Spotlight on preLights - shortlisted for the 2019 ALPSP Awards for Innovation in Publishing

We will be announcing the winner of this year's ALPSP Awards for Innovation in Publishing at the ALPSP 2019 Conference.  In this series, we meet the finalists...

In this post, we speak to Claire Moulton, Publisher at The Company of Biologists, and Mate Palfy, Community Manager for preLights.

Tell us a bit about your organisation.

The Company of Biologists is a not-for profit publishing organisation dedicated to supporting and inspiring the biological community. We publish five journals in the life sciences, we host workshops and meetings and provide a wide range of charitable grants. Community initiatives are important to us, for example we support a long-standing blog (the Node) for the developmental biology community, and our latest community project launched in February 2018 is preLights. preLights is just 18 months but has already gained significant name recognition in the biology community.

What is the project/product that you submitted for the Awards?

We submitted preLights, which is a community platform for preprint highlights. An early-career team selects preprints of interest across the biological sciences, provides relevant comment, and engages authors in further discussion. The preprint highlight and comments are freely available on https://prelights.biologists.com/ .

Tell us a little about preLights and the team behind it.

At the heart of preLights is a team of early-career researchers (called ‘preLighters’) who come from four continents and work in many different research fields. They select which preprints to feature and then highlight the key findings of the preprint. These highlights are somewhat similar to ‘news and views’ articles in that they give a background to the topic and summarize the results in the context of the literature. But preLights posts also have some unique features. For example, the preLighters give their personal opinion on the preprint and directly question preprint authors about their work. The resulting discussions are published at the end of the article – we know that authors find the discussion process useful, as some have provided feedback on resulting revisions to their preprints/ published articles.

A dedicated community manager helps build the community of early-career researchers around preLights, provides them with support, and is involved in evolving and promoting this initiative.

In what ways do you think it demonstrates innovation?

So far there has been very little public commenting happening on preprints, even though preprints could open up discussion of non-peer-reviewed research. preLights promotes such discussions by getting young scientists to write about the work and engaging preprint authors. Therefore, as the first platform of its kind, we believe preLights will change the way in which scientists engage with preprints.

preLights is also innovative in that it builds on a community of early-career researchers, who are often not asked directly by journals to take part in peer-review. preLights gives them an opportunity to hone their scientific writing skills, helps build their profile and credibility, and at the same time harnesses ideas from them for extending the product.

What are your plans for the future?

We have just launched a new feature on the preLights website called preLists in order to further help scientists navigate the preprint literature. These curated lists of preprints follow two main themes: preprints on a specific topic (e.g. CRISPR technology) or preprints which have been presented at a given scientific meeting. Following feedback from the community, we are now planning to make the creation of preLists open to any scientist.

We plan to expand preLights posts into new areas; for example now that medRxiv has launched we expect to have more team members covering biomedical fields.

We also plan to utilize preLights as a platform to provide educational insights into the peer-review process. The posts automatically link to the published version of the article, and we are planning to engage preprint authors to comment on the most important parts of their paper that changed during the peer-review process. We believe this can serve as a useful teaching resource for young scientists and help open up the ‘black box’ of peer-review.

Websites:
https://prelights.biologists.com/
https://prelights.biologists.com/prelists/

Twitter handles:
@preLights
@Co_Biologists

The ALPSP Annual Conference and Awards 2019 will be held at the Beaumont Estate, Old Windsor, UK from 11-13 September. #alpsp19
The ALPSP Awards for Innovation in Publishing 2019 are sponsored by MPS Ltd.

Spotlight on Annotation for Transparent Inquiry - finalist for 2018 ALPSP Awards for Innovation in Publishing

On 13 September we will be announcing the winner of the 2018 ALPSP Awards for Innovation in Publishing, sponsored by MPS Limited, at the annual ALPSP Conference.  In this series of posts leading up to the Awards ceremony we meet our six finalists and get to know a bit more about them.


In this blog, we speak to Nisha Doshi, Senior Digital Development Publisher at Cambridge University Press, Heather Staines, Director of Partnerships at Hypothesis and Sebastian Karcher, Associate Director of the Qualitative Data Repository.

Tell us a bit about your company

One of the things that makes Annotation for Transparent Inquiry unique is that it isn’t the product of one company but the result of a collaboration between three non-profit, mission-driven organizations: Cambridge University Press, Hypothesis and the Qualitative Data Repository (QDR).

Cambridge University Press dates from 1534 and is part of the University of Cambridge; our mission is to unlock people's potential with the best learning and research solutions and we published the first articles that make use of Annotation for Transparent Inquiry (ATI). 

Hypothesis is a non-profit open source technology company, and they provide the annotation tool that powers ATI. 

QDR is a domain repository dedicated to curating, preserving and publishing the data underlying qualitative and multi-method research in the health and social sciences. 

What is the project/product that you submitted for the Awards?

We submitted Annotation for Transparent Inquiry (ATI), which creates a digital overlay on top of content on publisher web pages and connects specific passages of text to author-generated annotations. The ATI annotations include ‘analytic notes’ discussing data generation and analysis, excerpts from data sources, and links to those sources stored in trusted digital repositories. These data sources can be interview transcripts, audio clips, scanned telegrams, maps and so forth – all sorts of different types of material which wouldn’t usually be accessible to the reader. Readers are able to view annotations immediately alongside the main text, removing the need to jump to footnotes or separate appendices.

Tell us more about how it works and the team behind it

A passage of the article is highlighted to indicate there’s an annotation, and the annotations are displayed as a collapsible right-hand panel alongside the content. Each annotation created by the author generates a unique persistent web address for the details and analysis shared with the reader. The passage in the publication is linked to the source material, which is archived by QDR – a trusted digital repository. Readers can also shift into an Activity Page where they can view, search, and filter all of the annotations created on the project. From this page, researchers can explore other portions of the content as well as connected resources.

ATI has been a collaborative effort both within and between our three organisations. At Cambridge University Press, launch of ATI has involved colleagues in editorial, digital publishing, the Cambridge Core platform team and marketing, to name but a few. 

At Hypothesis, with our dedication to supporting researcher workflow through open annotation, input and technical expertise has come from partnerships, marketing, and product development.

And at QDR, transparency in qualitative research is central to our mission and ATI involves the whole team. QDR is run by active researchers, who conceptualized ATI based on ongoing debates in qualitative methods. The repository’s curators provide advice and support to researchers interested in using QDR.

Why do you think it demonstrates publishing innovation?

Recent years have seen significant advances in transparency and reproducibility for quantitative analyses, but progress has much slower for the qualitative analyses central to so much research. ATI brings transparency to qualitative research. ATI allows readers to interrogate qualitative sources in a way that has not hitherto been possible without, for example, travelling to archives or museums to access the original material themselves. It also allows readers to understand authors’ analytic processes in depth, verify their evidence and thus properly evaluate their findings. By utilizing an annotation layer, authors are no longer constrained by word limits and thus can elaborate on aspects of the project which are important to them, providing rich media and additional links as needed.

What are your plans for the future?

We originally launched ATI in April 2018 with eight articles published by Cambridge University Press, followed by a 9^th article published in May. We are now working to integrate ATI with books published by Cambridge, as well as material from other publishers and preprint servers. Although ATI was launched by Cambridge University Press, Hypothesis and QDR, it makes use of open standards and open source technology and the aspiration is that it can go on to be used by different publishers, different annotation tools and/or different data repositories. For example, a further eight articles with annotations on five other publishing platforms are pending publication. The founding partners of ATI are also exploring how best to embed ATI upstream in the research and authoring process.

Lastly (for now), to further promote ATI and explore how authors will conduct research and write with these annotations in mind, QDR launched the “ATI Challenge”. The winners receive an honorarium to help them finalize their manuscript with ATI annotations and, from our point of view, working with those authors in a variety of disciplines and understanding how they want to use ATI will help us further improve workflows, instructions and technology. QDR received more than 80 applications across disciplines in the humanities, social sciences and STM and from across five continents and announced the winning proposals in early August. We believe that the wealth and quality of applications to the ATI challenge shows that Annotation for Transparent Inquiry really does serve a need recognized by qualitative researchers worldwide.

Nisha Doshi is Senior Digital Development Publisher at Cambridge University Press, where she leads the digital publishing team across academic books and journals.

@CambridgeUP
@nishadoshi








Heather Staines is Director of Partnerships at Hypothesis, working with publishers, platforms and technology companies to integrate annotation into their workflow.

@heatherstaines
@hypothes_is






Sebastian Karcher is the Associate Director of the Qualitative Data Repository, where his work focuses on data curation and technological strategy.

@adam42smith
@qdrepository

https://qdr.syr.edu/ati
https://www.cambridge.org/core/services/authors/annotation-for-transparent-inquiry-ati
https://qdr.syr.edu/ati/ati-challenge

The ALPSP Annual Conference and Awards 2018 will be held at the Beaumont Estate, Old Windsor, UK from 12-14 September. #alpsp18

Spotlight on Code Ocean - shortlisted for the 2018 ALPSP Awards for Innovation in Publishing

On 13 September, at the ALPSP Conference, we will be announcing the winners of the 2018 ALPSP Awards for Innovation in Publishing, sponsored by MPS Limited.  In this series of posts leading up to the Awards ceremony, we meet our six finalists and get to know a bit more about them.

In this blog, we speak to Simon Adar about Code Ocean - a cloud-based computational reproducibility platform that provides researchers an easy way to share, discover, and run code.

Tell us a bit about your company

More and more of today's research includes software code, statistical analysis, and algorithms that are not included in traditional publishing. These are often essential for reproducing an article’s research results and for enabling future research. Code Ocean addresses this major roadblock for researchers, and was incubated at the 2014 Runway Startup Postdoc Program at the Jacobs Technion Cornell Institute.

What is the project/product that you submitted for the Awards?

We submitted the Code Ocean platform codeocean.com. The platform offers researchers and scientists the option to upload a working instance of their code and data along with the associated article, at no cost to the researcher.

Tell us more about how it works and the team behind it 

Code Ocean is an open access platform for code and data, which can all be downloaded without charge. In addition, Code Ocean enables users to execute all published code on the platform, eliminating the need to install software on personal computers. Everything runs in the cloud on CPUs or GPUs, according to the user needs. We make it easy to change parameters, modify the code, upload data, run things again, and see how the results change.

Code Ocean was founded based on experiences I had during my Ph.D. Part of my research was spent exploiting airborne and spaceborne multispectral and hyperspectral images for the purpose of environmental monitoring. This meant building on previously published works, but as me and my colleagues got deeper into the project, we faced multiple roadblocks, particularly in trying to get other researchers’ code up and running. We found that researchers develop algorithms, software simulations, and analysis in a wide variety of programming languages (and each language often has multiple versions, creating further compatibility issues). Code also depends on different files, packages, scripts, and installers in order to run properly, and getting all these pieces working is a time-consuming and complicated endeavor that takes away from research. I soon discovered that these “reuse” difficulties were part of a wider problem that many call the  "Reproducibility Crisis" in science. I realized that certain recently developed technologies, properly used and adapted, could help address this crisis led to the founding of Code Ocean.

We are now a team of over twenty women and men dedicated to working with the scholarly publishing community in make code execution easier for researchers, so they can continue building upon their work and the work of others. 

Why do you think it demonstrates publishing innovation?

For the first time, researchers and scientists can upload code and data in any open source programming language (plus MATLAB and Stata) and link executable code with published articles. For many years the scholarly publishing community has been looking to move beyond the PDF, provide interactivity to their users and treat critical artifacts such code and data as first class citizens.  Code Ocean provides self-contained executable ‘compute capsules’ that include code, data, and the computational environment that can be embedded into articles. These compute capsules saves researchers time and allows them to iterate on and interact with code, for instance, bringing  in new datasets, changing variables, and extending existing code. Code Ocean's platform eliminates the need to set up or debug coding environments, allowing researchers to spend more time on their research.

Our current partnerships with the IEEE, F1000, Cambridge University Press, Taylor and Francis, and others demonstrate how embedding executable code within publications provides interactivity, validation, and research transparency. 

What are your plans for the future?

We are continually updating the platform with new features and have a substantial update in the works that will expand functionality for our researchers. One recent development is that researchers can download an entire capsule, comprising its code, data, results, metadata, and a recipe for the complete computational environment. This will allow researchers to use Code Ocean compute capsules outside of the platform on users’ preferred machines.

We are also testing a new peer review workflow with three Nature journals—Nature Methods, Nature Biotechnology and Nature Machine Intelligence— to enable authors to share fully-functional and executable code alongside submitted articles to facilitate peer review.

Simon Adar is the founder and CEO of Code Ocean which was originally incubated at Cornell Tech. He was a Runway postdoc awardee at the Jacobs Technion-Cornell Institute and holds a PhD from Tel-Aviv University in the field of Hyperspectral image processing. Simon previously collaborated with the DLR - the German Space Agency on the European FP7 funded EO-MINERS project to detect environmental changes from airborne and spaceborne sensors.

Website: www.codeocean.com

Twitter:@CodeOceanHQ 

The ALPSP Awards for Innovation in Publishing 2018 are sponsored by MPS Ltd. 

Spotlight on Springer Nature SharedIt - shortlisted for the 2017 ALPSP Awards for Innovation in Publishing

In this blog we talk to Sarah Greaves of Springer Nature about their shortlisted entry to tell us the story behind SharedIt.

Tell us a bit about your company

Springer Nature was formed through the merger of Nature Publishing Group, Palgrave Macmillan, Macmillan Education and Springer Science+Business Media in 2015. It is a leading global research, educational and professional publisher, home to an array of respected and trusted brands providing quality content through a range of innovative products and services. The company numbers almost 13,000 staff in over 50 countries.

Our brands are some of the most trusted and respected in their fields, with Springer founded by Julius Springer in 1842, Nature first published in 1869 and Macmillan Education a leading publisher for over 150 years.

What is the project that you submitted for the Awards?

The project Springer Nature submitted to the Awards is SharedIt. SharedIt is a content-sharing initiative that provides links to view-only, full-text subscription research articles which can be posted anywhere - including on social media platforms, author websites and in institutional repositories – allowing researchers to share research, legally and freely, with colleagues and general audiences.

Tell us more about how it works and the team behind it

SharedIt uses technology provided by ReadCube, part of DigitalScience, to create a readable PDF version of the published paper – but one that cannot be downloaded – and creates a unique ‘SharedIt’ link which authors, and subscribers, can then forward on to other researchers.

Why do you think it demonstrates publishing innovation?

SharedIt is the first initiative by a global STM publisher to encourage authors to promote and use a free sharing facility – meaning anyone can access the published version of record if they have the SharedIt link. By not limiting the amount of times a paper can be shared this increases access to the published literature across the globe and through our own analysis we see many students and post-docs taking advantage of this sharing facility. Authors are also encouraged to share their links on social networking sites knowing that the research community will always have access to the final published version of record.

What are you plans for the future?

We plan to continue developing SharedIt and are currently trialling the use of sharing for books and book chapters. We are also looking into the use of SharedIt for our peer reviewer community. We are keen to listen to the community and expand SharedIt based on their needs and expectations around content sharing.

Sarah Greaves, PhD, is an experienced science publisher at the cutting edge of innovation and product development - having led successful journal launches and numerous other profitable projects in both traditional and new business models. During 18 years at Nature Publishing Group and now Springer Nature, Sarah has moved from being an editor at Nature Cell Biology, to the Nature publishing team; becoming the Nature publisher in 2007.

Since 2010 Sarah has focussed exclusively on innovation and new product launches and drove the launch of open access titles across Nature Publishing Group and has recently launched Recommended, a primary paper pan-publisher recommendation service across the Springer Nature platforms as well as helping to lead the SharedIt initiative.

www.springernature.com/sharedit
https://twitter.com/SpringerNature

See the ALPSP Awards for Innovation in Publishing Finalists lightning sessions at our Annual Conference on 13-15 September, where the winners will be announced. 

The ALPSP Awards for Innovation in Publishing 2017 are sponsored by MPS Ltd. 

Fast Track Content from Author to Reader: Collaborative workflow management systems that work

Rahul Arora, Chief Executive Officer at MPS Limited, draws on many years’ experience, including the development of MPSTrak, a core component of their flagship cloud-based Digital Publishing Platform – DigiCore – that streamlines, automates, and optimizes the publishing process.

In this guest post he considers the need to implement a collaborative workflow management system to manage the complete author-to-reader value chain, and the associated benefits for publishers.

"A publishing workflow is a sequence of activities performed by individuals or groups to make the content available to the reader. Participation is required from the author, editorial team, reviewers, and production staff; with the publisher managing and owning the complete process in near real time.

In the past seven to eight years, much has changed in publishing workflow management. New technology, publishing models, workflows, demand from authors, and growing competition have created a demand for increased automation, efficiency, standardization, faster publishing, global visibility, and cost savings.

Publishers need a flexible and adaptable publishing workflow management system that deals with any existing multiplicity in publishing processes without creating any echo, supports future business workflow requirements, provides global visibility, and allows the business to make any required changes with no or minimum dependency on the technology team.

We have seen publishers struggling with various challenges in their workflows: repetitive data entry in different systems, inadequate data validation, no control on processes, challenges in managing user notifications and reminders, tracking work from author and providing visibility on work status, article-based or custom publishing, issue make-up, schedule management, managing payments, and integrating different internal and external components.

In some cases, publishers had over 30 production workflows, with more than 80% repetition in data entry. The resultant issues and productivity inhibitors with apparently simple looking processes would see staff doing something in a far more complex way than was necessary.

When we start to work with clients, we always carry out a “workflow discovery” workshop at the start of each system implementation. Invariably we find that many times staff don’t have a strong rationale behind following the existing process steps. The response to most of questions turns out to be “Someone asked us to do this way and we never thought too deeply about it”. In addition, there are always loose boundaries between editorial and production work and different teams doing the same things in different ways.

We recommend publishers adopt an automated workflow system through a capable and experienced partner without waiting for the struggle to peak and creating barriers in growth.

Because one thing remains true: successful organizations, the ones that ‘disrupt’ the old guard, are the ones that have figured out an end-to-end creative process that enables them to beat their competition.

The major things to consider are the platform’s flexibility to incorporate changes and a knowledgeable team that can lead and drive change. We advise clients to expect:

• Intuitive user interface with global visibility across the publishing process 
• Faster time to market 
• Increased transparency between publishing process stakeholders 
• Support for flexible business models 
• Increase in staff work handling capacity.

We were delighted to hear from one of our customers who reported absorption of three year growth in production volume without adding any production staff when they implemented MPSTrak. Another reported a 46% increase in article-handling capacity of a production editor. Whichever system you work with, make sure it helps you deliver the capacity, flexibility and adaptability to deal with an increasingly complex publishing workflow."

Rahul Arora is the Chief Executive Officer at MPS Limited. He graduated from Babson College, Massachusetts and has a MBA from the Indian School of Business in Hyderabad. Rahul led the transformation of his family’s print-focused publishing business to a larger, professionally-driven B2B media enterprise. He has led and grown some of Gallup’s most innovative consulting partnerships in the APAC region. As CEO of MPS, he manages the current operations in India and the United States, while continuing to actively engage with their client base.

MPS Limited has provided platforms and services for content creation, full-service production, and distribution for over 46 years. The business division, MPS Technologies, is a leading partner for global publishers and caters to the rapidly changing technological requirements of the publishing workflow. MPSTrak is a core component of their flagship cloud-based Digital Publishing Platform – DigiCore – that streamlines, automates, and optimizes the publishing process.

MPS Limited are sponsoring the 2016 ALPSP Awards for Innovation in Publishing. The winners will be announced at the ALPSP Conference 14-16 September. Book now and follow #alpsp16 #alpspawards for details.