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.

###

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

###

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

License: Public Domain

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 ZooKeysPhytoKeys, 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.”

The Open Science Pyramid

###

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.

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”.

###

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

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.”

###

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

###

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.