PART 2: The ARPHA Writing Tool: Adding Value to RIO

Last week, we presented some basic features of the ARPHA Writing Tool (AWT), focusing on the collaborative authoring process. This post will add the novelties that ARPHA has adopted when it comes to submission and post-submission processes.




Checks are a must whenever high-quality, professional writing is concerned. Shortly before submitting their manuscripts via ARPHA, the authors are free to initiate the first step of the validation process at any time. As a result, an automated technical check runs through the manuscript to verify its consistency and compliance with the JATS (Journal Article Tag Suite) standard as well as key elements of the journal’s policy.

After the automated checks, there is a second-layer of human checks made by RIO editorial assistants in order to bring the manuscript to a pre-publication level. They check compliance with further elements of the journal’s policy as well as linguistic consistency and work with the authors before finalising it altogether.



Even after submission, collaboration continues. With the peer-review stage being as transparent and open as the whole vision of RIO is, this step is no less straightforward and organised. All peer reviews are automatically consolidated into a single online file that makes the editorial process simple and pleasant. This is made possible by the XML-based workflow in the AWT.


PEER-REVIEW evolution:

Last week, we mentioned that an author can invite reviewers during the authoring stage itself. Let us elaborate here by saying that the ARPHA Writing Tool provides a functionality for pre-submission peer review(s) performed during the authoring process. These peer reviews are submitted together with the manuscript, so that the editorial evaluation and publication can be significantly sped up.

Post-publication UPDATES:

Even after an article is brought to life, ARPHA continues to play a role in it. Because of the XML workflow, authors are able to publish updated versions of their articles at any time. Once they request such an update, their work is returned to the ARPHA Writing Tool, where authors and peers are to collaborate once again. Eventually, the two versions are linked via CrossMark, so that nothing is lost.   

As you might have already noticed, just like RIO, the new ARPHA Writing Tool is constructed entirely around the needs of its authors. Why not find out yourself by giving ARPHA & RIO a try when they open for submission early next month?


PART 1: The ARPHA Writing Tool: Adding Value to RIO

The online, collaborative ARPHA Writing Tool (AWT) is an innovative, entirely Web-based, authoring, submission, peer-review, publication & dissemination authoring platform. While flexible to accommodate more traditional journal concepts, it clearly fits neatly with RIO’s novel approach to research publishing.

In the following two-part blog post, we will explain how the newly updated AWT will be integrated with RIO to provide a number of great features for unique user-experience.

ARPHA_part_1 (2)

All About User Friendliness:

The ARPHA Writing Tool did not appear out of nowhere. Pensoft has been developing its own writing tool since 2012, and the AWT is an updated version of this prototype, the Pensoft Writing Tool. The AWT builds onthe experience we have accumulated during the 3-year lifespan of its predecessor, and is designed to make the user experience as seamless and pleasant as possible.

How we did that? The AWT features a modern and intuitive design, where all features are listed and just a click away for the authors to use. The tool runs in one mode, showing real-time changes, comments and updates. Comments are left inline and automatically navigate through the text to make review and correcting easy.

awt-screen-shot (2)


RIO is all about collaboration, and within the ARPHA Writing Tool, this is now easier than ever. Authors can not only work collaboratively on a manuscript with their co-authors, but can also invite external contributors, such as mentors, pre-submission reviewers, linguistic and copy editors, or just colleagues, who may modify the manuscript or comment on it before submission. The system allows for such external contributors to not be listed as co-authors of the manuscript.

ARPHA_part_1 (3)

The collaborative peer-review process provides easy communication through track-change functionality, comments and replies, and automated, but customizable email and social network notification tools.

TEMPLATES for all needs

The AWT provides a large set of predefined, but flexible article templates covering many types of research outcomes. At the moment, the list fits the needs of the existing Pensoft journals, but with RIO coming soon, the choice of templates will grow to accommodate the needs of publishing full research cycles across a wide range of disciplines.

ARPHA_part_1 (4)

Adding CONTENT and REFERENCING made easy

A set of Web-based services and tools in AWT allows, e.g. for search and import of literature or data references, cross-referencing of in-text citations, import of tables, upload of images and multimedia, assembling images for display as reusably composite figures,  and even add videos to your article.


All the author needs to do to add content to an article is to select the right type from the side menu and then navigate through the instructions in the pop-up window. If in doubt, the authors can also consult the ‘Tips and Tricks’ on our website.

So far, we have explained some of the main features of the AWT that are useful throughout the authoring process, but there is much more to explore! In next week’s post, we will look at what happens after your manuscript is completed and ready for submission.

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!

RIO will emphasise the social impact of research

Most funding agencies now require researchers to specify and think about the broader, societal impacts of their proposed research. This makes a lot of sense, since approximately 80% of research is publicly-funded either by governments or charities.

Thus, the outputs of most academic research should ideally make some kind of contribution towards wider societal impact, even if tenuous or long-term.

Here at RIO, we don’t think the potential societal impact of research is well surfaced by most traditional journals, and this is something we’d like to improve upon. So, as one of the many innovative features of RIO, we’re going to experiment with social impact labelling and categorization of research outputs based upon internationally-recognised external criteria such as the EU Societal Challenges (the priorities of EU Horizon 2020 funding), and the United Nations’ Sustainable Development Goals (SDGs). Recognizing that the mapping of a given piece of research to such impact categories may be difficult at times, we strongly encourage the use of this feature, but do not require it.

E SDG Poster_A4

More detail about the UN SDGs is available at: . This image is copyright of the United Nations Department of Economic and Social Affairs. Permission for re-use is granted by the UN.

How will it work, in practice?

SDGs on RIOAuthors will have the option to choose societal impact badges from a preset list provided by RIO (see the Filter image for an example). The badges indicate impact categories that are or may be relevant to their submitted work. Reviewers and editors can assess the appropriateness of these badges, and if accepted, these badges will be pinned on the published output, so that they are clearly seen on the landing page of the work.


We think this will benefit authors, readers and funders of research.

  1. For Authors: It will better advertise the intended societal impact of their work – sometimes this can be quite indirect, so we think this expressive labelling will aid the recognition of potential social impact.
  2. For Readers: It will hopefully encourage more interdisciplinary reading. When searching for work relevant to ‘Zero Hunger’ (SDG #2), articles from vastly disparate subject areas will be more cohesively surfaced: social sciences, biology, chemistry, and engineering may all be relevant here, amongst others. Outputs from these different disciplines will no longer be siloed away from each other in vastly different journals.
  3. For Funders: Interesting research outputs that are relevant to specific societal challenges, some of which may be ideas not yet funded(!) may now be more clearly and relevantly presented.

Enabling the filtering of a diverse range of research ideas and outcomes by societal impact is thus clearly desirable, and while RIO is the first to implement such a system, we would encourage the wider community to join us in highlighting the connection between research and societal impact more systematically.

Do you want the potential societal impact of your research to be more clearly signalled to the world upon publication? Submit your research to Research Ideas & Outcomes (RIO) – we’ll start accepting submissions in November.  

P.S. The RIO team listens to constructive feedback on the journal from the global community. We are therefore delighted to acknowledge and thank our advisory board member Susan Reilly (LIBER) and Stuart Hamilton (IFLA) for emphasising the UN Societal Development Goals. We have taken that on board and will be using these and other internationally recognised societal goals as the basis for societal impact labelling at RIO.

Peer Review at RIO: Part 2

Having explained our pre-submission peer-review last week, in this post we’re going to explain our post-publication peer-review.

Why use open post-publication peer-review?

  • Removes unnecessary delay
  • Provides much needed transparency

Most journals use post-submission peer-review and only make the work public online once this process is completed. This results in long delays before the work is made public, often many months or even years in the worst cases. These publication delays (see figure below) are largely unnecessary: making a work public and operating a peer-review process on that work are two separate processes that do not need to interfere with each other.

publication delays chart


Daniel Himmelstein (2015). Publication delays at PLOS and 3,475 other journals. Zenodo. 10.5281/zenodo.19117 Licensed under the Creative Commons Attribution License.

By publishing almost immediately after pre-submission review, RIO Journal will help researchers establish the priority of their research outputs. We aren’t the first to use this system: F1000Research have been successfully using post-publication peer review since 2012 and everyone including PubMed accepts the validity of articles published this way.

Why is open reviewing a good idea?

Very few think that single-blind reviewing is optimal. Some think that double-blind reviewing results in fairer outcomes but we believe that this only treats the symptoms and does not address the causes of improper or poor reviewing. At RIO Journal, all post-publication reviews will be open, in addition to pre-submission reviews which go public as well – there will be no option to provide non-public review, pre-submission or post-publication. Furthermore, all reviews will be made available under the Creative Commons Attribution License (CC BY), so that the reviews are open access and attributed to their authors, just like the published works.

Again, it’s important to note that open and published reviews are not a radical ‘new’ thing in some subject areas. For instance, the British Medical Journal (BMJ) has identified reviewers since 1999, and Biology Direct has been successfully using open and published peer-review since 2006. For subject areas where open, published peer-review is a novel concept we suggest – try it for yourself with us!

Open and published reviews have benefits for both authors and reviewers – this is particularly important to consider given that reviewers do their work as an unpaid service to scholarship. To be able to have a citable, open record of contributed reviews, it is desirable to provide small and impartial reward for reviewers.

How does it work?

The main difference in our model of open post-publication review from those used by other journals, for example F1000Research, is that:

  • Post-publication review at RIO is just the 3rd step of checks on a manuscript. The first step is the pre-submission peer-review (see our previous blog) while authoring, the second is the technical and editorial evaluation in-house. The result of all this is that authors have the chance to revise and improve their manuscripts several times.
  • After a manuscript is published, the authors have the option to request  journal-arranged post-publication peer-review and editorial validation or to keep the publication in its first version, submitted and published after pre-submission review and technical/editorial checks.
  • Authors can also decide at any point to request publication of revised versions. So, they have the chance to improve their works if post-publication reviews are negative.  Only RIO Journal editors can provide the stamp of Validation on an output once sufficient, acceptable post-publication reviews have been received.

post-publication peer review chart

Next week we will blog about our plans for societal impact labelling on outputs to facilitate cross-disciplinary reading and collaboration. If you have any questions in the meantime, please don’t hesitate to contact us via the comments section, Twitter @RIOJournal, or via email.

Peer Review at RIO: Part 1

In this post we shall explain our much anticipated use of pre-submission peer-review.
This is not the only model of peer-review we will operate. Next week we will explain our post-publication peer-review.

You may be asking yourself – how can peer-review happen before submission?

This is a good question. Almost all traditional journals only arrange for peer-review to happen after submission. Manuscript review, immediately prior to submission can take place at RIO because of our unique authoring platform: ARPHA.

We think this will fit-in well with the normal research practices of many, as researchers often send off manuscripts to colleagues immediately prior to submission for checking with ‘a fresh pair of eyes’ anyway. All RIO seeks to do is to make this natural process more formal and transparent. Indeed, why spend so much precious time on pre-publication review and revisions, when this work could be done in an user-friendly online collaboration environment still during the authoring process?

The concept is this:

  • The author(s) write or load their documents in our what-you-see-is-what-you-get writing tool: ARPHA
  • When they think it is ready, they ask one or more colleagues to read the work and give a basic assessment of whether it is fit-to-publish in it’s current form. ARPHA provides Google Docs-like functionality for making inline comments and highlighting as well as ‘general’ comments.
  • This colleague (the pre-submission reviewer), logs into ARPHA from their own account, reads the work on ARPHA, and fills out a simple form declaring the work worthy of being made public to the world in RIO.
  • Final review statement and the name of the colleague is made public alongside the work after publication.

RIO will not publish outputs that it thinks are pseudoscience, that have unresolved ethical issues, or are otherwise not appropriate for an academic journal. This applies even if a pre-submission reviewer thinks that the output is ‘OK’ for publication. Checks by RIO technical and subject editors are performed both before and after submission to the journal, if serious problems are found, publication may be prevented.

For clarity, we have produced a diagram of the proposed pre-submission workflow below.

pre submission workflow diagram

Outputs that must undergo pre-submission peer-review include:

Research Articles, Review Articles, Replication Studies, Methods, Case Studies, Opinion Articles, Data Papers, Questionnaires, and Software Descriptions.

Outputs for which pre-submission peer-review is optional include*:

Research Ideas, Research Proposals, PhD Project Plans, PhD Theses, Small Grant Proposals, Grant Proposals, Data Management Plans, Software Management Plans, Single-figure publications, Research Posters, Research Presentations, Conference Abstracts, Correspondence, Project Reports, Policy/Communication Briefs, and Wikipedia Articles.

Next week, we will blog about our processes for post-publication peer-review. If you have any questions in the meantime, please don’t hesitate to contact us via the comments section, Twitter @RIOJournal, or via email.

*Even though pre-submission review is optional for a few manuscript types, the authors will be strongly encouraged to seek peer-review.

Counting days and tweets: What’s happened to RIO Journal so far?

So, here we are, counting days and Twitter impressions since Research Ideas & Outcomes (or, RIO for short) our new open access journal was officially announced on 1st September 2015. As much as we were excited to take this long-prepared and anticipated stand in the spotlight, we are still holding our breath ahead of the big event – the launch itself, scheduled for November 2015.

In the meantime, when not busy welcoming our very first subject editors, we have our ear to the ground, so that we can make sure to provide everyone with the best services and insight. The truth is, we don’t only value attention, we deeply appreciate your opinion and respect your needs and concerns.

So, here below we provide a short summary of the eventful first week of RIO Journal:

It all started on 1st September on Twitter. Among the constantly growing list of our first followers, there were a lot of welcoming retweets, sounding just as excited as we were:

Then, the time came for the world media to give its verdict:

This week sees the birth of a new type of scientific journal, one that will publish not only study results and data, but also research ideas and proposals. It’s called Research Ideas and Outcomes (RIO).
/The Scientist, 3rd September/

With so many science journals already in existence, it is rare for a new title to draw attention. But researchers and publishing experts are taking notice of Research Ideas and Outcomes, or RIO, an open-access journal that launched on 1 September.
/Nature, 3rd September/

Understandably, the hottest discussion points were RIO’s initiatives:

> To present openly the whole process of the research cycle especially including research proposals
> To publish such ideas regardless of them being eventually approved or rejected for funding
> To apply a transparent, public, and open peer-review policy

Stephen Curry, a structural biologist at Imperial College London shared on Twitter that in his opinion RIO is “bringing a new sense of transparency and collaboration to research”, while he voiced his strong support for preprint publications and open feedback in his Guardian blog. “Preprints can help to refocus attention where it matters – on the work itself, not where it is published. In so doing, they have the potential to revitalize the scientific enterprise”, his column reads.

“I like the idea of getting “publishing-credit” for my research proposals and other research output. Roughly speaking for every proposal I write, I write one paper less”, points out computational chemist at the University of Copenhagen Jan Jansen on explaining why he accepted the invitation to become one of RIO’s subject editors.

At the end of the day, some of RIO’s innovations couldn’t escape being challenged by some criticisms. A librarian and known extreme critic of open access journals, Jeffrey Beall questioned the freedom given to RIO’s authors to make their own choice of reviewers.

One of the RIO’s own subject editors, Ivo Grigorov, a marine scientist at the Technical University of Denmark also raised his concerns on the matter. Yet, he and our ever growing list of editors and advisory board are sticking with us:

In his turn, Ross Mounce, a postdoc at the Natural History Museum, London and a founding editor of RIO, explained how the new open access journal seeks to improve the “immensely wasteful” traditional research process in his piece on the popular LSE Impact blog.

Ross also gave a podcast interview for Beta Pleated Chic, he spoke in detail about the whole list of innovative tools and strategies.

If you know of any other press mentions or blogs about RIO Journal, please don’t hesitate to forward them to us on Twitter @RIOJournal.

Opening-up the early stages of research – LSE blog about RIO

Research Ideas & Outcomes (RIO) is now featured on the LSE Blog and here is what we shared with them.

Few like to admit it, but the traditional process of research is immensely wasteful. Inefficiency occurs in every part of the research cycle, perhaps none more so than the research proposal stage. For example, nearly 90% of EU Horizon 2020 grant proposals were rejected. Many of these proposals are extremely good works, written by teams, over many months of work. Significant effort goes into crafting research proposals, yet as research outputs in themselves, they are hugely under-utilised. After the proposals are scored and either funded or not funded, typically via closed processes, what happens to these documents? Most stay hidden, never to be seen again, regardless of whether they were funded or not

What if we treated proposals like other outputs of the research cycle: like data, like software, like research articles? What if we published proposals in a journal, regardless of whether they were funded or not, to enable the citation of ideas not yet tested, to foster collaboration, to demonstrate the quality of proposed research, and to help others see what good proposals look like…

Launched yesterday, a new journal called Research Ideas & Outcomes (RIO) has been created specifically to enable and encourage the entire research cycle to be published, from start to finish, specifically including research proposals and ideas; the earliest stages that rarely get published (see the video below for more explanation).

Efficient publishing technology does away with the need for typesetting

The innovations provided by RIO journal do not stop there though. Another of the major features of the journal is its authoring, reviewing and publishing system called ARPHA for short. This system is a revolution in itself: if used fully, it eliminates the need for an outsourced typesetting process and all the associated errors that entails which frustrate authors and delay publication. It also speeds up the publishing process; no delay waiting for typesetters, and it reduces the cost of production as good typesetters charge a non-negligible sum per page.

I remember only too well getting manuscript proofs back from a different publisher and seeing that the typesetting process had converted the word ‘Phylomatic’ into ‘phlegmatic’ (see tweet above) – the latter word was not in any submitted author version! This error had been introduced by mistake during the shadowy typesetting process, something publishing companies typically keep very quiet about as it’s a remarkable inefficiency in the publishing process. Typesetting is arguably an anachronism and doesn’t need to exist if authors use tools that are specifically designed to produce structured academic outputs. Don’t take my word for this: memorably, Dr Kaveh Bazargan, who runs a high-quality, successful typesetting business (River Valley) stood-up at a conference in 2012 and said of typesetting: “It’s madness. I’m here to say I really shouldn’t be in business”.

Pensoft have cracked the authoring tools problem with a solid solution that has been successfully developed & tested with the Biodiversity Data Journal and shown to be a robust system. By combining the ARPHA publishing system, with a broad subject-scope, a philosophy of publishing the entire research cycle, and low cost open access publishing, I genuinely think RIO journal offers a distinctive and attractive option for authors, significantly better in production workflow than most other journals. Alongside Dr Daniel Mietchen, I am proud to be a founding editor of this visionary new journal.

Originally posted in the LSE Blog at:

All you can publish: go à la carte with Research Ideas and Outcomes Journal (RIO)

Science is Awesome!

This is something we truly believe in at Pensoft.

But, like everything in this world, science needs funding to sustain itself. Out there, some great minds are turning countless ideas into research proposals every year, yet only a small proportion would eventually get funded.

Sadly, most of the time few get to hear about a particular idea if it gets rejected.

RIO Journal – get credit for all your work

The Research Ideas and Outcomes (RIO) journal is created to provide a positive enhancement to a frequently inefficient funding system.  

RIO publishes all outputs of the research cycle: starting from the project proposals, through to data, methods, workflows, software, project reports and research articles. And it all comes together on a single collaborative platform, encompassing all areas of academic research, including science, technology, humanities and the social sciences. Learn more about our vision in the RIO video.


Why publish a research proposal?

Behind a proposal there’s always:

  • a good idea,
  • long hours of research
  • huge collaborative effort by scientists.

But when it comes to funding decisions, it all turns to a pile of paper with either an approval or rejection stamp on it. Wafer-thin decision margins mean that great projects often don’t get funded at the first time of asking.

We created RIO as an alternative that allows scientists to get credit for their ideas as citable publications. Thus, they can share the outcomes from the vast research effort spent on producing non-traditional research outputs such as proposals that are otherwise lost to science and society.

All published ideas and outputs on RIO have public article level metrics and comment sections – so the stamp of approval is now in the hands of the real end users: the community.

New thinking: science for society

The journal takes a step ahead with a collaborative platform that allows all ideas and outputs to be labelled with Impact Categories based upon UN Millennium Development Goals (MDGs) and EU Societal Challenges.

These categories provide social impact-based labelling to help funders discover and finance relevant research.

Application FormAs RIO publishes research from across a wide range of disciplines, it is expected that the new Impact Category labels will help the journal to foster interdisciplinary research, allowing scientists from different fields to have their work discovered in novel-ways beyond traditional disciplinary boundaries,  providing real value for society. RIO is currently actively looking for editors from across disciplines, fill in a simple Editor Application Form and join us!

Innovation non-stop

RIO offers the most transparent, open and public peer-review process thus building trust in the reviewed outcomes.

The journal is published through ARPHA, the first publishing platform ever to support the full life cycle of a manuscript, from authoring through submission and public peer-review to publication and dissemination, within a single, fully-integrated online collaborative environment. RIO launches several innovative publishing features – a comprehensive list of these is available here.

And all that comes a-la-carte

Through RIO and ARPHA you can tailor our services towards your needs.

For a long time publishers ‘dictated the rules’ for the products and services that researchers  get. At Pensoft we believe in the opposite –  scientists, funders and communities should dictate to us their needs and we should aim to provide products and services to cover those needs.

Following this philosophy, at RIO you can choose exactly which publishing services you want according to your needs and budget.

You can write a manuscript in the RIO authoring tool, or submit it in other formats. Authors can also supply as many pre-submission reviews with your manuscript as you want and choose the style of peer-review that is appropriate for their output. They can also opt in and out from a number of additional services, such as proofreading or the services of our press office and many more. All options are available here.

Join us in the future

From the get-go Pensoft has always aimed to revolutionise the publishing field supplying authors with the latest innovations.

With RIO we are actively looking to expand. Not just in scope, by servicing all areas of academic research, including science, technology, humanities and the social sciences. But also to expand the mindset of a system haunted by old-fashioned prejudices.

RIO smashes the status-quo by publishing ALL research ideas & outcomes that constitute the research cycle, including: project proposals, data, methods, workflows, software, project reports and research articles. It’s simply a more accurate reflection of the real process of research.

All this supported by the latest innovations and tailored to your needs!

Visit the pre-launch webpage at: