Active data storage | Edinburgh Research Data Blog

Active data storage | Edinburgh Research Data Blog
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This is a guest blog from
Dr Ann Wheeler, Head of the Institute of Genetics and Cancer  Advanced Imaging Resource,
showcasing their exemplar for metadata capture and data management workflows
When the Edinburgh Bioimaging team, a group of technical specialists and core facility staff, first convened, the question of “What to do with all the data?” was a hot topic. The University of Edinburgh has invested over £50 million in bioimaging equipment, which can generate terabytes of data annually. Managing such large datasets presents significant challenges.
During the COVID period, leaders in the bioimaging field addressed these challenges by publishing metadata recommendations for experiments:
REMBI- Recommended Metadata for Biological Images
. Additionally, the European Bioinformatics Institute launched
the Bioimage Archive
, a repository for extensive imaging data, which some journals now require for data submission prior to publication. This is important for those of us who generate, or own bioimaging data to note!
A guide to capturing Recommended Metadata for Biological Images (REMBI)
While this is all great for the wider community, for those of us supporting data generation in Edinburgh, challenges remain:
Bioimaging core facility staff aren’t the data owners.
Data storage methods vary widely across departments.
Using community data repositories like OMERO would require substantial restructuring.
Re-provisioning costs are high in terms of both staff time and finances.
So, how can we promote data management consistent with FAIR (Fair, Accessible, Interoperable and Reusable) and REMBI (Recommended Metadata for Biological Images) principles at no cost?
Fortunately, collaboration between Bioimaging staff, College of Medicine and Veterinary Medicine (CMVM) data managers, and IT colleagues focused on data management, provided a solution.
We decided on a system involving a form and two tables to record metadata not captured by bioimaging equipment:
The form
: Describes the experiment (e.g., cell types, preparation for imaging).
Table 1
: Details imaging data acquisition methods (e.g., microscope type, live or fixed experiments).
Table 2
: Outlines image data analysis methodology. This is separate as analysis can occur later and may involve different personnel.
Example of data management form.
At its simplest, CMVM data managers can distribute these forms to data owners, who can fill them out and store them with their data. The next step was developing a WebApp for core facility SharePoint sites. This app facilitates easy data entry and sends submissions to the data owner and the relevant CMVM data manager. Submissions can be downloaded and stored alongside the data or within any chosen data management structure. The forms are flexible, allowing for updates or multiple entries if data are analysed in different ways.
The workflow, created in consultation with Bioimage Archive staff, complies with REMBI standards. Completing the forms thoroughly generates metadata, simplifying data uploads to the Bioimage Archive, and compliance with FAIR principle regardless of storage method.
This flexible, no-cost solution meets the needs of all CMVM departments and is potentially beneficial for colleagues in the College of Science and Engineering and the broader community. It’s easy to implement, use, and was well-received by the CMVM community.
Research Services, IT Infrastructure Division, are pleased to report that a project that allows researchers to transfer terabytes of data between the University of Edinburgh and external collaborators has been completed. The service uses a transport mechanism known as Globus to set up multiple connections between host and client to transfer data instead of relying on a single point-to-point connection. This results in very large data being transferred between sites in parallel, allowing faster transfer.
The service is integrated with the University’s research data platform,
DataStore
, allowing researchers to specify specific folders that can be used as “endpoints” to the transfer. Many users have already taken advantage of the service, but it is key to note that this will not improve data transfer speeds within the University itself, rather that bottlenecks in the wider Internet can be mitigated.
For more information, University of Edinburgh users may view
the RSS Wiki
Mike Wallis
IS ITI
For 2023/2024, Digital Research Services have organised a new iteration of the Lunchtime Seminar Series. These
one-hour
hybrid
seminars will examine different slices of the research lifecycle and introduce you to the data and computing expertise at the University of Edinburgh.
The seminars have been designed to answer the most common questions we get asked, offering valuable bite-sized learning opportunities for research staff, postgraduate research students, and professional staff alike. You will gain an understanding of how digital research fits in with wider research support teams and good research practices. Your sessions will cover research funding, research planning, tailored skill development, data management and advancements in AI.
Oh, and did we mention there is free lunch for in-person attendees? That is truly the cherry on top.
DRS Lunchtime Seminars – 2024 Calendar
Have a look at the upcoming seminars:
Seminar 1: How to plan and design your research project better.                        22
nd
January 12:00 – 13:00
This session is all about making sure researchers head off with a strong start. Did you know that the University has tools that help you optimise your data management plan, with funder specific templates and in-house feedback? We will make sure you get the best use out of DMPOnline and the Resource Finder Tool. We will also introduce you to some key concepts in data management planning, research funding and digital skill development.
Seminar 2: How to store and organise your data properly.                                    27
th
February 12:30-13:30.
Discover how to best store and organise your data using University of Edinburgh’s tools: DataStore, DataSync and GitLab. If you work in a wet lab, you might be particularly interested in electronic lab notebooks. We will introduce you to the functionalities of RSpace and protocols.io. Finally, the University has just launched an institutional subscription to the Open Science Framework (OSF). You will discover that it is much more than a tool for data storage, as it can help manage complex workflows and projects as well.
Seminar 3: How to interpret and analyse your data efficiently.                              13
th
March 12:00-13:00
This seminar is mainly about big computers, such as UoE’s Eddie and Eleanor. Through EPCC, researchers can get also access to large scale national supercomputers, such as Archer and Cirrus. At the same time, we will show a glimpse on some developments on the AI front.
Seminar 4: How to manage, publish, share and preserve your work effectively.  2
nd
April 12:00-13:00
The final seminar is all about making sure your work is published and preserved in the best way. We will talk you through different (open access) publishing pathways such as Journal Checker, Edinburgh Research Archive, Read & Publish journal list, Edinburgh Diamond. We will also be talking about data repositories (e.g. DataVault, DataShare) and our research output portal, Pure.
For info and booking:
Blog post by Dr Sarah Janac
Research Facilitator – The University of Edinburgh
Awesome news! The Research Data Service has a fantastic new addition to its
Open Research toolbox
! Fresh from the Centre for Open Science (COS) comes our institutional membership to Open Science Framework (
): a powerful tool for supporting staff and students at the University of Edinburgh.
OSF is a free, open platform that provides full integration and sharing across the entire data lifecycle. Among many other things, it streamlines workflows with customisable project organisation and automated version control. It also enhances collaborative research, making it easy to find and connect with other UoE users and their research projects. But wait, there’s more! OSF enables easy management of private and public aspects of a project, so sharing with project teams as well as the wider research community couldn’t be simpler; it’s ideal for sharing preprints and preregistered reports. Best of all, with centralised storage for documents, data, and code, it eliminates the need to scramble around hunting for that one file you need right now: no more trawling through email chains to recover lost data!
To launch the new platform we’ve been running Free Lunch Lunchtime sessions, with Free Lunch in the Main Library. The Centre for Research Collections were kind enough to let us use their rooms on the 6
th
floor, so obviously, all our attendees used the stairs and worked up a proper appetite for their Free Lunch.
The first event was held on August 30
th
to a packed house, or room. After the Free Lunch and a bit of professional mingling, Gretchen Gueguen from the Centre for Open Science Zoomed in to give us a brief introduction to and overview of OSF: what it is, how it works, and why it’s such an excellent addition to any research toolbox. Gretchen was followed by Emma Wilson, PhD student, UoE representative for ReproducibiliTea, and Open Research Intern extraordinaire. Emma provided the first of two user-perspectives, talking about her experience of using OSF for her projects, presentations, and posters. The second pair of boots on the ground belonged to Mark Lawson, Data Governance Manager for the Childlight project currently being run out of Moray House School of Education and Sport. Being another long time-user of OSF, as well as being a fan of such tools, Mark spoke with great enthusiasm about the use of OSF to support the data management and project management aspects of his work.
Emma Wilson presenting during the OSF introduction event in August.
The second event wasn’t quite as packed as the first, but it was still nice to see those who managed to make it through the December wind and rain. Once again, Gretchen was there to provide the introduction and overview; and Emma, likewise, returned to talk about her experience as an OSF user. This time, the afternoon was rounded off by Gillian Currie who outlined the OSF training she and Eirini Theofanidou were ready and able to deliver. Before the close of the session Gillian had secured several bookings for her training sessions. Sadly, and despite having organised the event – and the Free Lunch – RDS won’t receive any commission for these bookings.
However, we will soon be in vigorous competition with Gillian and Eirini because we’re preparing to offer OSF Winter and Summer Schools. These sessions will be delivered remotely by COS to an in-person cohort of researchers over two or three days. If all goes to plan, we may even be recording the session recordings for future use. And yes, in case you’re wondering, there will, once again, be a Free lunch for attendees.
To learn more about the University OSF membership go to:
. Questions about OSF? Email us:
data-support@ed.ac.uk
Dr Simon Smith – Research Data Support Officer
Research Data Support, Library & University Collections
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