Tag Archives: Wellcome Trust

Open Research Pilot project: the funder view

Case study, Funder, ,

This is the sixth and final piece in our series of blogs to mark the end of the Open Research Pilot Project – a two-year initiative through which four University of Cambridge research groups worked with University Research Support and the Wellcome Trust’s Open Research Team to assess what would be needed to make all their research outputs openly available. In this blog, David Carr, Programme Manager for Open Research at Wellcome, provides his perspectives on the project.

START OF THE PROJECT

As a global research foundation dedicated to improving health for everyone through enabling great ideas to thrive, the Wellcome Trust has been a long-standing and passionate champion of open access to research publications and research data sharing. We are committed to ensuring that the outputs of the research we support can be accessed and used by bright minds around the world to help accelerate research and its application to improve health.

When we were approached by the team at Cambridge in 2016 with the idea for the Open Research Pilot, we were in the process of establishing a new dedicated Open Research team at Wellcome to help spearhead our work to advance openness. We were in the process of developing a new policy on managing and sharing data, software and materials (which was subsequently published in July 2017). We had also just launched Wellcome Open Research with F1000 as a new platform to enable our funded researchers to rapidly publish any research finding they wished to make available using a fully open and transparent review process.

We were quick to accept their proposal and join forces. The Pilot offered a chance to explore the opportunities and challenges facing our funded researchers in adopting open approaches, and the resources and support they require to do this. It also offered the potential to explore whether the Wellcome Open Research platform could help researchers in making their outputs available.

 

PROJECT IN PROGRESS

Our main input during the Pilot was through periodic update meetings with the research groups and Cambridge team to review progress and discuss emerging themes and issues. I found these discussions enormously valuable.

There is simply no substitute to hearing about and discussing the practical challenges and barriers to open science first hand from our researchers. As the previous posts have described, these highlighted important issues around data size and complexity; incentives and recognition; skills and training; and the funding and sustainability of data resources. These conversations were very timely for us and have helped to inform the development of several aspects of our Open Research activity at Wellcome.

The Pilot also helped to build on our relationship with the research support team at Cambridge and provided valuable insights on the issues facing universities in supporting researchers to manage and share their research outputs. The expertise and dedication of the team to supporting the researchers with whom they work was hugely impressive, and they must take considerable credit for proactively initiating and taking forward this project. It is great to see that Cambridge has now formalized its support for open research at an institutional level through its recently-published position statement, and I hope it continues to adopt a leadership role in this space.

While I think the Pilot was hugely worthwhile, inevitably there were challenges and lessons to learn. Personnel changes in the team at Cambridge inevitably caused some minor disruptions, and it is fair to say that from Wellcome’s perspective other priorities sometimes meant our contribution and focus on the Pilot was sometimes less than it could have been. On reflection, there were probably opportunities to better align and link the Pilot with other activities at Wellcome that were missed.

We were a little disappointed that the Groups involved didn’t utilize our new publishing platform, although delighted that the first Wellcome Open Research data note resulting from the Pilot has now arrived (as highlighted in the first blog in this series). We hope that other Wellcome funded research groups at Cambridge will consider trying out Wellcome Open Research, and see if it adds value for them in rapidly and openly sharing their research findings.

 

LOOKING AHEAD

Wellcome is committed to supporting our researchers in adopting open research approaches in ways that maximise the value of research outputs and enrich the research enterprise.

Through our Open Research programme, we are taking forward a range of activities to support this goal, including:

  • providing the Research Enrichment – Open Research funding scheme to enable existing Wellcome grantholders to apply for additional funds to enhance the impact of their funded research through opening up their research outputs;
  • running the Open Research Fund – an annual competition to support cutting-edge, innovative approaches to open research around the world;
  • enhancing our support for researchers to manage and share data, including through an ongoing pilot with Springer-Nature to make its Research Data Support service available to our funded researchers;
  • taking a lead as a funder in incentivizing open research and working with others to accelerate implementation of the San Francisco Declaration on Research Assessment (DORA);
  • developing our guidance on developing and funding output management plans as part of grant applications, and introducing new approaches;
  • continuing to develop the Wellcome Open Research platform as a venue for Wellcome researchers to share their research findings.

In addition, of course, we are also focusing on accelerating the global transition towards full and immediate open access to research publications with our partners in cOAlition S.

We are committed to continuing to work with our funded researchers and institutions to advance open research. We got a lot out of our participation in this Pilot, and look forward to continuing to work closely with our colleagues at Cambridge and across the institutions we support.

 

Published 13 March 2019

Written by David Carr, Programme Manager for Open Research at The Wellcome Trust

Creative Commons License

The Open Research Pilot – one year in

Uncategorized, , , ,

As we close in on the halfway point for the Open Research Pilot between the University of Cambridge and the Wellcome Trust, how are things going?

Well, in many ways exactly as expected. The primary issues that we are facing are a lack of sustainable support for infrastructure and a lack of reward and incentive to work openly. None of this is news, and while no new issues are being surfaced by the Open Research Pilot, having the dialogue is helping the participating researchers exchange ideas and the Wellcome Trust develop new services and policies.

This was the take home message from the second full meeting of the Open Research Pilot participants held in London at the Wellcome Trust on 13 September. Given 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, it seems the Pilot is on track.

This blog summarises the discussions and ideas that arose at the event. A full write-up and the presentations are now available in the Open Research Pilot collection in Apollo, the University repository. The notes are also available from the pilot kick-off meeting held in January in Cambridge.

As a memory jogger, information about the Pilot and the different people and research projects involved are available. A blog describing the kick off meeting is also online as part of our new Open Adventures blog platform.

Outcomes of the meeting

Main issues raised:

  • Today a successful researcher and a good researcher are not necessarily the same thing
  • Time is a big issue. It takes time to annotate data sets to be made useable to others
  • The current incentive and reward structure is a barrier to change
  • The ethos needs to change with regard to the need to publish in particular journals
  • There is a need to re-define what is valuable and this may need to be defined at the discipline level
  • There is a mismatch between the reliance the research community have on certain resources and the availability of funding for long-term sustainability
  • There is a need for dedicated staff to manage sharing of research at the institute or department level

Possible solutions:

  • The new publishing platform, Wellcome Open Research is cheaper and faster than traditional publishing outlets
  • There are movements towards international approaches to collectively funding scientific infrastructure
  • The participants have found having access to library colleagues through this Open Research Pilot Project has been useful for figuring out where to put their research data – this does raise questions about future library services
  • We need strong leadership to drive the change to Open Research and given the risk adverse nature of institutions, change needs to be led by funders

    

Summary of the discussions

Wellcome Open Research update

Robert Kiley and David Carr gave a progress report on what had been happening in open science at the Wellcome Trust. They gave an update on the new Wellcome Trust open publishing platform, Wellcome Open Research.

When Wellcome Open Research was launched, ‘success’ was defined as 25-30 publications in a year. However in less than a year, more than 100 items have been published on this platform from a broad range of institutions. While half the publications are research articles, the rest are other output types such as data notes, software studies and protocols. This is important, given the new requirement of the Wellcome Trust to share all research outputs.

The platform is relatively popular as well. A comparison of the volume of Wellcome Trust funded publications across the range of publications showed Wellcome Open Research was found to be the fourth most used after Scientific Reports, PLoS ONE and Nature Communications.

This is significant because the average cost of publication on the Wellcome platform is of the order of £700, which is significantly lower than the average cost of the other named publications (generally around £2000).  It is not just cheaper, it is faster as well. Robert described an example where an item was submitted, reviewed, approved, published and made discoverable and then requests were received for the data within a three week period.

Open data, Funding and Sustainability

Recently as part of this Pilot, the OSC published a series of blogs discussing the problem of supporting infrastructure, from the researcher perspective, the funder perspective, and that of the university library. The group discussed the serious problem with infrastructure being funded at a grant level but the data is used by the whole community. Funders do not necessarily fund ongoing infrastructure which is in competition with new requests to fund new ideas. Another question is whether it is even the funder’s job to provide long-term sustainability?

The point was raised that there is a mismatch between a reliance on certain resources on the one hand, but a reluctance to fund for long-term sustainability.  For example, when arXiv (an e-print service, operated by Cornell University) asked the physics community to provide support, they thought that it was the library’s responsibility to provide funding, not theirs.  Similarly, Canadian Health Research heavily rely on GenBank, but do not contribute to the costs of this resource.

This problem is recognised internationally and there are some attempts to address the problem. Earlier this year there was a meeting of several major funding organisations, from which a strong consensus emerged that core data resources for the life sciences should be supported through a coordinated international effort(s) that better ensure long-term sustainability and that appropriately align funding with scientific impact. There is also some work to to build a stable and sustainable infrastructure for biological information across Europe

Support for Open Research activities

One question posed to the researchers in the group was: what support from their institutions and funders would they want to make their data more accessible? It was commented that time was a big issue. For example, it takes time to annotate data sets to be made useable to others.  One group said that they could write protocols and a series of articles to put on Wellcome Open Research, which would be a good thing, but it would take the team a long time.

There appears to be a need for dedicated staff to manage sharing of research at the institute or department level.  It was commented that having had access to library colleagues through this Open Research Pilot Project has been useful for figuring out where to put their research data. An action was taken for the library component of the group to think about what support is being provided in this context (and into the future).

Open Research and Culture

In the current climate it is easy to identify a successful researcher.  A successful researcher has prizes, publishes in particular journals with high impact factors and has grants and funding. But a successful researcher and a good researcher are not necessarily the same thing. One of the blockers for a future Open Research environment seems to be the research community itself.  For example, the current incentive and reward structure is a barrier to change and there is a need to re-define what is valuable and this may need to be defined at the discipline level.

Some suggestions that arose in the discussion were:

  • a data re-use prize by Wellcome Trust
  • only provide grants or Fellowships to institutions or departments that have signed or support the Declaration on Research Assessment (DORA)
  • travel fellowships awards for good Open Research practices (noting that credit should be given to the individual winning the award and not the head of the laboratory who was the recipient of the original grant)

By ‘fighting on different fronts’, slowly the research environment might change. We need strong leadership to drive the change to Open Research, and the leadership needs to come from funders and institutions for the researchers to align themselves with working openly. But institutions are very risk adverse with activities that could jeopardise funding, so change needs to be led by the funders.

The hybrid question

While open access could be a vehicle for improving open research, the route to achieve this is debatable. The group asked whether funders could insist on green open access or only pay for truly open access journals. If payment for articles in hybrid journals, for example, was stopped, the money saved could be used to invest in other aspects of open research.

An alternative option discussed was whether the value given for APCs be limited, say to $1000? But this would be very difficult to implement, as an indicator, the SCOAP3 project took five years to get off the ground.

The question arose: if Wellcome Trust stopped paying for open access in hybrid journals, would researchers stop applying for funding? The feeling was no. But researchers perceive that when applying for grants, their record for publications in particular journals is very important.  The ethos needs to change with regard to the need to publish in particular journals.

Next steps

The Office of Scholarly Communication is coordinating an “In Conversation” event on 5 December to give researchers the opportunity to talk to Wellcome Trust representatives about their Policy on data, software and materials management and sharing.

We are also looking to find evidence that data is reused.

The Wellcome Trust will be using the group as scoping group for a proposal that the Wellcome Trust build a repository by sharing the draft requirements.

      

Published 10 November 2017
Written by Dr Danny Kingsley, based on notes by Dr Debbie Hansen
Creative Commons License

Sustaining open research resources – a funder perspective

Uncategorized, , ,

Originally published 26 July 2017, Written by David Carr, Wellcome Trust

This is the second in a series of three blog posts which set out the perspectives of researchers, funders and universities on support for open resources. The first was Open Resources, who should pay? In this post, David Carr from the Open Research team at the Wellcome Trust provides the view of a research funder on the challenges of developing and sustaining the key infrastructures needed to enable open research.

As a global research foundation, Wellcome is dedicated to ensuring that the outputs of the research we fund – including articles, data, software and materials – can be accessed and used in ways that maximise the benefits to health and society.  For many years, we have been a passionate advocate of open access to publications and data sharing.

I am part of a new team at Wellcome which is seeking to build upon the leadership role we have taken in enabling access to research outputs.  Our key priorities include:

  • developing novel platforms and tools to support researchers in sharing their research – such as the Wellcome Open Research publishing platform which we launched last year;
  • supporting pioneering projects, tools and experiments in open research, building on the Open Science Prize which with the NIH and Howard Hughes Medical Institute;
  • developing our policies and practices as a funder to support and incentivise open research.

We are delighted to be working with the Office of Scholarly Communication on the Open Research Pilot Project, where we will work with four Wellcome-funded research groups at Cambridge to support them in making their research outputs open.  The pilot will explore the opportunities and challenges, and how platforms such as Wellcome Open Research can facilitate output sharing.

Realising the long-term value of research outputs will depend critically upon developing the infrastructures to preserve, access, combine and re-use outputs for as long as their value persists.  At present, many disciplines lack recognised community repositories and, where they do exist, many cannot rely on stable long-term funding.  How are we as a funder thinking about this issue?

Meeting the costs of outputs sharing

In July 2017, Wellcome published a new policy on managing and sharing data, software and materials.  This replaced our long-standing policy on data management and sharing – extending our requirements for research data to also cover original software and materials (such as antibodies, cell lines and reagents).  Rather than ask for a data management plan, applicants are now asked to provide an outputs management plan setting out how they will maximise the value of their research outputs more broadly.

Wellcome commits to meet the costs of these plans as an integral part of the grant, and provides guidance on the costs that funding applicants should consider.  We recognise, however, that many research outputs will continue to have value long after the funding period comes to an end.  Further, while it not appropriate to make all research data open indefinitely, researchers are expected to retain data underlying publications for at least ten years (a requirement which was recently formalised in the UK Concordat on Open Research Data).  We must accept that preserving and making these outputs available into the future carries an ongoing cost.

Some disciplines have existing subject-area repositories which store, curate and provide access to data and other outputs on behalf of the communities they serve.  Our expectation, made more explicit in our new policy, is that researchers should deposit their outputs in these repositories wherever they exist.  If no recognised subject-area repository is available, we encourage researchers to consider using generalist repositories – such as Dryad, FigShare and Zenodo – or if not, to use institutional repositories.  Looking ahead, we may consider developing an orphan repository to house Wellcome-funded research data which has no other obvious home.

Recognising the key importance of this infrastructure, Wellcome provides significant grant funding to repositories, databases and other community resources.  As of July 2016, Wellcome had active grants totalling £80 million to support major data resources.  We have also invested many millions more in major cohort and longitudinal studies, such as UK Biobank and ALSPAC.  We provide such support through our Biomedical Resource and Technology Development scheme, and have provided additional major awards over the years to support key resources, such as PDB-Europe, Ensembl and the Open Microscopy Environment.

While our funding for these resources is not open-ended and subject to review, we have been conscious for some time that the reliance of key community resources on grant funding (typically of three to five years’ duration) can create significant challenges, hindering their ability to plan for the long-term and retain staff.  As we develop our work on Open Research, we are keen to explore ways in which we adapt our approach to help put key infrastructures on a more sustainable footing, but this is a far from straightforward challenge.

Gaining the perspectives of resource providers

In order to better understand the issues, we did some initial work earlier this year to canvas the views of those we support.  We conducted semi-structured interviews with leaders of 10 resources in receipt of Wellcome funding – six database and software resources, three cohort resources and one materials stock centre – to explore their current funding, long-term sustainability plans and thoughts on the wider funding and policy landscape.

We gathered a wealth of insights through these conversations, and several key themes emerged:

  • All of the resources were clear that they would continue to be dependent on support from Wellcome and/or other funders for the long-term.
  • While cohort studies (which provide managed access to data) can operate cost recovery models to transfer some of the cost of accessing data onto users, such models were not appropriate for data and software resources who commit to open and unrestricted access.
  • Several resources had additional revenue-generation routes – including collaborations with commercial entities– and these had delivered benefits in enhancing their resources.  However, the level of income was usually relatively modest in terms of the total cost of sustaining the resource. Commitments to openness could also limit the extent to which such arrangements were feasible.
  • Diversification of funding sources can give greater assurance and reduce reliance on single funders, but can bring an additional burden.  There was felt to be a need for better coordination between funders where they co-fund resources.  Europe PMC, which has 27 partner funders but is managed through a single grant is a model which could be considered.
  • Several of the resources were actively engaged in collaborations with other resources internationally that house related data – it was felt that funders could help further facilitate such partnerships.

We are considering how Wellcome might develop its funding approaches in light of these findings.  As an initial outcome, we plan to develop guidance for our funded researchers on key issues to consider in relation to sustainability.  We are already working actively with other funders to facilitate co-funding and make decisions as streamlined as possible, and wish to explore how we join forces in the future in developing our broader approaches for funding open resources.

Coordinating our efforts

There is growing recognition of the crucial need for funders and wider research community to work together develop and sustain research data infrastructure.  As the first blogin this series highlighted, the scientific enterprise is global and this is an issue which must be addressed international level.

In the life sciences, the ELIXIR and US BD2K initiatives have sought to develop coordinated approaches for supporting key resources and, more recently, the European Open Science Cloud initiative has developed a bold vision for a cloud-based infrastructure to store, share and re-use data across borders and disciplines.

Building on this momentum, the Human Frontiers Science Programme convened an international workshop last November to bring together data resources and major funders in the life sciences.  This resulted in a call for action (reported in Nature) to coordinate efforts to ensure long-term sustainability of key resources, whilst supporting resources in providing access at no charge to users.  The group proposed an international mechanism to prioritise core data resources of global importance, building on the work undertaken by ELIXIR to define criteria for such resources.  It was proposed national funders could potentially then contribute a set proportion of their overall funding (with initial proposals suggesting around 1.5 to 2 per cent) to support these core data resources.

Grasping the nettle

Public and charitable funders are acutely aware that many of the core repositories and resources needed to make research outputs discoverable and useable will continue to rely on our long-term funding support.  There is clear realisation that a reliance on traditional competitive grant funding is not the ideal route through which to support these key resources in a sustainable manner.

But no one yet has a perfect solution and no funder will take on this burden alone.  Aligning global funders and developing joint funding models of the type described above will be far from straightforward, but hopefully we can work towards a more coordinated international approach.  If we are to realise the incredible potential of open research, it’s a challenge we must address

Originally published 26 July 2017,
Written by David Carr, Wellcome Trust

Creative Commons License

Open Resources: Who Should Pay?

Uncategorized, , , , , ,

Originally published 23 June 2017 Written by Dr Lauren Cadwallader

This blog is the first in a series of three which considers the perspectives of researchers, funders and universities in relation to the support for open resources, coordinated and written by Dr Lauren Cadwallader. This post asks the question: What is the responsibility of national funders to research resources that are internationally important?

In January 2017 the Office of Scholarly Communication and Wellcome Trust started an Open Research Pilot Project to try to understand how we could help our researchers work more openly and what barriers they faced with making their work open. One of the issues that is a common theme with the groups that we are working with is the issue of the sustainability of open resources.

The Virtual Fly Brain Example

Let’s take the Connectomics group I am working with for example. They investigate the connections of neurons in fly brains (Drosophila). They produce a lot of data and are committed to sharing this openly. They share their data via the Virtual Fly Brain platform (VFB).

This platform was set up in 2009 by a group of researchers in Cambridge and Edinburgh; some of the VFB team are now also involved in the Connectomics group so there is a close relationship between these projects. The platform was created as a domain-specific location to curate existing data, taken from the literature, on Drosophila neurons and for curating and sharing new data produced by researchers working in this area.

Initially it was set up thanks to a grant from the Biotechnology and Biological Sciences Research Council (BBSRC). After an initial three year grant, the BBSRC declined to fund the database further. One likely reason for this is that the BBSRC resources scheme explicitly favours resources with a large number of UK users. The number of UK researchers who use Drosophila brain image data is relatively small (<10 labs), whereas the number of international researchers who use this data is relatively large, with an estimated 200 labs working on this type of data in other parts of the world.

Subsequently, the Wellcome Trust stepped in with funding for a further three years, due to end in September 2017. Currently it is uncertain whether or not they will fund it in the future. By now, almost eight years after its creation, VFB has become the go-to source for openly available data on Drosophila brain information and images integrated into a queryable platform. No other resource like it exists and no other research group is making moves to curate Drosophila neurobiology data openly. The VFB case raises interesting and important questions about how resources are funded and the future of domain specific open infrastructures.

The status quo

On the one hand funders like the Wellcome Trust, Research Councils UK and National Institutes of Health (NIH) are encouraging researchers to use domain specific repositories for data sharing. Yet on the other, they are acknowledging that the current approaches for these resources are not necessarily sustainable.

A recent review on building and sustaining data infrastructures commissioned by the Wellcome Trust acknowledges that in light of the FAIR principles “it is clear that data is best made available through repositories where aggregation can add most value”, which is arguably in a domain-specific repository. Use of domain-specific repositories allows data to be aggregated with similar data recorded using the same metadata fields.

It is also clear that publishers can influence where data is deposited, with publishers such as Nature Publishing Group, PLOS and F1000 all recommending subject-specific repositories as the first choice place for deposition. If no subject-specific repository is available then unstructured repositories, such as Dryad or figshare are often recommended instead, which complicates infrastructure needs and therefore provisions.

The economic model for supporting data infrastructures is something the Wellcome Trust are considering, with reports recently published by other funding agencies (here, here and here). The Wellcome Trust’s commissioned review noted that project-based funding for data infrastructures in not sustainable in the long term.

However, historically funders have encouraged, and still encourage, the use of domain specific resources, which have been born from project-based funding because of a lack of provision elsewhere. This has created a complex situation – researchers created domain specific data infrastructures using their project funding; these have become the subject norm; funder’s encourage their use, but now don’t have the mechanisms to be able to pledge sustained long-term funding.

National interests?

What is the responsibility of national funders to research resources that are internationally important? Academic research is collaborative. It crosses borders and utilises shared knowledge regardless of where it was generated and this is acknowledged by funders who see the benefits of collaboration. Yet, the strategic goals of funders, such as the BBSRC, are often focused on the national level when it comes to relevance and importance.

On the one hand it is understandable that funders concentrate on national interests – taxpayers’ money goes into the funder’s coffers and therefore they have a responsibility to those taxpayers to ensure that the money is spent on research that benefits the nation.

But, one could argue that international collaboration is in the national interest. The US-based NIH funds resources that are of international importance, including most of the model organism databases and genomic resources, such as the Gene Expression Omnibus. These are highly used by US researchers so one could argue that NIH are acting in the national interest but they are open to researchers all over the world and therefore constitute a resource of international importance.

Wellcome Trust do have a global outlook when it comes to funding, with 21% of their total spend (2015-6) going to projects outside of the UK. Yet, the VFB resource is still vulnerable despite being an internationally important resource.

One of the motivations for the Connectomics group to to participate in the Open Research Pilot is to open a dialogue with the Wellcome Trust about these issues. The Wellcome Trust are committed to strategically investing in Open Research and encourage the use of domain-specific resources. The Connectomics group are interested in how will this strategic investment translate into actual funding decisions now and into the future.

Issues on which researchers would like clarification

All the researchers who are part of the Open Research Pilot have had the opportunity to contribute to questions on open resources sustainability. Posts on the funder’s and University’s perspective will be published as parts 2 and 3 of this blog.

  1. What do you think is the responsibility of national funders towards research resources that are of more international benefit than national?
  2. How do you think the funding landscape will react to the move towards open research in terms of supporting the sustainability of resources used for curating and sharing data?
  3. Researchers are asked to share their data in domain specific resources if they are available. There are 1598 discipline specific repositories listed on re3data.org and each one needs to be supported. How big does a research community need to be to expect support?
  4. What percentage of financial support should be focussed on resources versus primary research?
  5. If funders are reluctant to pay for domain specific resources, is there a need to move to a researcher pays model for data sharing rather than centrally funding resources in some circumstances? Why? How do they envisage this being paid for?
  6. How can we harmonise the approach to sustainable open resources across a global research community? Should we move to centralised infrastructures like the European Open Science Cloud?
  7. More generally how can funders and employers help to incentivise open research (carrot or stick?)
  8. Wellcome often tries to act in a way to bring about change (e.g. open access publishing): Do they envisage that the long term funding of open research (10-20 years from now) will be very different from the situation over e.g. the next 5 years?

Originally published 23 June 2017
Written by Dr Lauren Cadwallader

Creative Commons License

Open at scale: sharing images in the Open Research Pilot

Uncategorized, , ,

Originally published 8 May 2017 Written by Rosie Higman and Dr Ben Steventon
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.

Originally published 8 May 2017
Written by Rosie Higman and Dr Ben Steventon

Creative Commons License

Open Research Project, first thoughts

Uncategorized, ,

Originally blogged 14 February 2017 Written by Dr Laurent Gatto 

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 planfor 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.

Originally blogged 14 February 2017
Written by Dr Laurent Gatto 

Creative Commons License

Piloting more openness at the University of Cambridge

Uncategorized,

Marta Teperek describes a new pilot project being undertaken at the University of Cambridge with the aim of finding out what can be done to bring about more open research practices. Originally published 10 February 2017

The problem: reproducibility crisis and lack of transparency in research

There have been a lot of discussions 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. University of Cambridge researchers have clearly indicated that the lack of incentives is one of the main reasons that discourages them from adopting a more open research practice.

Joining forces with the Wellcome Trust

As a way of addressing this issue, we approached the Open Research team at the Wellcome Trust. The Wellcome Trust are natural allies, as they always promoted the virtues of greater openness to their researchers. As one of the first funding bodies to introduce policies on open access and on data management and sharing, they have been leaders in this area, so it seemed natural to speak to them about this.

The Wellcome Trust has started to make moves in proactively supporting open research beyond enforcing their open access compliance requirements. To promote immediate and transparent research sharing, they recently launched Wellcome Open Research. This publication platform that allows researchers to submit articles about virtually any research output and get published in a matter of days with author-led open peer review occurring afterwards. The Wellcome Trust is now considering making open research one of their strategic priorities.

From our discussions, we quickly realised that we have a lot of shared interests, and joining forces to tackle the reluctance to adopting open research practices made a lot of sense. The final result was the idea to launch the Open Research Pilot Project at Cambridge.

 

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

We conceive the project as being a two-year experiment, which would allow us to gain an understanding of what is needed for researchers to share their research results 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 their research outputs, including resource and time implications, as well as what the incentives are. The Project aims to utilise the Wellcome Open Research, together with other channels, to share these outputs.

An 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 case studies about their experience of taking part in the pilot.

Recruiting researchers

One of our biggest questions was whether how willing would people be to participate in the pilot. We have not offered any incentive other than encouraging researchers to contribute to the greater good. Support is offered by the Wellcome Trust and Cambridge Open Research team members for those who have agreed to be part of this experiment, but no financial aid to prospective participants has been offered. 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.

To our surprise, we received several fantastic applications from individual researchers and research groups who demonstrated a great interest and willingness to practice 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 carries our research in computational biology, with a special focus on proteomics data. From his participation, we aim to find out, how to effectively share the research data and the code needed to reproduce them.
  • Dr David Savage researches the molecular pathogenesis of the consequences of obesity. Through his participation, we aim to identity what the problems are with sharing data coming from human participants.
  • Dr Benjamin Steventon is a developmental biologist generating and analysing large-scale imaging datasets. We intend to find out from his participation if there are image repositories that allow the sharing of large image datasets in a re-usable way.
  • Dr Marta Costa and Dr Greg Jefferies (and others) are researchers leading the work on two collaborative projects: Connectomics and Virtual Fly Brain, which will create interactive tools to interrogate Drosophila neural network connections. By being part of this pilot they will inform us of the issues with sharing complex interactive datasets, and help answer questions around the long-term preservation of complex digital objects.

Identifying researchers

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 – in 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 throughout 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 them. Every six months all project members will meet to discuss barriers to sharing outputs that have been identified through the pilot 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 with case studies describing what we have discovered while working together. There will also be an update from each research group every six months.

We will also be publicly sharing all main outputs of the Project. To date, we have shared the archived call for participants and the presentation from the kick off meeting on 27 January.

We are all extremely excited about  beginning this openness and we suggest that anyone interested in the open research practice watches this space – you can keep up to date on all aspects of this project here.

A version of this blog has also been posted on University of Cambridge Office of Scholarly Communication’s blog “Unlocking Research“.

tags: , 

We are going OPEN – the Open Research experiment has begun!

Uncategorized, ,

Originally published 08 February 2017
Written by Dr Marta Teperek

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 theOpen 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.

Originally published 08 February 2017
Written by Dr Marta Teperek
Creative Commons License