-selective neurons within a single patient, multiple novel pairings of objects can be studied,” author Dr. Andrey Vyshedskiy explains. “Furthermore, morphing of more than two objects into one mental frame can also be investigated”.

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Original source:

Vyshedskiy A, Dunn R (2015) Mental synthesis involves the synchronization of independent neuronal ensembles. Research Idea and Outcomes (RIO) Journal: doi: 10.3897/rio.1.e7642

05/01/201610/05/2023

New DFG grant proposal for a software quality control able to stand the test of time

For a software to be maintained in an optimal condition, as well as in track of any necessary updates and innovations, it needs to be kept in check constantly. This appears to be the only way for any potential quality problems that may arise to be detected and handled momentarily well before a user can encounter them.

A new grant proposal, addressed to the German Research Foundation (DFG), authored by Prof. Dr. Stefan Wagner, University of Stuttgart, and published in the open-access journal Research Ideas & Outcomes (RIO), suggests a new persistent set of quality control approaches meant to start analysing a software both manually and automatically during its creation and well before it has even been introduced.

The proposed methods, which Prof. Dr. Stefan Wagner envisions as a solution to software quality decay, provide thorough, contextual and focused feedback to the developers, who in their turn need less time and efforts to make sense of the new information. To achieve this, novel tools are to initiate regular analyses even before the implementation of the software changes and go on during the changes.

Previous knowledge and experience from similar problem-detection tools and practices are to be utilised as well. “Contemporary quality models, dynamic slicing and online discussions could even provide rationales for the feedback to support its acceptance and understandability,” explains the German researcher.

A particular issue addressed by the Professor of Software Engineering in his present publication are the so-called ‘co-changes’, which are changes to source code files that need to occur together. For example, if developers introduce a new feature it will cause changes in the functional part of the source code as well as the user interface. Such co-changes can lead to a defect when the change to the user interface is omitted. Giving such information on co-changes is especially useful to give the developers directly while the perform the change.

“Advances in static analysis, test generation and repository mining allow us to give further feedback to developers, potentially just-in-time while performing changes,” Prof. Dr. Stefan Wagner points out. “These analyses have not been incorporated into a joint feedback system that gives focused hints.”

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Original source:

Wagner S (2015) Continuous and Focused Developer Feedback on Software Quality (CoFoDeF). Research Ideas and Outcomes 1: e7576. doi: 10.3897/rio.1.e7576

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Additional information:

The DFG is the largest independent research funding organisation in Germany. It promotes the advancement of science and the humanities by funding research projects, research centres and networks, and facilitating cooperation among researchers.

The mission of RIO is to catalyse change in research communication by publishing ideas, proposals and outcomes in order to increase transparency, trust and efficiency of the whole research ecosystem. Its scope encompasses all areas of academic research, including science, technology, the humanities and the social sciences.

The journal harnesses the full value of investment in the academic system by registering, reviewing, publishing and permanently archiving a wider variety of research outputs than those traditionally made public: project proposals, data, methods, workflows, software, project reports and research articles together on a single collaborative platform offering one of the most transparent, open and public peer-review processes.

23/12/201510/05/2023

An Open Science plan: Wikidata for Research

Wikidata is to databases what Wikipedia is to encyclopedias – the free version that anyone can edit. Both aim to share “the sum of all human knowledge” across the world in a multitude of languages, and while Wikidata is younger and has a smaller community, it attracts the collaboration of more than 16,000 volunteer contributors globally each month (up from 14,000 a year ago).

Meanwhile, recent years have witnessed a constantly increasing demand and support for Open Access and Open Science across professional research communities and citizen scientists. Therefore, a Horizon 2020 project plan was put together by a team of six European partners led by the Museum für Naturkunde Berlin to integrate research workflows with Wikidata into a new virtual research environment (VRE) for Open Science, called Wiki4R. The plan combined approaches to make Wikidata useful for researchers both across disciplines and for several specific use cases, e.g. chemistry.

The cross-disciplinary aspects included standard ways for handling scholarly references in Wikidata and for asking questions of Wikidata, whereas the chemical part focused on how to describe Wikidata entries for chemical topics like molecules, solvents or reactions and pathways, how to link this information to scholarly databases and publications, and how to ask chemical questions of Wikidata. These technical parts of the proposal were complemented by parts on how to bring Wikidata together with citizen science projects, on what the value proposition of openness is for institutions, and on training activities.

The grant proposal was submitted in January and ultimately rejected, but its drafters believe it contains a range of ideas that may still be worth pursuing. In fact, efforts to handle scholarly references through Wikidata are ongoing, and Wikidata can now be queried for things like a list of countries ordered by the number of their cities with a female mayor.

“The idea of a closer integration between Wikidata and research workflows is not itself rejected, and we believe that it is useful for both the research and Wikimedia communities to continue to explore the opportunities here, to pilot them and to keep talking to funders and other stakeholders about the value that such infrastructure would provide to society, so they can consider making the necessary resources available,” comments Dr. Daniel Mietchen, who spearheaded the effort.

In order to stimulate such activities, the Wiki4R proposal is among the first ones published via the new open-access journal Research Ideas & Outcomes (RIO). The innovative platform accepts submissions of scholarly works from the entire research life-cycle, including research ideas and proposals that are deemed to be valuable to scholarly research and its future.

“Our proposal focuses on the needs of open science and empowering researchers to work together across disciplines in an open environment,” explains Dr. Daniel Mietchen. “The concept of open science is central to this proposal. Open science is highly inclusive, inviting collaboration from professional peers as well as other interested parties, including citizen scientists. It is also open with respect to the process, providing access to research as it unfolds, allowing anyone to engage with it right away.”

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Original source:

Mietchen D, Hagedorn G, Willighagen E, Rico M, Gómez-Pérez A, Aibar E, Rafes K, Germain C, Dunning A, Pintscher L, Kinzler D (2015) Enabling Open Science: Wikidata for Research (Wiki4R). Research Ideas and Outcomes 1: e7573. doi: 10.3897/rio.1.e7573

Additional Information:

The mission of RIO is to catalyse change in research communication by publishing ideas, proposals and outcomes in order to increase transparency, trust and efficiency of the whole research ecosystem. Its scope encompasses all areas of academic research, including science, technology, the humanities and the social sciences.

21/12/201510/05/2023

New proposal published in RIO tackles problematic trial detection in ClinicalTrials.gov

Clinical trials are crucial in determining the effectiveness of treatments and directly influence practical and policy decisions. However, their results could be even detrimental to real-life patients if data is fabricated or subject to errors. While it is about 2% of all researchers that admit to having manipulated their data, a new Dutch Fulbright project proposal, published via the innovative Research Ideas & Outcomes (RIO) Journal, suggests new methods to tackle these issues and to apply them to results reported in the ClinicalTrials.gov database.

Decisions based on bad data, both clinical and policy ones made by medical doctors and governmental institutions, respectively, can pose direct risks on treated patients and the population in general. Such was the case of beta-blockers, for instance, used to be prescribed to cardiac patients in order to decrease perioperative mortality. However, a subsequent meta-analysis detected erroneous data in the related clinical trials. Moreover, it turned out that beta-blockers actually increase the risk of mortality.

The new Dutch Fulbright proposal led by Chris HJ Hartgerink, Tilburg University, Netherlands, and Dr. Stephen L George, Duke University, United States, proposes new additional statistical methods for erroneous data detection to provide an additional quality control filter for clinical trial results reported in the ClinicalTrials.gov database.

Unfortunately, misleading data is not simply the product of bad practice, but could also result from human error or inadequate data handling. It is not even clear enough how often such mistakes or manipulations occur and have occurred in reality, let alone their prevalence in any science in particular. What is beyond doubt, however, is that additional methods and procedures of detecting bad data are needed in order to minimize the risk of bad decisions being taken when health and wellbeing are at stake.

“Detecting problematic data is a niche field with few experts around the world, despite its importance,” further explains Chris HJ Hartgerink. “Systematic application remains absent and this project hopes to push this field into this area. New estimates of how prevalent problematic data are welcome, because we currently rely on self-report measures, which suffer from human bias.”

Recently submitted to Fulbright, the 6-month project proposal has now been made open-access by the authors with RIO Journal, an innovative platform publishing all outputs of the research cycle, including: project proposals, data, methods, workflows, software, project reports and research articles.

“A grant proposal is a research output like any other but is only rewarded when it results in funding,” says Chris HJ Hartgerink. “We know that many good proposals are rejected and consequently not rewarded. Publishing the grant proposal shows the output, makes it rewardable and can help improve it by post-publication peer review.”

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Original Source:

Hartgerink CHJ, George SL (2015) Problematic trial detection in ClinicalTrials.gov. Research Ideas and Outcomes 1: e7462. doi: 10.3897/rio.1.e7462

Additional Information:

The Research Ideas and Outcomes (RIO) Journal publishes all outputs of the research cycle, including: project proposals, data, methods, workflows, software, project reports and research articles together on a single collaborative platform offering one of the most transparent, open and public peer-review processes. Its scope encompasses all areas of academic research, including science, technology, the humanities and the social sciences.

18/12/201510/05/2023

Austrian Science Fund grant proposal goes public with RIO Journal

Controlled manipulation of matter on the scale of atoms is the topic of a new cutting edge Austrian Science Fund (FWF) project “Heteroatom quantum corrals and nanoplasmonics in graphene” (HeQuCoG), led by Finnish-born physicist Toma Susi. The project is the first to openly publish its proposal via the innovative platform of the Research Ideas & Outcomes (RIO) Journal, designed to uncover the entire research cycle.

The mission of RIO is to catalyse change in research communication by publishing ideas, proposals and outcomes in order to increase transparency, trust and efficiency of the whole research ecosystem. The journal harnesses the full value of investment in the academic system by registering, reviewing, publishing and permanently archiving a wider variety of research outputs than those traditionally made public.

RIO offers one of the most transparent, open and public peer-review processes, including pre-submission and post-publication peer-review options. The journal is designed to encourage collaboration between scientists within and across disciplines by making the entire research cycle open, and by mapping the social impact for its publications.

Dr. Susi, based at the University of Vienna in Austria, shares why he chose to make his research accessible to peers and the wider public from the proposal stage. “I must be honest: it was an instinctively scary prospect to publish a grant proposal, even a funded one. However, once I carefully weighed the potential pros and cons and discussed the idea with my close peers, I concluded that those fears most likely were unfounded. Moreover, there really can be no doubt that science as a whole would benefit if this became common practice.”

The aim of the HeQuCoG project is to create atomically precise structures consisting of silicon and phosphorus atoms embedded in the lattice of graphene using a combination of ion implantation, first principles modeling and electron microscopy. The expected outcome is a systematic demonstration of atomic-level material design and the creation of freestanding “quantum corral” structures for the first time.

“We are happy to have such an exciting and ambitious project as one of the first to publish its proposal in RIO. This goes to show that the platform is an ideal hub for forward-thinking young researchers wishing to take science to a new level of collaboration and real-world impact” comments Prof. Lyubomir Penev, co-founder of RIO.

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Original source:

Susi T (2015) Heteroatom quantum corrals and nanoplasmonics in graphene (HeQuCoG). Research Ideas and Outcomes 1: e7479. doi: 10.3897/rio.1.e7479

Additional information:

The Austrian Science Fund FWF is devoted to the support of the ongoing development of Austrian science and basic research at a high international level. In this way, the FWF makes a significant contribution to cultural development, to the advancement of a knowledge-based society, and to the creation of value and wealth in Austria and abroad.

14/10/201510/05/2023

Would you like some experience of basic editorial work at RIO Journal?

Warming up for its first set of research ideas, proposals, articles, software suggestions and a lot more types of scientific work to be submitted in November, RIO Journal is on the lookout for early career researchers to lay the basis of the one-of-a-kind project that Research Ideas and Outcomes (RIO) Journal is.

What is an Editorial Apprentice?

At RIO Journal, we want to help researchers gain an understanding of editorial roles, by experience, from an early stage in their careers. Editorial Apprentices perform basic technical checks and execute the validation of a manuscript right before it is submitted to RIO.

RIO uses a unique platform – ARPHA, along with its associated authoring tool, the ARPHA Writing Tool (AWT). The platform is the first end-to-end, narrative- and data-integrated publishing solution that supports the full life cycle of a manuscript, from authoring to reviewing, publication and dissemination.

To ensure high quality of content, manuscripts on ARPHA go through a two-step validation process. First, the system provides an automated technical check, but a human “fine tuning” on a manuscript is often still needed. The editorial assistant keeps an eye on the text consistency, whether the references and the language are in compliance with the high standards of RIO, and if data underlying a manuscript are published according to the journal’s policy.

Why should I apply for an Editorial Apprentice at RIO?

If you are a PhD student or a Postdoc, you should be looking for some first-hand experience of more senior academic roles. It’s good to improve your own understanding of the academic system, as well as good for your CV. As an Editorial Apprentice at RIO you’ll gain experience of paper reviewing and publishing processes, and you will also be given the right atmosphere to advance your editorial skills and improve your knowledge of the publishing process.

What else do I want to know about RIO?

RIO is the first open-access peer-reviewed journal that makes it possible to publish research across all stages of the research cycle in disciplines ranging from humanities to science. RIO uses a novel, entirely public process of quality assurance checks, technical validation and formal peer-review, including options for pre-submission and post-publication peer-reviews.

How to apply?

If you are a PhD student or a Postdoc and wish to continue your career in academia or in the academic publishing industry, you are more than welcome to apply for an Editorial Apprenticeship via our online application form (Also available as PDF).

Please, note you will need to spend a few hours per week for a period of one year or more. We are looking for candidates who have published or submitted at least two scientific articles. High-level proficiency with written English is a must.

We look forward to working with you!