Open Research Spotlight: In Conversation with Dr. Ramiro Bravo
In this Open Research Spotlight, Open Research Specialist Josh Emsley (he/him) speaks with Research Data Manager Dr. Ramiro Bravo (he/him) about the opportunities of using Protocols.io to enhance research transparency and reproducibility. This conversation is part of a wider project led by the which is engaging researchers and research support staff across the University of 优蜜传媒 (UoM) to explore how are being applied in different research contexts.
Promoting good data management: Ramiro鈥檚 role in research workflows
Dr. Ramiro Bravo is a Research Data Manager based in the Core Facilities (CF) within the Faculty of Biology, Medicine and Health (FBMH) at the University of 优蜜传媒 (UoM). As a Research Data Manager, Ramiro collaborates with the CF team, Principal Investigators (PIs), and health researchers to promote good data management practices. With a background in both biomedical engineering and computer science, Ramiro brings a strong technical background to his role. He provides technical assistance for research data storage, oversees project management of research data lifecycles, and collaborates with Open Research Ambassadors in the in FBMH.
Ramiro is a strong advocate for Open Research (OR) practices, positioning them as essential to ensuring research data transparency, reproducibility, and collaboration across research teams. Given that a large proportion of research data in FBMH originates from CF, Ramiro鈥檚 role is crucial in driving and promoting OR among these facilities and the broader research community. Ramiro explains his collaborative approach:
鈥淐ollaborating with Core Facilities to ensure data is provided to researchers in the most effective way is essential. This approach encourages researchers to maintain strong data management practices, including proper documentation, metadata creation, preparation of analysis results, and tracking of software usage. By adhering to the FAIR (findable, accessible, interoperable and reusable) principles, we can foster a culture of good data management and Open Research from the start of research projects through to publication, data storage and eventual data destruction.鈥�
For Ramiro, one way to foster greater OR practices across research workflows is using the right tools 鈥� which is why he is an advocate for .
鈥淓nsuring transparency and reproducibility鈥�: How Protocols.io is opening up research workflows
Protocols.io is an OR management tool designed to support research projects and enable collaboration in the development and sharing of detailed research . Through UoM鈥檚 institutional membership arranged by The Office for Open Research, staff and students can create private individual and team spaces for method development, collaboration and the tracking of protocol execution records.
There are multiple pathways to publishing a protocol on Protocols.io. Users can start from scratch with a blank template or import content from existing documents using an AI-assisted tool. As the Office for Open Research has established an institutional membership for Protocols.io, UoM staff and students can access a premium import service where the platform鈥檚 team will enter a protocol on behalf of a user. Users can also discover and adapt (鈥榝ork鈥�) existing public protocols on the platform, enabling ongoing refinement and reuse. Ramiro shares some of the key benefits of using Protocols.io below.
The power of detailed documentation
鈥淧rotocols.io is a valuable tool for maintaining records of how data is generated by Core Facilities.鈥�
Ramiro believes detailed documentation is foundational to good research data management. Protocols.io allows CF teams to record, refine and share the step-by-step processes by which data is generated 鈥� from sample preparation through to analysis. This moves beyond the limitations of traditional methods reporting in journal articles, which is often restricted by word limits and lacks sufficient detail required for reproducibility.
With Protocols.io, researchers can develop comprehensive protocols that remain private for internal review until ready for public sharing. This enables teams to collaboratively review and improve research workflows, while ensuring access to accurate, up-to-date procedures.
Ramiro highlights that sample traceability remains a persistent challenge in CF, particularly when samples are submitted without accompanying preparation documentation. Protocols.io helps resolve this issue by documenting how a sample was prepared, making it easier to connect upstream preparation with downstream analysis.
鈥淧rotocols.io allows researchers to share their protocol records with Core Facilities, detailing how their samples were prepared. This fosters better collaboration, standardisation, and adherence to best practices.鈥�
By embedding these documentation practices into research workflows, Ramiro sees Protocols.io as a powerful enabler of the FAIR data sharing principles, even if researchers aren鈥檛 explicitly aiming to align with them. He shares a as a primary example.
Enhanced discoverability and version control
Two further benefits to using Protocols.io Ramiro highlights are enhanced discoverability and version control. When a protocol is published, it becomes publicly available and receives a unique DOI (Digital Object Identifier). Ramiro explains how the DOI feature makes protocols independently citable research outputs:
鈥淲hen a paper needs to describe the methods, the Core Facility could provide the DOI of the protocol they used and published, ensuring proper credit鈥︹��
If a published protocol is reused or forked by others on Protocols.io, the original remains fully traceable and credited, supporting transparency and appropriate recognition of authorship. Each version of a protocol is archived, and refinements over time are logged, linked and can be compared, allowing researchers to demonstrate how a method has evolved overtime. Protocols.io also tracks engagement with published protocols through metrics such as views, comments, runs, and version forks, providing insights into protocol engagement.
Ramiro points out that protocols published on Protocols.io are distinct research outputs, with their own authorship and citation history. This can create opportunities for early career researchers and research methodologists to gain first-author recognition for methodological contributions 鈥� strengthening visibility and facilitating future research collaborations. Linking protocol DOIs to research profiles and publications also helps to build a visible record of technical expertise and demonstrate impact beyond traditional journal articles.
Concluding thoughts
Through his advocacy and work in research data management, Ramiro is playing a key role in promoting OR practices across CF in FBMH. His insights emphasise that OR is not only about making data accessible, but also ensuring that research workflows are transparent, reproducible, and well-documented across the entire lifecycle.
"Open Research tools like Protocols.io are essential for improving data transparency, documentation, and collaboration across research teams. By integrating these tools into research workflows, we can ensure that research is more reproducible, accessible, and aligned with FAIR principles."
Are you using Protocols.io or other OR tools in your work at 优蜜传媒? We鈥檇 love to hear from you! with the Office for Open Research to share your experiences and insights on how these tools are supporting your research.