Wednesday, 5 September 2018

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.


graphic Annotation for Transparent Inquiry


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 9th 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.




photo Nisha Doshi
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






photo Heather Staines

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

@heatherstaines
@hypothes_is




photo Sebastian Karcher

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

Friday, 31 August 2018

Spotlight on IP Intrusion - shortlisted for the 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 ALPSP Annual 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.


logo IP Intrusion

In this post, we speak to Andrew Pitts, a partner and co-founder of PSI Ltd.



Tell us a bit about your company


PSI is the brainchild of two veterans of the publishing world who, between them, hold over 40 years of STM publishing experience. It was while working for major publishers that they recognised a number of problems facing the industry that could only be overcome through communication, collaboration and innovation. PSI is an independent company. Through our work to enable publishers, membership societies, and libraries to work together securely and confidentially towards common goals, PSI has found itself in a unique position to encourage collaboration across the academic research community.

PSI is the developer of both the IPregistry.org and IP-intrusion.org and also the STM endorsed Due Diligence Bureau. With the IPRegistry.org, publishers and libraries can save time and streamline processes, eliminate errors, improve the reliability of usage metrics and ensure the right content is accessible to the right users.
With 
IP-intrusion.org publishers, and soon libraries, can join the community driven fight against cybercrime. With the Due Diligence Bureau publishers can demonstrate compliance and protect their reputation.

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


The product we submitted for the innovation award is our IP Intrusion Service database. PSI’s IP Intrusion Service is a community liaison hub where publishers and libraries can exchange information and warn each other about threats via IP-intrustion.org in REAL time.


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


PSI’s IP Intrusion Database is a new tool that will help both publishers and libraries by preventing intrusions of their secure IT systems. This new service will help protect publishers’ copyrighted content, universities’ intellectual property, and researchers’ personal data and identities. With the IP intrusion service, the academic research community can work together to fight against hackers, spammers, password crackers, scrapers and, most importantly, it will combat piracy and spear-phishing attacks. The PSI IP Intrusion Database exposes cyber-crime across the academic research community, with the added benefit of reducing service interruptions resulting from these malicious threats.  

PSI IP Intrusion Database was developed by PSI Ltd in collaboration with the AAP (American Association of Publishers) and a number of major STM publishers including IEEE, AMA, AWS, Taylor and Francis, SAE, Elsevier, ASME and ASTM. The service has been built using software developed by technology partner, Adactus Ltd.


Why do you think it demonstrates publishing innovation?


PSI IP Intrusion Database allows publishers and libraries to share detailed information about intrusions so they can protect themselves from future threats. Each day users of the service receive details of the latest intrusions across the industry allowing them to block the attacks at source.

graphic IP Intrusion threat notifications

As well as providing users with a block list, the database also cross-references activity against the 1.5 billion verified IP addresses held within theIPregistry.org for over 60,000 academic institutions, in effect the most comprehensive “white list” of verified institutional data available. This information is used to alert publishers that the attacks are being made via a legitimate organisation, allowing them to treat these intrusions differently, for example, by reaching out to the library before blocking access. Libraries can then be asked to review logs to determine the level of intrusion, alert users that credentials have been compromised and determine what may have been stolen. The IP-intrusion steering group will be able to assess all attacks on a regular basis in order to evaluate potential opportunities for group action.


graphic IP Intrusion

Libraries using the service are alerted in real time to breaches involving their IT systems. They will be prompted to investigate the real source IP of the intrusion and to share these details so that other libraries and institutions can block cyber-attacks from these sources before they even happen.

What are your plans for the future?


Th PSI IP Intrusion Database offers the academic research community a unique opportunity to work together to fight all forms of cyber-crime. Every intrusion reported within the database will provide the academic community with an opportunity to fight back. Having the IP-intrusion steering group evaluate all attacks on a regular basis will enable the community to take group action much faster. This will give the industry an opportunity to think ahead and try to stay one step ahead of the cyber-criminals. The consequences of not protecting published content, intellectual property, and personal data do not bear thinking about.


photo Andrew Pitts
Andrew Pitts is a partner and co-founder of PSI Ltd, he has worked in the field of STM publishing for over 20 years and has worked closely with most of the major STM publishers during that time.  

Websites:

Twitter: @PubSolutionsInt, @ip_registry


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

Tuesday, 28 August 2018

Spotlight on Kopernio - shortlisted for the 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 ALPSP Annual 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.

logo kopernio

In this blog, we speak to Ben Kaube, co-founder and Managing Director of Kopernio




Tell us a bit about your company. 


Kopernio is the brainchild of Jan Reichelt and myself, the co-founders of Mendeley and Newsflo, respectively. The idea for Kopernio came to me whilst I was writing up my PhD. I was working at home and in cafes and was growing frustrated at having to repeatedly log into various platforms over and over again in order to access papers.

On one hand, I could easily play any song I wanted in Spotify, but found myself with 40 browser tabs open to access all the papers I needed. It occurred to me that this was a wider problem – in fact some 10 million researchers worldwide endeavor to access 2.5 billion journal articles each year. It was then that we started thinking about how much more convenient it would be if there was a tool to access papers with a single click, wherever you are.

Kopernio does just this. It alleviates the hassle researchers currently have “hunting” for journal-article PDFs across the web. Kopernio eliminates the frustrating clicking, link chasing, and waiting on redirects and re-authentication delays that researchers currently face, and allows academics to spend more time focusing on their research. 


What is the project or product you submitted for the awards? 


Kopernio gives researchers one-click, legal access to journal articles anywhere and anytime. Kopernio’s aim is to create the definitive publisher-neutral platform for accessing research for scientific researchers, publishers and institutions worldwide. Through Kopernio, publishers are able to deliver their content, both subscription and OA, direct to researchers wherever they happen to be. Our vision is to dramatically improve and facilitate access to scientific knowledge.


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


Despite the millions invested by libraries in content and discovery solutions, journal articles are often not conveniently available to researchers at the point of need. As such, researchers are often forced to follow circuitous and time-consuming routes to access journal articles, and often don’t end up with the publisher’s version of record. This problem is compounded by the fact that typical researchers use 20 or more different online platforms each month as part of their literature discovery and access workflows.

Not only do these barriers waste time and cause frustration, they are stifling the pace of scientific innovation. If 10 million researchers spend an hour per year (a very conservative estimate!) trying to navigate clunky paywalls and university login pages just to read a few articles, it equates to 10 million hours (or 416,667 days) per year of wasted time that could be better used in actually conducting research.

Rather than trying to funnel users into “yet another destination site,” Kopernio enhances established workflows and travels with the researcher as they search and discover journal articles across 20,000 online platforms including discovery platforms, repositories and even scholarly collaboration networks.


Kopernio co-founder and new Managing Director for Clarivate’s Web of Science, Jan Reichelt discusses how Kopernio helps solve a major pain-point for 10 million researchers globally.

Kopernio integrates with existing institutional authentication systems to surface subscription content at the point of need for the researcher. This is done in a consistent and convenient user experience across many different platforms, and both on- and off-campus.
In April 2018 Kopernio was acquired by Clarivate Analytics, a data and analytics company with a desire to collaborate and solve problems across the research ecosystem.


Why do you think it demonstrates publishing innovation? 


Kopernio automatically detects institutional subscriptions a user already possesses and facilitates one-click access to these, giving convenient access to the publisher’s version of record across 20,000 platforms.


Kopernio co-founder and new Managing Director for Clarivate’s Web of Science Jan Reichelt on Kopernio’s benefit for publishers.

This is useful for researchers, who benefit from having professionally typeset, citable articles which are sure to contain all corrections from peer review (which is important for reproducibility). Publishers see increased utilisation of content (both OA and subscription) and can identify and meet new demand for their content. Both libraries and publishers can better understand journal usage and how the content needs of researchers can best be served. 


What are your plans for the future? 

Kopernio complements Clarivate's existing digital product portfolio, which is used by millions of researchers. The scale, reach and unique data at the heart of Web of Science, combined with the Kopernio researcher-facing platform, will allow us to build novel tools which we hope will delight researchers and support them as they work on some of society’s most important problems.

The future will see the investment and scaling of Kopernio and the integration with other Clarivate products and services. This will enable us continue building tools which we hope will delight researchers, and develop the business by building out commercial offerings for publishers and academic institutions.


Ben Kaube is a co-founder and the Managing Director of Kopernio, acquired by Clarivate Analytics in 2018. He obtained his PhD in computational physics from Imperial College London in 2017 and previously founded research 


Website: https://kopernio.com
Twitter: @kopernio @clarivate 

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

Friday, 24 August 2018

Spotlight on JPPS - 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.

logo JPPS
In this post, we speak to Sioux Cumming of INASP, and Susan Murray of African Journals Online (AJOL) about Journal Publishing Practices and Standards (JPPS).


Tell us a bit about your companies


INASP is an international development organisation with over 25 years’ experience of working with a global network of partners in Africa, Latin America and Asia. Research and knowledge have a crucial role to play in addressing global challenges. Many of these challenges affect the Global South most acutely, but we believe that these challenges will not be addressed without Southern research and knowledge.

To realise this potential, we strengthen research and knowledge systems by addressing issues of power and supporting individuals and institutions to produce, share and use research. Broadly speaking, we have six areas of work: academic publishing; evidence for policy; gender & equity; higher education & learning; information access; and research communication.

African Journals Online (AJOL) was the first JOL platform and has been managed by a South African non-profit organisation of the same name since 2005. AJOL provides a highly visible online library of African-published, peer-reviewed scholarly journals, allowing global access to the research output of the continent. AJOL also works with journal partners throughout Africa to facilitate their capacity building in publishing best practices, and provides various technical services that many journals might not be able to afford or implement on their own. 

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


Journal Publishing Practices and Standards (JPPS) was established – and is managed - by AJOL and INASP to provide detailed assessment criteria for the quality of publishing practices of Global South journals.  
Northern journals dominate global research, leading to an underrepresentation of knowledge from the South. Championing Southern journals is essential for redressing imbalance in the dissemination of global research.
JPPS levels give readers assurance that the journals meet an internationally recognised set of criteria. The detailed feedback from the JPPS assessment helps editors identify ways to improve their publishing practices and standards.  

The initiative and its first awards have been widely welcomed by Southern journal editors and have already prompted significant improvements. 

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

image logo JPPS badge

The JPPS assessment process evaluates these journals based on 108 internationally accepted criteria. The result is one of six badges that are displayed on the official JPPS site and on the JOL platforms. These badges give guidance and reassurance to researchers as they are choosing which journals to read, cite and publish in.

image editor at deskBut JPPS goes further than this: the other output of the assessment process is a detailed, customised report for each journal editor highlighting the areas of journal publishing that could be improved. This feedback is supported by the Handbook for Journal Editors, which gives practical guidance on things like how to run editorial processes, communicate with authors, and improve a peer review system. 

Why do you think it demonstrates publishing innovation?


JPPS has several important, unique features. Firstly and crucially, JPPS isn’t just a metric; it’s also a framework to help improve quality. The aim of JPPS is to increase equity in global publishing and to help this by recognising and supporting legitimate journals. The detailed reports from JPPS are intended to not only highlight what is missing but also to help journals to improve.

It was developed in consultation with journal editors in Africa and it recognises the contexts that these editors operate in, and provides support and guidance appropriate to the contexts. However, although the focus is on the Global South, the standards expected in JPPS are global ones; journals awarded JPPS stars will have publishing standards and processes similar to other journals around the world.

What are your plans for the future?


On the technical side, we are working towards an online form (and database) to streamline the assessment process. This would be a tool that new journals could use in applying to join a JOL platform and also that journals already on the platforms could use in their applications for reassessment. 
Extensions to JPPS might also include going beyond the JOLs platforms in partnership with other journal platforms. In addition, we hope to roll out a full online course in journal quality following feedback and refinement from a recent pilot. 

AJOL and INASP have been grateful for funding and encouragement from Sida and DFID over many years to support the development of the JOLs platforms and, more recently, the JPPS initiative. We are pleased to have continued support from Sida for this work over the next year but are also keen to discuss other funding opportunities to extend this work. 


Sioux Cumming (left in photo) has worked on and managed INASP’s Journals Online project since 2003 and has helped establish and maintain eight JOLs platforms. She has also been instrumental in bringing international standards and initiatives such as DOIs, eISSNs, the anti-plagiarism software CrossCheck, article-level metrics and Kudos to the journals. In collaboration with African Journals Online, she helped to develop and is implementing the Journal Publishing Practices and Standards (JPPS) framework to help journals improve their publishing quality.


photo Sioux Cumming and Susan MurraySusan Murray (right in photo) is Executive Director of African Journals OnLine (AJOL). AJOL is a South African based non-profit organization working toward increased visibility and quality of African-published research journals. AJOL hosts the world’s largest online collection of peer-reviewed, African-published scholarly journals and is a sponsoring member of CrossRef. Ms Murray is also a member of the Advisory Committee of the Directory of Open Access Journals (DOAJ) and a member of the Advisory Board for the Public Knowledge Project’s current study on Open Access Publishing Cooperatives. She has an abiding interest in the role that access to research outputs can play in economic development in low income and emerging economies, as well as the practicalities of attaining this.

Website: www.journalquality.info

Twitter: @INASPinfo @AJOLinfo

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

Wednesday, 22 August 2018

Introducing 'Platform Strategies' - a new kind of industry conference

by Jake Zarnegar

image Platform Strategies logo
From the list of finalists for the Awards for Innovation in Publishing to conference sessions like "Expanding the Scholarly Record: Technology and Tools for Today's Content," it is clear that ALPSP and its members have technology on the brain.

Publishers of all sizes today deploy a variety of specialized technology platforms to create, market, and deliver scholarly content. These technology choices used to be compartmentalized, or rather, “departmentalized" - delegated to the individual departments that would most often interact with the platform. (Or, worse, delegated to the folks in internal IT procurement.) But now more organizations are practising coordination and strategic planning around their technology platforms. And though we have begun to see more seminars, articles, and tracks at conferences devoted to technology platforms, there has not yet been a meeting exclusively devoted to examining strategy and integration of these pivotal pieces of the publishing ecosystem.

This is what Silverchair aims to bring to publishers with the inaugural Platform Strategies, a free-to-attend conference to explore strategic options for the core technology platforms used by publishers. Our goal is to bring together large and small publishers, commercial and not-for-profit publishers, and leaders from relevant research and technology fields to discuss our common challenges and opportunities - offering attendees an informed picture of the (rapidly) evolving platform space from experts and peers.

The day-and-a-half program will focus both on technology itself (with sessions on search and discovery, machine learning, content enrichment, and more) as well as broader topics concerning platforms and partnerships (e.g. “Technology Leadership Roundtable” and "Scale and Survival: Is the Future of Scholarly Publishing Exclusively Commercial?"). Registrations have already exceeded expectations (and have us looking for additional space!), which confirms our belief that this event addresses a growing need in our industry.

If you have questions about the meeting, find me at ALPSP in a couple of weeks, and I’ll be glad to chat. You can also reach out to us at strategies@silverchair.com. If you can’t attend, we’ll have recordings of the meeting available online, so we look forward to continuing the conversation with you beyond September.

Platform Strategies will be held September 26 - 27, 2018 in Washington, DC. Visit the website to learn more.

photo Jake Zarnegar
Jake Zarnegar leads the development of The Silverchair Platform. After joining Silverchair as an intern in 1996 while still in college, Jake gained hands-on experience with structured content workflows, software development, and semantic enrichment technologies. He has subsequently served in a variety of senior leadership roles at Silverchair, including Chief Technology Officer and President.

https://twitter.com/silverchairnews



Silverchair is a proud Silver Sponsor for the ALPSP 2018 Annual Conference 12-14 September which is being held at the De Vere Beaumont Estate, Old Windsor, UK




Monday, 20 August 2018

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.


logo code ocean

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.



photo Simon AdarSimon 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

Tuesday, 14 August 2018

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

On the 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.

logo Dimensions

In this blog, we speak to Daniel Hook, MD of Digital Science, and Christian Herzog, CEO of ÜberResearch, about Dimensions.


An Introduction to Digital Science 

Set up in 2010 by a team from Nature, Digital Science was established with the aim of investing in startups that originated in academia and that created software tools to help researchers to do their best research. 

An independent company since the Springer Nature merger of 2015, Digital Science continues to pursue the vision of its founders: working closely with the research community to improve workflows, provide new insights, and develop alternative technologies that can better meet their needs.

Many of the Digital Science team either come from a research background, supported researchers in their previous roles, or simply have a love of research and science. It is this ethos that keeps us close to the researcher and to the broader scholarly community. 

Today, the Digital Science portfolio has grown to include now-familiar services Altmetric, Figshare, and Symplectic Elements, amongst others. These tools, widely adopted by publishers, institutions and funders around the world, have helped to evolve the way that scholars work and scholarly information flows. 

Dimensions: re-imagining discovery and access to research 

Launched in January 2018 and built in partnership with over 100 research organisations from around the world, Dimensions is a research insights platform that aims to re-imagine discovery and access to research, transforming the way the scholarly community navigates the global research landscape.

In developing Dimensions, Digital Science wanted to achieve 3 key things: 

  • A more complete view across the research lifecycle, with the focus no longer so much on publications alone
  • A more open approach to content and metrics that puts the power of data back into the hands of the scholarly community 
  • A tool that meets the needs of all stakeholders in scholarly research: institutions, funders, publishers and of course researchers

Dimensions breaks down barriers to discovery and enhances the visibility of research by connecting over 133 million grants, publications, patents and clinical trials for the first time, enabling users to explore over 4 billion links between them to gather new insight into the multi-dimensional aspects of research activity. 

It provides vital information that publishers, institutions, funders and corporate R&D can use to analyze the outcomes and impacts of past work, inform their strategic planning, and strengthen their research programs. 


image Dimensions Plus


A free version of the platform for researchers provides openly-available search across the publication records and their associated metrics, and paid-for versions Dimensions Plus and Dimensions Analytics deliver extended functionality and analytical tools to institutions, funders, publishers and corporate research organisations. 

Dimensions was designed with specific publisher benefits in mind. Publication detail pages in both the free and licensed versions link directly to the publisher site, driving traffic to the best available version of the article. For our publisher partners with whom we have indexing agreements - as well as Open Access publishers - we offer the dynamic Dimensions badges, which can be easily added to publisher article pages to showcase citations. The Dimensions citation metrics API, freely available for non-commercial use, can further be used commercially by our publisher content partners, enabling them to use citations data internally or on their platform. 
image Dimensions badges

To make it easy for researchers to consume the publisher’s preferred, legitimate version of an article, Digital Science has also launched Anywhere Access, a technology that enables libraries to provide one-click access to Open Access and licensed content. Anywhere Access ensures that all publications are more easily discoverable and that researchers are delivered the best, legally available version of the content every time. 

Behind the scenes

Dimensions is a study in what can be done with open data, unique identifiers, modern machine learning, some friendly publisher-partners, a great set of development partners and a highly dedicated team. It also relies on the technologies that Digital Science has been investing in over the last 8 years with companies such as Altmetric, Readcube and Figshare.  

Built by a distributed and diverse team located in countries mostly around Europe, the technical group is orchestrated by our CTO, Mario Diwersy, from Frankfurt. Much of the team is specialised in machine learning and artificial intelligence. 

An extensive data enrichment process has ensured that search results are both comprehensive and meaningful. Organisation identification, researcher disambiguation, natural language processing and reference extraction mean Dimensions is able to respond accurately to complex search queries. 

Using Dimensions, users are able to draw out insights that would not previously have been possible to uncover, and trace the research process from ideas to eventual impacts for the first time. 

visual of linked content

Just two dedicated staff members were newly hired to work on Dimensions: the rest has come from collaboration between existing teams - pulling together expertise from across the portfolio. 

These contributions included marketing and the development of the Dimensions badges, led by Altmetric; the application development and data science, directed by ÜberResearch; the close partnerships formed by the Digital Science Consulting team and Symplectic that helped to create the development partner programme; and the underpinning publication and infrastructure made possible by ReadCube.

It has been amazing to see the teams evolve and find new ways to work together, sharing different and multifaceted experiences to enable the rapid development and launch of a mature and well-thought-through product that keeps researchers and institutional users as a key focus. 

A 'game-changing' innovation

Until Dimensions, data sets that are highly relevant to one another were often fragmented, or situated in silos, making them difficult to compare. Existing market structures and data monopolies were preventing innovation in a space that needed up to date tools. 

In building Dimensions, we aimed to trigger an evolution in how researchers think about research information, and to address some key problems that had become apparent through our interactions with scholars, funders, institutions and publishers: 

  • Difficulties in getting access to content 
    Connecting researchers to the content that they need has been a poorly solved problem for many years. With Anywhere Access, which provides one-click access to OA and licensed content, Dimensions offers the fastest way yet for a researcher to find the article that they’re looking for and to get access to the legal, full text version. Dimensions is also the first freely available publication and citation data source where users can have full visibility of the data that drives the system, and that has been written to meet specific academic use cases.
  • Increasing demands on researchers
    There has been a slow but significant shift in what is asked of a researcher. Now, they must find places for PhD students who wish to continue studying, seek out collaborations, identify grant opportunities and craft responses, help to hire other academics in their institutions and ensure that their research is original, translatable and well “marketed”. In essence, they must run their own mini-startup around their research. Dimensions gives them the data to start managing all these facets of their research life. 
  • Going beyond publications and citations
    Research institutions, funders, publishers, governments and industry have all focussed on bibliometrics to form some kind of measure of the parts of the research enterprise that are relevant to them, and to help inform their future strategies. With Dimensions, we move to give a broader view and enable users to easily trace the links and analyse connections between content from across the research lifecycle - providing much more comprehensive context on which to base decisions.
  • Excessive barriers to innovation
    A core aspect of Dimensions is to put decisions and control back in the hands of the research community. In an era where metrics are so easily misused, metrics must be developed and owned by the community based on a datasource that can be fully audited. In commitment to this, the full Dimensions API is made freely available to bibliometrics researchers as well as to clients, enabling them to build on the data as they wish. 

Crucially, we did not do this alone. Beyond the development partners we have taken the approach of incorporating existing industry standards and data sources, with the aim of furthering a more collaborative scholarly ecosystem.

This includes publications data from Crossref (along with many publishers who actively supported the project), citation data from the Initiative for Open Citations (I40C), OA discovery via Unpaywall, and a partnership with ORCID that makes it possible for authors to supplement how they appear in Dimensions and claim publications directly to their ORCID account from within the platform. 

Our plans for the future

The launch of Dimensions was only the starting point for a continued joint development with the large group of development partners and users, including publishers.

Our aim now is to provide a constantly growing research information database that continues to link elements and content consistently together, providing a data landscape that reflects the complexity of the research process, outcomes and impacts.

In early August we integrated supplementary data from Figshare to publication pages within the platform, and in the next month we expect to add over 330,000 policy documents, offering valuable insights for social science scholars and those looking to understand the societal impacts of research.

In the meantime, we hope that the wider research community will grasp the opportunity to provide feedback and build on the infrastructure that exists today, and look forward to seeing where new ideas might lead!

Daniel Hook, MD Digital Science photo Daniel Hook

Daniel has been CEO of Digital Science since 2015. Holding a PhD in Theoretical Physics from Imperial College London, Daniel was a founder of Symplectic and served as its Managing Director from its foundation in 2003 until 2013, when he moved into a senior management role at Digital Science.


photo Christian HerzogChristian Herzog, CEO ÜberResearch 

Christian is the lead on the Dimensions project at Digital Science and CEO of ÜberResearch, which he co-founded. A medical doctor by training, Christian was also one of the co-founders of Collexis, and later became Vice President Product Management for SciVal.


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