Tag: open science

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RIO Journal 5 years on: over 300 published outcomes from all around the research cycle

Five years on, the Open Science-driven journal Research Ideas and Outcomes (RIO) published an editorial that looks back on the 300 research ideas and research outcomes it has published so far.

Since its early days, RIO has enjoyed quite positive reactions from the open-minded academic community for its innovative approach to Open Science in practice: it provides a niche that had long been missing, namely the publication of early, intermediate and generally unconventional research outcomes from all around the research cycle (e.g. grant proposals, data management plans, project deliverables, reports, policy briefs, conference materials) in a cross-disciplinary scientific journal. In fact, several months after its launch, in 2016, the journal was acknowledged with the SPARC Innovator Award.

‘Alternative’ research publications

In times when posting a preprint was seen as a novel and rather bold practice across many fields, RIO facilitated much deeper dives into the research process, in order to unveil scientific knowledge and the process by which it is gathered, well before any final conclusions have been drawn. Long story short, to date, RIO has published 33 Research Ideas, 78 Grant Proposals, 16 Data Management Plans, 33 Workshop Reports and 5 PhD Project Plans, in addition to plenty of other early, interim and final non-traditional research outcomes, as well as conventional articles. Over time, RIO has kept adding additional article types to its list of publication types, with a few more expected in the near future.

What’s more, over the years, we’ve already observed how papers published in RIO successfully followed up on the continuity of the research process. For example, the Grant Proposal for the “Exploring the opportunities and challenges of implementing open research strategies within development institutions” project, funded by the International Development Research Centre (IDRC), was followed by the project’s Data Management Plan a year later.

Five years later, the figures reflecting the usage and engagement with the content published in RIO are evidently supportive of the value of having non-final and unconventional academic publications. For instance, the Grant Proposal for the COST Action DNAqua-Net, a still ongoing project dedicated to the development of novel genetic tools for bioassessment and monitoring of aquatic ecosystems, is the article with the most total views in RIO’s publication record to date. In the category of sub-article elements, whose usage is also tracked at the journal, the most viewed figure belongs to a Project Report and illustrates a sample code meant to be used in future neuroimaging studies. Similarly, the most viewed table ever published in RIO is part of a Workshop Report that summarises ASAPbio‘s third workshop, dedicated to the technical aspects of services related to the promotion of preprints in the biomedical and other life science communities.

Response to societal challenges

A unique and defining staple for RIO since the very beginning has also been the pronounced engagement with the Sustainable Development Goals (SDGs), as formulated by the United Nations right around the time of RIO’s launch. In order to highlight the societal impact of published research, RIO lets authors map their articles to the SDGs relevant to their paper. Once published, the article displays the associated badge(s) next to its title. Readers of the journal can even search RIO’s content by SDG, in the same way they would filter articles by subject, publication types, date or funding agency. Next on the list for RIO is to add another level of granularity to the SDGs mapping. The practice has already been piloted by mapping relevant RIO articles to the ten targets under SDG14 (Life below water).

Taking transparency, responsibility and collaboration in academia and scholarly publishing up another notch, RIO requires for reviews to be publicly available. In addition, the journal supports post-publication reviews, where peers are free to post their review anytime. In turn, RIO registers each review with its own DOI via CrossRef, in order to recognise the valuable input and let the reviewers easily refer to their contributions. A fine example is a Review Article exploring the biodiversity-related issues and challenges across Southeast Asia, which currently has a total of three public peer reviews, one of which is provided two years after the publication of the paper.

Public, transparent and perpetual peer review, pre- and/or post-publication

What’s more striking about peer review at RIO, however, is that it is not always mandatory. Given that the journal publishes many article types that have already been scrutinised by a legitimate authority – for instance, Grant Proposals that have previously been evaluated by a funder or defended PhD Theses – it only makes sense to avoid withholding these publications and duplicating associated evaluation efforts. On such occasions, all an author needs to do is provide a statement about the review status of their paper, which will be made public alongside the article.

On the other hand, where the article type of a manuscript requires pre-publication review, to avoid potential delays caused by the review process and editorial decisions, RIO encourages the authors to post their pre-review manuscript as a preprint on the recently launched ARPHA Preprints platform, subject to a quick editorial screening, which would only take a few days.

Further, RIO has now abandoned the practice of burdening the journal’s editors with the time-consuming task of finding reviewers, and instead requiring the submitting author to invite suitable reviewers upon submission, who are then immediately and automatically invited by the system. While significantly expediting the editorial work on a manuscript, this practice doesn’t compromise the quality of peer review in the slightest, since the reviews go public, while the final decision about the acceptance of the paper lies with the editor, who is also overlooking the process and able to intervene and invite additional reviewers anytime, if necessary.

Project-driven knowledge hub

The most significant novelty at RIO, however, is perhaps the newly assumed role of the journal as “a project-driven knowledge hub“, targeting specifically the needs of research projects, conference organisers and institutions. For them, RIO provides a one-stop source for the outputs of their scientists, in order to comply with the requirements of their funders or management, or simply to facilitate the discoverability, reusability and citability of their academic outputs and to highlight their interconnectedness.

Unlike typical permanent article collections, already widely used in scholarly publishing, with RIO, collection owners can take advantage of the unique opportunity to add a wide range of research outputs, including such published elsewhere, in order to provide even greater context to the assembled research outputs in their project- or institution-branded article collection (see the Horizon 2020 Project Path2Integrity‘s project collection as an example).

A permanent topical collection in RIO Journal may include a diverse range of both traditional and unconventional research outputs, as well as links to publications from outside the journal (see What can I publish on the journal’s website). 

For example, a project coordinator could open a collection under the brand of the project, and start by publishing the Grant Proposal, followed shortly by Data and Software Management Plans and Workshop Reports. Thus, even at this early point in the project’s development, the funder – and with them everyone else – would already have strong evidence of the project’s dedication to transparency and active science communication. Later on, the project’s participants would all be able to easily add to the project’s collection by either submitting their diverse research outputs straight to RIO and having it accepted by the collection lead editor, or providing metadata and link to their publication from elsewhere, even preprints. If the document is published outside of RIO, its metadata, i.e. author names and affiliations, article title and publication date, show up in the collection, while a click on the item will lead to the original publication. As the project progresses, the team behind it could add more and more outputs (e.g. Project Reports, Guidelines and Policy Briefs), continuously updating the public and the relevant stakeholders about the development of their work. Eventually, the collection will be able to provide a comprehensive and fully transparent report of the project from start to finish.

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Centrally-managed collections & Peer review flexibility: what’s new at RIO

In 2015, Research Ideas and Outcomes (RIO) was launched to streamline dissemination of scientific knowledge throughout the research process, recognised to begin with the inception of a research idea, followed by the submission of a grant proposal and progressing to, for example, data / software management plans and mid-stage project reports, before concluding with the well-known research and review paper.

In order to really expedite and facilitate access to scientific knowledge, the hurdles for engagement with the process need to be minimized for readers, authors, reviewers and editors alike. RIO aims to lay the groundwork for constructive scientific feedback and dialogue that would then lead to the elaboration and refinement of the research work well in its early stage. 

Recently, RIO published its 300th article – about a software for analyzing time series data from a microclimate research site in the Alps – and at that occasion, the RIO team wrote an editorial summarizing how the articles published in RIO so far facilitate engagement with the respective research processes. One of the observations in this regard was that while providing access to the various stages of the research cycle is necessary for meaningful engagement, there is a need for the various outcomes to be packed together, so that we can provide a more complete context for individual published outcomes.

Read the new editorial celebrating RIO’s 5th anniversary and looking back on 300 publications.

RIO introduced updates to its article collection approach to evolve into a “project-driven knowledge hub”, where a project coordinator, research institution or conference organiser can create and centrally manage a collection under their own logo, so that authors can much more easily contribute. Further, research outputs published elsewhere – including preprints – are also allowed, so that the collection displays each part of the ‘puzzle’ within its context. In this case, the metadata of the paper, i.e. title, authors and publication date, are displayed in the article list within the collection, and link to the original source.

Apart from allowing the inclusion of the whole diversity of research outcomes published in RIO or elsewhere, what particularly appeals to projects, conferences and institutions is the simplicity of opening and managing a self-branded collection at RIO. All they need to do is pay a one-time fee to cover the setup and maintenance of the collection, whereas an option with an unlimited number of publications is also available. Then, authors can add their work – subject to approval by the collection’s editor and the journal’s editorial office – by either starting a new manuscript at RIO and then assigning it to an existing collection; pasting the DOI of a publication available from elsewhere; or posting an author-formatted PDF document to ARPHA Preprints, as it has been submitted to the external evaluator (e.g. funding agency). In the latter two cases, the authors are charged nothing, in order to support greater transparency and contextuality within the research process.

Buttons on RIO Journal’s homepage allow users to create a new collection or add a document to an existing collection by either submitting a new manuscript via RIO Journal or pasting a DOI link of a publication from elsewhere, thus allowing for the collection to link to the original source and display the article’s metadata, i.e. title, authors and publication date.

Find more information about how to edit a collection at RIO and the associated benefits and responsibilities on RIO’s website.

Another thing we have revised at RIO is the peer review policy and workflow, which are now further clarified and tailored to the specificity of each type of research outcome.

Having moved to entirely author-initiated peer review, where the system automatically invites reviewers suggested by the author upon submission of a paper, RIO has also clearly defined which article types are subject to mandatory pre-publication peer review or not (see the full list). In the latter case, RIO no longer prompts the invitation of reviewers. Within their collections, owners and guest editors can decide on the peer review mode, guided by RIO’s existing policies.

While pre-publication peer review is not always mandatory, all papers are subject to editorial evaluation and also remain available in perpetuity for post-submission review. In both cases, reviews are public and disclose the name of their author by default. In turn, RIO registers each review with its own DOI via CrossRef, in order to recognise the valuable input and let the reviewers easily refer to their contributions. 

Both pre- and post-publication reviews at RIO are openly published alongside the paper and bear their own DOI. All papers in RIO remain available for post-publication review in perpetuity (see example).

For article types where peer review is mandatory (e.g. Research Idea, Review article, Research Article, Data Paper), authors are requested to invite a minimum of three suitable reviewers upon the submission of the paper, who are then automatically invited by the system. While significantly expediting the editorial work on a manuscript, this practice doesn’t compromise the quality of peer review in the slightest, since the editor is still overlooking the process and able to invite additional reviewers anytime, if necessary. 

For article types where peer review is not mandatory (e.g. Grant Proposal, Data Management Plan, Project Report and various conference materials), all an author needs to do is provide a statement about the review status of their paper, which will be made public alongside the article. Given that such papers have usually already been scrutinised by a legitimate authority (e.g. funding agency or conference committee), it only makes sense to not withhold their publication and duplicate academic efforts.

By the time it is submitted to RIO, a Grant Proposal like this one has often already been assessed by a legitimate funder, so it only makes sense to not undergo the process again at RIO and thereby slowing down its public dissemination.

Additionally, where the article type of a manuscript requires pre-publication review, RIO encourages the authors to click a checkbox during the submission and post their pre-review manuscript as a preprint on ARPHA Preprints, subject to a quick editorial screening, which would only take a few days.

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Further reading:

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RIO shifts gears to serve as project-driven knowledge hub

Research Ideas and Outcomes (RIO Journal) upgrades its unique concept to appeal to scientific projects, conference organisers and research institutions

Over the last few years, we’ve been increasingly observing how major funders of research around the world, including the likes of the European Commission, Wellcome, U.S. National Institutes of Health (NIH), Deutsche Forschungsgemeinschaft (DFG) and the Japan Society for the Promotion of Science (JSPS) recognise the research cycle as a continuum, rather than scattered standalone conclusions and reports. 

Hence, as a forward-looking, open science-driven journal Research Ideas and Outcomes (RIO) took it as its own responsibility to encourage scientific project teams, conference organisers and research institutions to bring together unconventional research outputs (e.g. grant proposals, data management plans, project deliverables, policy briefs, conference materials) as well as traditional (e.g. research or review papers, monographs, etc.), including such published elsewhere. To do so, RIO now provides the platform ready to be used as a research knowledge hub, where published outcomes are preserved permanently and easier to share, disseminate, reference and reuse.

Hence, RIO stepped up its game by turning permanent article collections into a one-stop source of diverse research items, where project coordinators, conference organisers or research institutions can not only publish early, interim and conclusive research items as they emerge within a research project, a series of events or the continuous scientific efforts at their lab, but also link relevant publications (i.e. preprints, articles or other documents, published elsewhere) available elsewhere through their metadata. As a result, they will receive a one-stop source under their own branding for every piece of scientific contribution ready to present to funding bodies or prospective collaborators and future research teams.

A permanent topical collection in RIO Journal may include a diverse range of both traditional and unconventional research outputs, as well as links to publications from outside the journal (see What can I publish on the journal’s website). 

Apart from bringing contextually linked research outcomes together, thus prompting findability, readership and citability en masse, RIO’s approach to collections ensures further accessibility by not only having RIO-published articles available in traditional PDF, semantically enriched HTML and minable XML format. The open-science journal has now made it possible for users to add to their collections preprints from ARPHA Preprints, as well as author-formatted PDFs (e.g. project deliverables, reports, policy briefs, etc.) and linked metadata to documents published elsewhere. Thanks to the integration of the journal with the general-purpose open-access repository Zenodo, all items in a collection are archived, and additionally indexed, disseminated and cited.

By focusing on article and preprint collections coming out from a research project, institution or conference, RIO provides a quite specific and unique combination of benefits to all actors of the research process: scientists, project coordinators, funders and institutions: 

  1. Project, institution or conference branding and promotion.
  2. One-stop point for outputs of a research project, institution or conference.
  3. Free publication of author-formatted project outputs (i.e. grant proposals, deliverables, reports, policy briefs, conference materials and others).
  4. Inclusivity through adding articles, preprints and other documents published elsewhere as easy as entering the DOI number of the document.
  5. Credit and recognition for the Collection and Guest editors, who take care to organise and manage the article collection.
  6. Easier discoverability and usability of topically related studies to benefit both authors and readers.
  7. Increased visibility of related papers in a collection, even when these might otherwise not have much exposure.
  8. Simultaneous citation of multiple articles related to a certain subject.
  9. Citation and referencing of the whole collection as a complete entity.
  10.  DOI and citation details for collections and individual articles.

Furthermore, RIO Journal maps all publications to the Sustainable Development Goals  (SDGs), in order to emphasise the real-world impact of each published contribution, by displaying the corresponding badge within the article list. 

Last, but not least, both collections and individual publications in RIO enjoy the variety of default and on-demand science communication services, provided by Pensoft.  

How do project coordinators, funders and institutions benefit from a collection in RIO?

At the time a grant proposal is submitted to a research funder for evaluation, the team behind the proposed project has already put in considerable efforts, resulting in a unique idea with the potential to make a great stride towards the resolution of an outstanding problem in science, if only given the chance. However, too many of these ideas are bound to remain locked away in the archives of those funders, not because they are lacking in scientific value, but due to limited funds.

So, with its launch back in 2015, RIO Journal made it possible to publish and shed light on grant proposals and research ideas in general, similar early research outputs regardless of whether they are eventually funded or not, a novelty in scholarly publishing which earned RIO the SPARC Innovator Award Winner in 2016. To date, the journal has already published 75 grant proposals. 

Then, imagine what a contribution to science it would make to bring together the whole continuum of knowledge and scientific work all the way from the grant proposal to data  and software management plans, workshop reports, policy briefs and all interim and final deliverables produced within the span of the project!

On the other hand, funders are increasingly evaluating a prospective project’s impact based on its communication strategy. So, why not publish a grant proposal at the time of the submission of your proposal, in order to prove to the funding body that your project is serious about optimising its outreach to both the public and academia? Furthermore, by having an academic journal host any subsequent project deliverable, as a coordinator, you can rest assured that the communication activities of your project remain consistent and efficient.

In an excellent example of a project collection, the EU-funded ICEDIG (Innovation and Consolidation for Large Scale Digitisation of Natural Heritage), led by several major natural history institutions, including the Natural History Museum of London, Naturalis Biodiversity Center (the Netherlands), the French National Museum of Natural History and Helsinki University, brought together policy briefs, project reports, research articles and review papers, in order to provide a fantastic overview of their own research continuum. As a result, future researchers and various stakeholders can easily piece together the key components within the project, in order to learn from, recreate or even build on the experience of ICEDIG.

Explore the ICEDIG Project Outcomes collection on RIO’s website.

Similarly, conference organisers can make use of their own branded collections to overcome the ephemerality of presented research by collating virtually all valuable conference outputs, including abstracts, posters, presentations, datasets and full-text conference talks. For further convenience, a collection can be divided into subcollections, in order to organise the contribution by type or symposium. What particularly appeals to conference participants is the ARPHA Writing Tool, an intuitive collaborative online environment, which practically guides the user through each step: authoring, submission and pre-submission review, within a set of pre-designed, yet flexible templates available for each type of a conference output, thus sparing them the hassle to familiarise themselves with specific and perplexing formatting requirements

For institutions, RIO offers the opportunity to continuously provide evidence of the scholarly impact of their organisation. To better serve the needs of different labs or research teams, an institution can easily organise their outputs into various subcollections, and also customise their own article types, as well as the available usage tracking systems. Furthermore, by making use of the available pre-paid plans, institutions can support their researchers by covering fully or partially the publication charges at a discounted rate.

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Find more information regarding the submission and review process, policies and pricing, visit RIO Journal’s website.

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The first microbial supertree from figure-mining thousands of papers

While recent reports reveal the existence of more than 114,000,000 documents of published scientific literature, finding a way to improve the access to this knowledge and efficiently synthesise it becomes an increasingly pressing issue.

Seeking to address the problem through their PLUTo workflow, British scientists Ross Mounce and Peter Murray-Rust, University of Cambridge and Matthew Wills, University of Bath perform the world’s first attempt at automated supertree construction using data exclusively extracted by machines from published figure images. Their results are published in the open science journal Research Ideas and Outcomes (RIO).

For their study, the researchers picked the International Journal of Systematics and Evolutionary Microbiology (IJSEM) – the sole repository hosting all new validly described prokaryote taxa and, therefore, an excellent choice against which to test systems for the automated and semi-automated synthesis of published phylogenies. According to the authors, IJSEM publishes a greater number of phylogenetic tree figure images a year than any other journal.

An eleven-year span of articles dating back to January, 2003 was systematically downloaded so that all image files of phylogenetic tree figures could be extracted for analysis. Computer vision techniques then allowed for the automatic conversion of the images back into re-usable, computable, phylogenetic data and used for a formal supertree synthesis of all the evidence.

During their research, the scientists had to overcome various challenges posed by copyrights formally covering almost all of the documents they needed to mine for the purpose of their work. At this point, they faced quite a paradox – while easy access and re-use of data published in scientific literature is generally supported and strongly promoted, common copyright practices make it difficult for a scientist to be confident when incorporating previously compiled data into their own work. The authors discuss recent changes to UK copyright law that have allowed for their work to see the light of day. As a result, they provide their output as facts, and assign them to the public domain by using the CC0 waiver of Creative Commons, to enable worry-free re-use by anyone.

“We are now at the stage where no individual has the time to read even just the titles of all published papers, let alone the abstracts,” comment the authors.

“We believe that machines are now essential to enable us to make sense of the stream of published science, and this paper addresses several of the key problems inherent in doing this.”

“We have deliberately selected a subsection of the literature (limited to one journal) to reduce the volume, velocity and variety, concentrating primarily on validity. We ask whether high-throughput machine extraction of data from the semistructured scientific literature is possible and valuable.”  

 

Original source:

Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589

 

Additional information:

The research has been funded by the BBSRC (grant BB/K015702/1 awarded to MAW and supporting RM).

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Legitimacy of reusing images from scientific papers addressed

It goes without saying that scientific research has to build on previous breakthroughs and publications. However, it feels quite counter-intuitive for data and their re-use to be legally restricted. Yet, that is what happens when copyright restrictions are placed on many scientific papers.

The discipline of taxonomy is highly reliant on previously published photographs, drawings and other images as biodiversity data. Inspired by the uncertainty among taxonomists, a team, representing both taxonomists and experts in rights and copyright law, has traced the role and relevance of copyright when it comes to images with scientific value. Their discussion and conclusions are published in the latest paper added in the EU BON Collection in the open science journal Research Ideas and Outcomes (RIO).

Taxonomic papers, by definition, cite a large number of previous publications, for instance, when comparing a new species to closely related ones that have already been described. Often it is necessary to use images to demonstrate characteristic traits and morphological differences or similarities. In this role, the images are best seen as biodiversity data rather than artwork. According to the authors, this puts them outside the scope, purposes and principles of Copyright. Moreover, such images are most useful when they are presented in a standardized fashion, and lack the artistic creativity that would otherwise make them ‘copyrightable works’.

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“It follows that most images found in taxonomic literature can be re-used for research or many other purposes without seeking permission, regardless of any copyright declaration,” says Prof. David J. Patterson, affiliated with both Plazi and the University of Sydney.

Nonetheless, the authors point out that, “in observance of ethical and scholarly standards, re-users are expected to cite the author and original source of any image that they use.” Such practice is “demanded by the conventions of scholarship, not by legal obligation,” they add.

However, the authors underline that there are actual copyrightable visuals, which might also make their way to a scientific paper. These include wildlife photographs, drawings and artwork produced in a distinctive individual form and intended for other than comparative purposes, as well as collections of images, qualifiable as databases in the sense of the European Protection of Databases directive.

In their paper, the scientists also provide an updated version of the Blue List, originally compiled in 2014 and comprising the copyright exemptions applicable to taxonomic works. In their Extended Blue List, the authors expand the list to include five extra items relating specifically to images.

“Egloff, Agosti, et al. make the compelling argument that taxonomic images, as highly standardized ‘references for identification of known biodiversity,’ by necessity, lack sufficient creativity to qualify for copyright. Their contention that ‘parameters of lighting, optical and specimen orientation’ in biological imaging must be consistent for comparative purposes underscores the relevance of the merger doctrine for photographic works created specifically as scientific data,” comments on the publication Ms. Gail Clement, Head of Research Services at the Caltech Library.

“In these cases, the idea and expression are the same and the creator exercises no discretion in complying with an established convention. This paper is an important contribution to the literature on property interests in scientific research data – an essential framing question for legal interoperability of research data,” she adds.

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Original source:

Egloff W, Agosti D, Kishor P, Patterson D, Miller J (2017) Copyright and the Use of Images as Biodiversity Data. Research Ideas and Outcomes 3: e12502. https://doi.org/10.3897/rio.3.e12502

Additional information:

The present study is a research outcome of the European Union’s FP7-funded project EU BON, grant agreement No 308454.

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Guidelines for scholarly publishing of biodiversity data from Pensoft and EU BON

While development and implementation of data publishing and sharing practices and tools have long been among the core activities of the academic publisher Pensoft, it is well-understood that as part of scholarly publishing, open data practices are also currently in transition, and hence, require a lot of collaborative and consistent efforts to establish.

Based on Pensoft’s experience, and elaborated and updated during the Framework Program 7 EU BON project, a new paper published in the EU BON dedicated collection in the open science journal Research Ideas and Outcomes (RIO), outlines policies and guidelines for scholarly publishing of biodiversity and biodiversity-related data. Newly accumulated knowledge from large-scale international efforts, such as FORCE11 (Future of Research Communication and e-Scholarship), CODATA (The Committee on Data for Science and Technology), RDA (Research Data Alliance) and others, is also included in the Guidelines.

The present paper discusses some general concepts, including a definition of datasets, incentives to publish data and licences for data publishing. Furthermore, it defines and compares several routes for data publishing, namely: providing supplementary files to research articles; uploading them on specialised open data repositories, where they are linked to the research article; publishing standalone data papers; or making use of integrated narrative and data publishing through online import/download of data into/from manuscripts, such as the workflow provided by the Biodiversity Data Journal. Among the guidelines, there are also comprehensive instructions on preparation and peer review of data intended for publication.

Although currently available for journals using the developed by Pensoft journal publishing platform ARPHA, these strategies and guidelines could be of use for anyone interested in biodiversity data publishing.

Apart from paving the way for a whole new approach in data publishing, the present paper is also a fine example of science done in the open, having been published along with its two pre-submission public peer reviews. The reviews by Drs. Robert Mesibov and Florian Wetzel are both citable via their own Digital Object Identifiers (DOIs).

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Original source:

Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017) Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431. https://doi.org/10.3897/rio.3.e12431

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New collection in RIO Journal devoted to neuroscience projects from 2016 Brainhack events

A new collection devoted to neuroscience projects from 2016 Brainhack events has been launched in the open access journal Research Ideas and Outcomes (RIO). At current count, the “Brainhack 2016 Project Reports” collection features eight Project Reports, whose authors are applying open science and collaborative research to advance our understanding of the brain.

Seeking to provide a forum for open, collaborative projects in brain science the Brainhack organization has found a like-minded partner in the innovative open science journal RIO. The editor of the series is Dr. R. Cameron Craddock, Computational Neuroimaging Lab, Child Mind Institute and Nathan S. Kline Institute for Psychiatric Research, USA. He is joined by co-editors Dr. Pierre Bellec, Unité de neuroimagerie fonctionnelle, Centre de recherche de l’institut de gériatrie de Montréal, Canada, Dr. Daniel S. Margulies, Max Planck Research Group “Neuroanatomy & Connectivity“, Max Planck Institute for Human Cognitive and Brain Sciences, Dr. Nolan Nichols, Genetech, USA, and Dr. Jörg Pfannmöller, University of Greifswald, Germany.

The first project description published in the collection is a Software Management Plan presenting a comprehensive set of neuroscientific software packages demonstrating the huge potential of Gentoo Linux in neuroscience. The team of Horea-Ioan Ioanas, Dr. Bechara John Saab and Prof. Dr. Markus Rudin, affiliated with ETH and University of Zürich, Switzerland, make use of the flexibility of Gentoo’s environment to address many of the challenges in neuroscience software management, including system replicability, system documentation, data analysis reproducibility, fine-grained dependency management, easy control over compilation options, and seamless access to cutting-edge software release. The packages are available for the wide family of Gentoo distributions and derivatives. “Via Gentoo-prefix, these neuroscientific software packages are, in fact, also accessible to users of many other operating systems,” explain the researchers.

While quantifying lesions in a robust manner is fundamental for studying the effects of neuroanatomical changes in the post-stroke brain while recovering, manual lesion segmentation has been found to be a challenging and often subjective process. This is where the Semi-automated Robust Quantification of Lesions (SRQL) Toolbox comes in. Developed at the University of Southern California, Los Angeles, it optimizes quantification of lesions across research sites. “Specifically, this toolbox improves the performance of statistical analysis on lesions through standardizing lesion masks with white matter adjustment, reporting descriptive lesion statistics, and normalizing adjusted lesion masks to standard space,” explain scientists Kaori L. Ito, Julia M. Anglin, and Dr. Sook-Lei Liew.

Called Mindcontrol, an open-source web-based dashboard application lets users collaboratively quality control and curate neuroimaging data. Developed by the team of Anisha Keshavan and Esha Datta, both of University of California, San Francisco, Dr. Christopher R. Madan, Boston College, and Dr. Ian M. McDonough, The University of Alabama, Mindcontrol provides an easy-to-use interface, and allows the users to annotate points and curves on the volume, edit voxels, and assign tasks to other users. “We hope to build an active open-source community around Mindcontrol to add new features to the platform and make brain quality control more efficient and collaborative,” note the researchers.

At University of California, San Francisco, Anisha Keshavan, Dr. Arno Klein, and Dr. Ben Cipollini, created the open-source Mindboggle package, which serves to improve the labeling and morphometry estimates of brain imaging data. Using inspirations and feedback from a Brainhack hackathon, they built-up on Mindboggle to develop a web-based, interactive, brain shape 3D visualization of its outputs. Now, they are looking to expand the visualization, so that it covers other data besides shape information and enables the visual evaluation of thousands of brains.

Processing neuroimaging data on the cortical surface traditionally requires dedicated heavy-weight software suites. However, a team from Max Planck Institute for Human Cognitive and Brain Sciences, Free University Berlin, and the NeuroSpin Research Institute, France, have come up with an alternative. Operating within the neuroimaging data processing toolbox Nilearn, their Python package allows loading and plotting functions for different surface data formats with minimal dependencies, along with examples of their application. “The functions are easy to use, flexibly adapt to different use cases,” explain authors Julia M. Huntenburg, Alexandre Abraham, Joao Loula, Dr. Franziskus Liem, and Dr. Gaël Varoquaux. “While multiple features remain to be added and improved, this work presents a first step towards the support of cortical surface data in Nilearn.”

To further address the increasing necessity for tools specialised to process huge high-resolution brain imaging data in their anatomical detail, Julia M. Huntenburg gathers a separate team to work on another Python-based software. Being a user-friendly standalone package, this subset of CBSTools requires no additional installations, and allows for interactive data exploration at each processing stage.

Developed at the University of California, San Francisco, Cluster-viz is a web application that provides a platform for cluster-based interactive quality control of tractography algorithm outputs, explain the team of Kesshi M. Jordan, Anisha Keshavan, Dr. Maria Luisa Mandelli, and Dr. Roland G. Henry. It.

A project from the University of Warwick, United Kingdom, aims to extend the functionalities of the FSL neuroimaging software package in order to generate and report peak and cluster tables for voxel-wise inference. Dr. Camille Maumet and Prof. Thomas E. Nichols believe that the resulting extension “will be useful in the development of standardized exports of task-based fMRI results.”

More 2016 Brainhack projects are to be added to the collection.

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In a nutshell: The four peer review stages in RIO explained

Having received a number of requests to further clarify our peer review process, we hereby provide a concise summary of the four author- and journal-organised peer review stages applicable to all research article publications submitted to RIO. 

 

Stage 1: Author-organised pre-submission review

Optional. This review process can take place in the ARPHA Writing Tool (AWT) during the authoring process BEFORE the manuscript is submitted to the journal. It works much like discussion of a manuscript within an institutional department, akin to soliciting comments and changes on a collaborate Google Doc file. The author can invite reviewers via the “+Reviewers” button located on the upper horizontal bar of the AWT. Then, the author(s) and the reviewers are able to work together in the ARPHA online environment through an inline comment/reply interface. The reviewers are then expected to submit a concise evaluation form and a final statement.

The pre-submission review is not mandatory, but we strongly encourage it. Pre-submission reviews will be published along with the article and will bear a DOI and citation details. Articles reviewed before submission are labelled “Reviewed” when published. Manuscripts that have not been peer-reviewed before submission can be published on the basis of in-house editorial and technical checks, and will be labelled “Reviewable”.

If there is no pre-submission review, the authors have to provide a public statement explaining why they do not have, or need a pre-submission review for this work (e.g. a manuscript has been previously reviewed; a grant proposal has already been accepted for funding, etc.).

 

Stage 2: Pre-submission technical and editorial check with in-house editors or relevant members of RIO’s editorial board

Mandatory. Provided by the journal’s editorial office within the ARPHA Writing Tool when a manuscript is submitted to the journal. If necessary, it can take several rounds, until the manuscript is improved to the level appropriate for direct submission and publication in the journal. This stage ensures format compliance with RIO’s requirements, as well as relevant funding-body and discipline-specific requirements.

 

Stage 3: Community-sourced post-publication peer review

Continuously available. All articles published in RIO are available for post-publication review, regardless of them being subject to a pre-submission review or not, or their review status (Reviewable, Reviewed, or RIO-validated). The author may decide to publish a revised version of an article anytime based on feedback received from the community. Putatively, even years after publication of the original work our system allows a review to be published alongside the paper.  

 

Stage 4: Journal-organized post-publication peer review

Optional. If the author(s) request it, the journal can additionally organize a formal peer review from discipline-specific researchers in a timely manner. Authors may suggest reviewers during the submission process, but RIO may not necessarily invite suggested reviewers.

Once an editor and reviewers are invited by the journal, the review process happens much like the conventional peer review in many other journals, but is entirely open and transparent. It is also subject to a small additional fee, in order to cover the management of this process. When this review stage is successfully completed and the editors have decided to validate the article, the revised article version is labelled “RIO-validated”.

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Robot to find and connect medical scientists working on the same research via Open Data

Sharing research data or Open Science, aims to accelerate scientific discovery, which is of particular importance in the case of new medicines and treatments. A grant proposal by an international research team, led by Dr Chase C. Smith, MCPHS University, and submitted to the Open Science Prize, suggests development of what the authors call The SCience INtroDuction Robot, (SCINDR). The project’s proposal is available in the open access journal Research Ideas and Outcomes (RIO).

Building on an open source electronic lab notebook (ELN) developed by the same team, the robot would discover and alert scientists from around the world who are working on similar molecules in real time. Finding each other and engaging in open and collaborative research could accelerate and enhance medical discoveries.

Already running and being constantly updated, the electronic lab notebook serves to store researchers’ open data in a machine-readable and openly accessible format. The next step before the scientists is to adapt the open source notebook to run SCINDR, as exemplified in their prototype.

“The above mentioned ELN is the perfect platform for the addition of SCINDR since it is already acting as a repository of open drug discovery information that can be mined by the robot,” explain the authors.

Once a researcher has their data stored on the ELN, or on any similar open database, for that matter, SCINDR would be able to detect if similar molecules, chemical reactions, biological assays or other features of importance in health research have been entered by someone else. If the robot identifies another scientist looking into similar features, it will suggest introducing the two to each other, so that they could start working together and combine their efforts and knowledge for the good of both science and the public.

Because of its ability to parse information and interests from around the globe, the authors liken SCINDR to online advertisements and music streaming services, which have long targeted certain content, based on a person’s writing, reading, listening habits or other search history.

“The potential for automatically connecting relevant people and/or matching people with commercial content currently dominates much of software development, yet the analogous idea of automatically connecting people who are working on similar science in real time does not exist,” stress the authors.

“This extraordinary fact arises in part because so few people work openly, meaning almost all the research taking place in laboratories around the world remains behind closed doors until publication (or in a minority of cases deposition to a preprint server), by which time the project may have ended and researchers have moved on or shelved a project.”

“As open science gathers pace, and as thousands of researchers start to use open records of their research, we will need a way to discover the most relevant collaborators, and encourage them to connect. SCINDR will solve this problem,” they conclude.

The system is intended to be tested initially by a community of researchers known as Open Source Malaria (OSM), a consortium funded to carry out drug discovery and development for new medicines for the treatment of malaria.

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Original source:

Smith C, Todd M, Patiny L, Swain C, Southan C, Williamson A, Clark A (2016) SCINDR – The SCience INtroDuction Robot that will Connect Open Scientists. Research Ideas and Outcomes 2: e9995. doi: 10.3897/rio.2.e9995

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Guiding EU researchers along the ‘last mile’ to Open Digital Science

Striving to address societal challenges in sectors including Health, Energy and the Environment, the European Union is developing the European Open Science Cloud, a complete socio-technical environment, including robust e-infrastructures capable of providing data and computational solutions where publicly funded research data are Findable, Accessible, Interoperable and Re-usable (FAIR).

Since 2007 The European Commission (EC) has invested more than €740 million in e-infrastructures through Horizon 2020 (the European Union Research and Innovation programme 2014-2020) and FP7 (the European Union’s Seventh Framework Programme for Research and Technological Development). They want to see this exploited in full.

Many research communities are, however, struggling to benefit from this investment. The authors call for greater emphasis on Virtual Research Environments (VREs) as the only way for researchers to capitalise on EC advances in networking and high performance computing. The authors characterise this as a “last mile” problem, a term borrowed from telecommunications networks and once coined to emphasise the importance (and difficulty) of connecting the broader network to each customer’s home or office. Without the last mile of connectivity, a network won’t generate a cent of value.

Some concerns around the transition to Open Digital Science refer to attribution and quality assurance, as well as limited awareness of open science and its implications to research. However, most difficulties relate to many e-infrastructure services being too technical for most users, not providing easy-to-use interfaces and not easily integrated into the majority of day-to-day research practices.

Trustworthy and interoperable Virtual Research Environments (VREs) are layers of software that hide technical details and facilitate communication between scientists and computer infrastructures. They serve as friendly environments for the scientists to work with complicated computer infrastructures, while being able to use their own set of concepts, ways of doing things and working protocols.

Helping them to solve the difficulties noted above, VREs could guide the skeptical research communities along the ‘last mile’ towards Open Digital Science, according to an international team of scientists who have published their Policy Brief in the open access journal Research Ideas and Outcomes (RIO).

The authors state “These domain-specific solutions can support communities in gradually bridging technical and socio-cultural gaps between traditional and open digital science practice, better diffusing the benefits of European e-infrastructures”. They also recognise that “different e-infrastructure audiences require different approaches.”

“Intuitive user interface experience, seamless data ingestion, and collaboration capabilities are among the features that could empower users to better engage with provided services,” stress the authors.

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Original source:

Koureas D, Arvanitidis C, Belbin L, Berendsohn W, Damgaard C, Groom Q, Güntsch A, Hagedorn G, Hardisty A, Hobern D, Marcer A, Mietchen D, Morse D, Obst M, Penev L, Pettersson L, Sierra S, Smith V, Vos R (2016) Community engagement: The ‘last mile’ challenge for European research e-infrastructures. Research Ideas and Outcomes 2: e9933. doi: 10.3897/rio.2.e9933>