Showing posts with label Code Ocean. Show all posts
Showing posts with label Code Ocean. Show all posts

Monday, 8 October 2018

2018 ALPSP Conference Report - From Adventures in Publishing to #MeToo

In this blog, Alastair Horne, Press Futurist and social media correspondent at this year's ALPSP Conference reports on a packed few days in Windsor hearing from the scholarly publishing community.


This year’s conference once again offered a range of perspectives from across the scholarly publishing ecosystem on the key issues that affect us.

photo Chris Jackson
Keynote - Professor Chris Jackson
Thursday’s opening keynote was given by Professor Chris Jackson, who shared his own experiences as a researcher who has engaged deeply with the industry, publishing more than 150 articles, acting as editor for three journals, and co-founding the EarthArXiv preprint server. In a wide-ranging talk, Jackson offered some advice for publishers drawn from his experience: to be transparent about APC pricing; to offer strongly reduced APCs to early career researchers in order to build an affinity with new authors; and to be clear about their views on metrics. On open access, though generally enthusiastic, he suggested that Plan S had caused concerns among academics and might create challenges for societies who relied on income from subscription or hybrid journals to fund their other activities.

Open access was, inevitably, a theme that persisted throughout the conference. The panel that followed Jackson’s talk asked how societies and publishers should ‘accelerate the transition’. Kamram Naim shared details of the ‘subscribe to open’ model used by non-profit publisher Annual Reviews, which addressed the twin problems of library policies on ‘donations’ often preventing the support of open access initiatives, and the fact that APCs don’t work for journals that publish invited contributions from scholars, rather than receiving submissions. Their ‘Subscribe to Open’ model, which bears some similarities to Knowledge Unlatched’s, sees libraries receive a discount on their journal subscriptions if they choose to participate in unlocking initiatives: if enough do so, then that volume’s issues of the journal become available through open access; if not, then only subscribing institutions have access. Naim’s fellow panellist Steven Hill, Director of Research at Research England, and architect of the new REF, insisted that the new requirement for open access monographs would not mandate any particular model. His position was strongly challenged, though, by the panel’s third speaker, Goldsmiths Press’ Sarah Kember, who asked why the transition to open access for monographs was happening at all, and called for a deceleration to allow time for more consideration of differences across the sector. Plan S, she suggested, totally disregarded the humanities and monographs, and posed a considerable threat to academic freedom by restricting where researchers could publish.

photo Conference Panel session
Panel debate on Open Access
The following day, a further session considered the impact of open access on library sales, strategies, and solutions, as library directors from Europe and the US shared some insights into their institutions’ recent cancellations of big deals. Wilhelm Widmark, Library Director of Stockholm University, suggested that the Swedish universities’ decision to reject what he described as a ‘good’ proposed deal with Elsevier was because it didn’t offer a sustainable route to full open access; the money saved is being redirected towards fully open access journals. Jean François Lutz, Head of the Digital Library at the University of Lorraine, and Adrian Alexander, Dean of the Library at the University of Tulsa, added that their own institutions’ decision to cancel some of their big deal contracts were prompted by budget constraints and unsustainable pricing increases.

Friday’s opening session considered another increasingly hot topic: customer data. Chris Leonard from Emerald shared insights from their work in mapping user journeys in accessing their content, and one key finding – that though a high proportion of people who visit their site discover it through Google, the majority of those people don’t have institutional access and so leave; people who come to the site via library discovery services are far more likely to continue their journey further. Lettie Conrad of Maverick Consulting spoke of the wealth of data available to publishers, both internal – customer service records, sales reports, customer data, market research findings, product testing and user studies – and external – competitor analysis, discovery journeys, and usage analytics. Transforming such data into usable information required strategic thinking and some investment, she suggested, but it wasn’t rocket science. The third panel member, David Hutcheson, told how BMJ had developed a strategy for using data to inform their decisions, drive user engagement and deepen user understanding. Working with consultants and stakeholders to create an overall plan, they started by deepening their understanding of their existing technology and resources and testing them to see what worked. Integrating their different platforms to connect their data, and developing partnerships with suppliers, the BMJ set up a small six-person data team to serve as a specialist centre of excellence, supporting the rest of the business, automating processes and delivering self-service reporting to enable and empower colleagues to make use of the data produced.

The parallel sessions offered the usual dilemma of which to attend, and though there’s too little space to describe them all here, a personal highlight was a fascinating panel on the digital humanities. Peter Berkery of the Association of University Presses, Paul Spence of King’s College London, and Etienne Posthumus of Brill all discussed recent experiments in finding modes of publishing that would support the complex needs of this growing sector. Spence spoke of the need to fix a common terminology for the different types of publications produced, while Berkery talked through four marquee digital projects by university presses: Rotunda at Virginia, Manifold at Minnesota, Fulcrum at Michigan, and .supDigital at Stanford; Posthumus spoke on Brill’s own initiatives in labs and data.
Revenues from rights formed the focus of the day’s final session, sponsored by Publishers’ Licensing Services: Rebecca Cook of Wiley emphasised the need for thorough documentation governing what can be done with content, while Clare Hodder urged publishers to invest in metadata.

Photo Awards Presentation
Code Ocean wins the ALPSP Awards for Innovation 2018
Then, at the evening’s gala dinner, the winners of two prestigious ALPSP Awards were announced: Richard Fisher was honoured for his Contribution to Scholarly Publishing over a long career, both at Cambridge University Press and in his retirement, busier than many people’s main careers; then the cloud-based computational reproducibility platform Code Ocean was named the winner of the ALPSP Award for Innovation in Publishing.

The final day of the conference was dominated by ethical questions. Professor Graham Crow of the University of Edinburgh explored issues in research and publishing ethics, before the closing panel session addressed ‘The #MeToo Era in Academic Publishing: Tackling harassment and the roots of gender bias’. Femi Otitoju of the Challenge Consultancy shared some lessons drawn from thirty years of experience working in this area, emphasising the need to create the right working culture by focusing on positive outcomes rather than problems – having a ‘dignity at work’ policy rather than one on harassment, for instance – and prominently highlighting such policies through posters rather than pages buried on the company intranet. Karen Phillips of SAGE spoke of the need for publishers to learn from each other, while Eric Merkel-Sobotta of De Gruyter emphasised the importance of economic arguments in convincing management of the need to address such problems. Dr Afroditi Pina shared the results of her research into sexual harassment and successful strategies for addressing it: the need to agree appropriate sanctions for unacceptable behaviour, the role that public apologies can play in such sanctions, and the importance of listening un-defensively to those reporting harassment.

photo Beaumont Estate
The Beaumont Estate

If you would like to hear more about this year's ALPSP Conference, you can find video footage, audio and speaker presentations at:

 

https://www.alpsp.org/2018-Programme


The ALPSP Conference and Awards 2019 will be held at Beaumont Estate, Old Windsor, UK on 11-13 September. Please save the date!



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