Tag Archives: Wellcome Trust

Open at scale: sharing images in the Open Research Pilot

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Dr Ben Steventon is one of the participants in the Open Research Pilot. He is working with the Office of Scholarly Communication to make his research process more open and here reports on some of the major challenges he perceives at the beginning of the project.

The Steventon Group is a new group established last year which looks at embryonic development, in particular focusing on the zebrafish. To investigate problems in this area the group uses time-lapse imaging and tracks cells in 3D visualisations which presents many challenges when it comes to data sharing, which they hope to address through the Wellcome Trust Open Research Project. Whilst the difficulties that this group are facing are specific to a particular type of research, they highlight some common challenges across open research: sharing large files, dealing with proprietary software and joining up the different outputs of a group.

Sharing imaging data 

The data created by time-lapse imaging and cell tracking is frequently on a scale that presents a technical, as well as financial, challenge. The raw data consists of several terabytes of film which is then compressed for analysis into 500GB files. These compressed files are of a high enough quality that they can be used for analysis but they are still not small enough that they can be easily shared. In addition the group also generates spreadsheets of tracking data, which can be easily shared but are meaningless without the original imaging files and specific software to allow the two pieces of data to be connected. One solution which we are considering is the Image Data Resource, which is working to make imaging datasets in the life sciences, which have not previously been shareable due to their size, available to the scientific community to re-use.

Making it usable

The software used in this type of research is a major barrier to making the group’s work reproducible. The Imaris software the group uses costs thousands of pounds so anything shared in their proprietary formats are only accessible to an extremely small group of researchers at wealthier institutions, which is in direct opposition to the principles of Open Research. It is possible to use Fiji, an open source alternative, to recreate tracking with the imaging files and tracking spreadsheets; however, the data annotation originally performed in Imaris will be lost when the images are not saved in the proprietary formats.

An additional problem in such analyses is the sharing of protocols that detail the methodologies applied, from the preparation of the samples all the way through data generation and analysis. This is a common problem with standard peer-review journals that are often limited in the space available for the description of methods. The group are exploring new ways to communicate their research protocols and have created an article for the Journal of Visualised Experiments, but these are time consuming to create and so are not always possible. Open peer-review platforms potentially offer a solution to sharing detailed protocols in a more rapid manner, as do specialist platforms such as Wellcome Open Research and Protocols.io.

Increasing efficiency by increasing openness

Whilst the file size and proprietary software in this type of research presents some barriers to sharing, there are also opportunities through sharing to improve practice across the community. Currently there are several different software packages being used for visualisation and tracking. Therefore, sharing more imaging data would allow groups to try out different types of images on different tools and make better purchasing decisions with their grant money. Furthermore, there is a great frustration in this area that lots of people are working on different algorithms for different datasets, so greater sharing of these algorithms could reduce the amount of time wasted creating algorithms when it might be possible to adapt a pre-existing one.

Shifting models of scholarly communication

As we move towards a model of greater openness, research groups are facing a new difficulty in working out how best to present their myriad outputs. The Steventon group intends to publish data (in some form), protocols and a preprint at the same time as submitting their papers to a traditional journal. This will make their work more reproducible, and it also allows researchers who are interested in different aspects of their work to access the bits that interest them. These outputs will link to one another, through citations, but this relies on close reading of the different outputs and checking references. The Steventon group would like to make the links between the different aspects of their work more obvious and browsable, so the context is clear to anyone interest in the lab’s work. As the research of the group is so visual it would be appropriate to represent the different aspects of their work in a more appealing form than a list of links.
The Steventon lab is attempting to link and contextualise their work through their website, and it is possible to cross-reference resources in many repositories (including Cambridge’s Apollo), but they would like there to be a more sustainable solution. They work in areas with crossovers to other disciplines – some people may be interested in their methodologies, others the particular species they work on, and others still the particular developmental processes they are researching. There are opportunities here for openness to increase the discoverability of interdisciplinary research and we will be exploring this, as well as the issues around sharing images and proprietary software, as part of the Open Research Pilot.

Published 8 May 2017
Written by Rosie Higman and Dr Ben Steventon

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Open Research Project, first thoughts

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Dr Laurent Gatto is one of the participants in the Office of Scholarly Communication’s Open Research Pilot. He has recently blogged about his first impressions of the pilot. With his permission we have re-blogged it here.

I am proud to be one of the participants in the Wellcome Trust Open Research Project (and here). The call was initially opened in December 2016 and was pitched like this:

Are you in favour of more transparency in research? Are you concerned about research reproducibility? Would you like to get better recognition and credit for all outputs of your research process? Would you like to open up your research and make it more available to others?

If you responded ‘yes’ to any of these questions, we would like to invite you to participate in the Open Research Pilot Project, organised jointly by the Open Research team at the Wellcome Trust and theOffice of Scholarly Communication at the University of Cambridge.

This of course sounded like a great initiative for me and I promptly filed an application.

We had our kick-off meeting on the 27th January, with the aim of getting to know each other and somehow define/clarify some of the objectives of the project. This post summarises my take on it.

Here’s how I introduced myself.

Who are you?

Laurent Gatto, Senior Research Associate in the Department of Biochemistry, physically located in Systems Biology and the Maths Department. SSI fellow and Software/Data Carpentry instructor and generally involved in the Open community in Cambridge, such as OpenConCam and Data Champions initiative.

What is your research about and what kind of data does your research generate?

My area of research is computational biology, with special focus on high-throughput proteomics and integration of different data and annotations. I use raw data produced by third parties, in particular the Cambridge Centre for Proteomics (mass spectrometry data), and produce processed/annotated/interactive data and a lot of software (and also here).

What motivated you to participate in the Pilot?

Improve openness/transparency (and hence reproducibility/rigour) in my research and communication, and participate in improving openness (and hence reproducibility/rigour) more widely.

What kind of outputs are you planning to share? Do you foresee any difficulties in sharing?

My direct outputs are systematically shared openly early on: open source software (before publication), pre-prints, improved data (as data packages). Difficulties, if any, generally stem from collaborators less willing to share early and openly.

A personal take on the project

It is a long project, 2 years, and hence a rather ambitious one, of a unique kind. Hence, we will have to define its overall goals as we go. The continued involvement of the participants over time will play a major role in the project’s success.

What are attainable goals?

It is important to note that there is no funding for the participants. We are driven by a desire to be open, benefit from being open and the visibility that we can gain through the project, and the prospect that the Wellcome Trust will learn from our experience and, implement any lessons learnt. We get to interact with each other and with research support librarians, who will help us throughout the duration of the project. We also commit to sharing of research outputs beyond traditional publications and to engage with the Project, by participating in Project meetings and contributing to Project publications.

A lot of our initial discussions centred around rewards for open research or, actually, lack thereof and perceived associated risks. Indeed, the traditional academic rewarding system and the competitiveness in research leaves little room for reproducibility and openness. It is, I believe, all participants hope that this project will benefit us, in some form or another.

A critical point that is missing is the academic promotion of open research and open researcher, as a way to promote a more rigorous and sound research process and tackle the reproducibility crisis. What should the incentives be? How to make sure that the next generation of academics genuinely value openness and transparency as a foundation of rigorous research?

Some desired outputs

Ideally, I would like that the Wellcome Trust’s famous Research investigator awards to be de facto Open research investigator awards. There’s currently a split (opposition?) between doing research and supporting open science when doing research. In every grant I have written, I had to demonstrate that the team had a track record, or was in a good position to successfully pursue to proposed project. Well, how about demonstrating a track record in being good in opening and sharing science outputs? Every researcher submitting a grant should convincingly demonstrate that they are, have been and/or will be proactive open researcher and openly disseminate all the outputs. By leading by example in the frame of this Open Research Project, this is something that the Wellcome Trust could take away from.

Unfortunately, it is a fact that open science is not on the agenda of many (most?) more senior researchers and that they are neither in a position to be open nor that open science is a priority at all. I find it particularly disheartening that many senior academics (i.e. those that will sit on the panel deciding if I’m worth my next job) consider investing time in open science and the promotion of open science as time wasted of actually doing research. A bit like time for outreach and promotion of science to the wider public is sometimes looked down at, as not being the real stuff.

Another desire is that this project will enable us to influence funders, such as the Wellcome Trust, of course, but also more widely the research councils.

As a concrete example, I would like all grants that are accepted to be openly published beyond the daft layman summary. Published grants after acceptance should include data management plan, the pathway to impact, possibly more, and these could then be used to assess to what extend the project delivered as promised.

This serves at least two purposes. First, it is a way to promote transparency and accountability towards the funder, scientific community and public. Also, it is a great resource for early career researchers. Unless there is specific support in place, writing a first grant is not an easy job, especially given the multitude documents to prepare in addition to the scientific case for support. And even for more experienced researchers, it can’t harm to explore different approaches to grant writing.

Another concrete output is the requirement for a dedicated software management plan for each grant that involves any software development. I certainly consider my software to be equivalent to data and document it as such in my DMPs, but there seems to be a need for clarification.

I believe that I do a pretty decent job in conducting open science: pre-prints, open access, release data, … In the frame of this project, I shall do a better job at promoting open science for its own sake.

I also hope that by bringing some of my projects under the umbrella of the the Open Research Project, I will benefit from a broader dissemination that will, directly or indirectly, be beneficial for my career (see the importance of benefits and rewards above).

Next steps

It is important to make the most out of this unique opportunity. We need to create a momentum, define ambitious goals, and work hard to reach them. But I also think that it is important to get as much input as possible from the community. Nothing beats collective intelligence for such open-ended projects, in particular for open projects.

So please, do not hesitate to comment, discuss on twitter or elsewhere, or email me directly if you have ideas you would like to promote and or discuss.

Published 08 March 2017
Written by Dr Laurent Gatto
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We are going OPEN – the Open Research experiment has begun!

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There has been much discussion recently about the reproducibility crisis and about the growing distrust among the public in the quality of research. As illustrated in our ‘Case for Open Research’ series of blog posts, one of the main reasons for this is that researchers are currently rewarded for the number of papers they publish in high impact factor journals, and not necessarily for the quality of work that they are doing.

Indeed, Cambridge researchers clearly indicated that the lack of incentives to do anything other than publishing in these types of journals is one of the main blockers discouraging them from adopting a more open research practice.

Joining forces with the Wellcome Trust

The Office of Scholarly Communication started talking about these problem with the Open Research team at the Wellcome Trust. The Wellcome Trust are natural allies, as they have consistently led their researchers towards greater openness. They were one of the first funding bodies to introduce policies on Open Access and on data management and sharing. Now the Wellcome Trust is moving towards proactively supporting Open Research beyond enforcing their compliance requirements.

To promote immediate and transparent research sharing, they have recently launched the Wellcome Open Research platform which allows researchers to submit articles about virtually any research output and get published within a couple of days. The Wellcome Trust is now considering making Open Research one of their strategic priorities.

We quickly realised that we have a lot of shared interests, and joining forces to tackle the problem together made a lot of sense. We came up with the idea to launch the Open Research Pilot Project.

The Open Research Pilot – understanding the barriers to “openness”

We conceived the project as a two year experiment, which would allow us to gain an understanding of what is needed for researchers to share and get credit for all outputs of the research process. These include non-positive results, protocols, source code, presentations and other research outputs beyond the remit of traditional publications.

The Project aims to understand the barriers preventing researchers from sharing (including resource and time implications), as well as what the incentives are. The Project aims to utilise the new Wellcome Open Research publishing platform, together with other channels, to share these outputs.

The invitation to take part in the Pilot was sent to all researchers at Cambridge funded by the Wellcome Trust. Participating researchers had to commit to sharing of research outputs beyond traditional publications and to engage with the Project, by participating in Project meetings and contributing to Project publications.

Is ‘doing the right thing’ enough incentive?

Our biggest question was whether anyone would be willing to participate in the Pilot. We did not offer any incentive other than encouraging researchers to contribute to the greater good. The only support available to those who wanted to take part in the project was that offered by the Wellcome Trust and Cambridge Open Research team members, but there was no financial aid available to prospective participants. We thought that regardless of the outcome, that inviting researchers would be a good exercise to go through – we thought that if no one applied, we would have learnt that doing ‘the right thing’ was not a good enough motivator.

Thankfully, we received several fantastic applications from individual researchers and research groups who demonstrated great interest in and motivation for Open Research. We initially planned to work with two research groups, but given the quality of applications received and passion for Open Research expressed by the applicants, we decided to extend the scope of the project to four research groups. We have selected researchers doing different types of research, with the aim of learning about distinct problems in sharing that are experienced in diverse research disciplines:

  •       Dr Laurent Gatto –is  doing computational biology research, with a special focus on proteomics data. His interest is: How to effectively share research data and the code needed to reproduce them?
  •       Dr David Savage – is researching molecular pathogenesis of the consequences of obesity. His question is: What are the problems with sharing data coming from human participants?
  •       Dr Benjamin Steventon – is a developmental biologist generating and analysing large-scale imaging datasets. He would like to know: Are there image repositories allowing one to share large image datasets in a re-usable way?
  •       Dr Marta Costa and Dr Greg Jefferis (and others) – researchers leading the work on two collaborative projects: Connectomics and Virtual Fly Brain, which will create interactive tools to interrogate Drosophila neural network connections. They would like to understand: What are the issues with sharing complex interactive datasets? How to ensure long-term preservation of complex digital objects?

Motivations

So what motivated these researchers to apply for the project? We asked this question at the application stage and were positively surprised by the altruistic answers that we received. Our researchers were largely driven by a desire to improve the research process. We have seen responses like:

  • “Openness in research, from data and software to publication, is a central pillar of good research.”
  • “I am very concerned (disappointed as a scientist) by the current wave of ‘unreproducible’ and/or ‘irrelevant’ research, and am very passionate about contributing to improving scientific endeavour in this regard.”
  • “I am very enthusiastic about exploiting new ways of sharing my research output beyond the established peer-review journal system.”
  • “I believe that sharing research outputs fully, including data and code are essential to accelerate research, and I have benefitted from it in my own research.”

Summarising, researchers expressed a great desire for contributing to a cultural change. Researchers wanted to change the way in which research was disseminated and to increase research transparency and reproducibility.

Let’s get to work

We all met (the researchers, Wellcome Trust and Cambridge Open Research teams) on Friday 27 January to officially start the two year project. Each research group was appointed a facilitator – a dedicated member of the Cambridge Open Research team to support researchers during the Project. Research groups will meet with their facilitators on a monthly basis in order to discuss shareable research outputs and to decide on best ways to disseminate these outputs. Every six months all project members will meet together to discuss the barriers to sharing discovered and to assess the progress of the Project.

One of the main goals of the Project is to learn what the barriers and incentives are for Open Research and to share these findings with others interested in the subject to inform policy development. Therefore, we will be regularly publishing blog posts on the Unlocking Research blog and on the Wellcome Open Research blog with case studies describing what we have discovered while working together. There will be an update from each research group every six months. We will also be publicly sharing all main outputs of the Project.

We are all extremely excited about going “Open” and we suggest that anyone interested in the Open Research practice watches this space.

Published 08 February 2017
Written by Dr Marta Teperek
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