Ep5 Reference managers: easing the pain of referencing

Niamh and Andrew are interviewed by Clare Baker from the Microbiology Society about their editorial on AI in Microbial Genomics research. Editorial on AI: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001049 Article for podcast: https://microbiologysociety.org/blog/microbe-talk-ai-a-useful-tool-or-dangerous-unstoppable-force.html

This episode was generated by ChatGPT 4, with the script read out by virtual voices. It is not our own words, but is a bit of fun nonetheless. In this episode, hosts virtual Andrew and virtual Niamh discuss the ethical considerations, best practices, potential risks, and benefits associated with using AI-generated content in academic research. Topics covered: Role of AI in academic research AI as a supportive tool Insights, suggestions, and idea generation Ethical considerations Plagiarism and intellectual property rights Bias in AI-generated content Authorship and responsibility Maintaining human judgment Best practices Using AI as a supportive tool Verifying originality and proper citation Acknowledging AI assistance Mitigating bias Maintaining human judgment Risks and benefits Risks: plagiarism, introduction of biases, compromised research quality, misattribution of authorship Benefits: increased efficiency, access to a broader range of information, assistance in generating ideas and writing, promoting collaboration and interdisciplinary research Key Takeaways: AI can be a valuable tool for academic research but should not replace human judgment and critical thinking. Researchers should be aware of the ethical considerations and adopt best practices when using AI-generated content. Understanding the potential risks and benefits can help researchers make responsible decisions when using AI-assisted research publishing.

It was announced that the White House Office of Science and Technology Policy has updated US policy guidance to make the results of taxpayer-supported research immediately available to the American public at no cost. We discuss this development in open research. Further information is available in this blog post by Niamh: https://unlockingresearch-blog.lib.cam.ac.uk/?p=3208 In this episode, we discuss the recent open access developments in the United States, particularly the new policies initiated by the Office of Science and Technology Policy (OSTP). The conversation delves into the potential impact of these policies on research, both in the US and internationally, including in the United Kingdom. It highlights the importance of open access in promoting knowledge sharing, facilitating research, and ensuring that taxpayer-funded research is accessible to all. We touch on the role of publishers in the research ecosystem, acknowledging that the value they add can vary widely depending on the discipline and the publisher's practices. We argue that some publishers may not provide significant value beyond copyediting and content curation. However, we recognize that learning societies and community-driven publishers can offer more valuable services in terms of connecting researchers with their peers and promoting a sense of shared community and passion. The conversation also covers the potential drawbacks and exceptions to open access. While we agree that open access is generally beneficial, we acknowledge that there are situations where it may not be appropriate to make certain data or research publicly available. For example, we mention cases involving sensitive data, such as indigenous data, commercial data, or personally identifiable medical information. The speakers emphasize the importance of striking a balance between openness and protecting sensitive information, recognizing that different disciplines may have unique considerations in this regard. The discussion also touches on the need for a cultural shift in research communities, moving away from the glamor of prestigious journals as a shorthand for quality. We point out that this change is already being promoted through initiatives like the Declaration on Research Assessment (DORA), which encourages research assessment based on the content and impact of research rather than where it is published. We stress that it is crucial for researchers, institutions, and funding agencies to actively work together to change the research culture and promote open access. We express hope that the OSTP's announcement will be a catalyst for further progress in the open access movement. We suggest that by 2030, the entire globe could be marching in the direction of more open, accessible, and affordable publication practices. To achieve this goal, we argue that more community governance, institutional hosting, and different ways of thinking about the values and needs of researchers in scholarly communication platforms are needed. In summary, the episode covers the following key points: 1. The OSTP's new open access policies have the potential to significantly impact research in the US and internationally, promoting greater knowledge sharing and accessibility of taxpayer-funded research. 2. Publishers can offer varying degrees of value to the research ecosystem, with some providing more valuable services in terms of community building and curation. 3. There are exceptions and drawbacks to open access, particularly when it comes to protecting sensitive or commercial data. 4. A cultural shift is needed in research communities to move away from focusing on the prestige of journals and toward the content and impact of research. 5. The OSTP's announcement may serve as a catalyst for further progress in the open access movement, leading to more open, accessible, and affordable publication practices worldwide by 2030.

In this episode of The Research Pages podcast, join hosts Andrew and Niamh as they delve into the world of academic publishing and explore how the process can be improved for researchers everywhere. They examine the complexities and inefficiencies of the current publishing landscape and envision a future where the systems are more user-friendly, allowing academics to focus on their research instead of navigating cumbersome publication processes. The conversation begins with a discussion on the challenges faced by researchers, such as managing multiple usernames and passwords across different journal websites and providing excessive amounts of personal information for submissions. Andrew and Niamh acknowledge the recent improvements brought by ORCID ID, which simplifies the login process and helps disambiguate researchers with similar names. As they explore ways to streamline the publishing process, the hosts emphasize that the primary goal for researchers is to have their work hosted permanently with a citable DOI, without the need for additional complications. They express their desire for a centralized hosting service that indexes uploaded papers and extracts metadata automatically, saving researchers time and effort. The episode also dives into the often opaque world of peer review, examining the lack of transparency in the process and sharing concerns about the quality of reviews. Andrew and Niamh question the value of peer review without transparency and discuss the pros and cons of signed, public peer reviews. They highlight the importance of striking a balance between anonymity for protection and openness for credibility. The hosts propose an ideal scholarly publishing landscape that includes a content hosting platform with search functionality, good metadata, and a transparent peer review system. They consider existing platforms like Faculty of 1000 and Journal of Open Source Software, which meet some of these criteria, but acknowledge that researchers may still hesitate to publish there due to concerns about journal prestige and quality perception. In the pursuit of reinventing the scholarly publishing landscape, Andrew and Niamh emphasize the need for open peer review, content filtering for relevance, and search functionality that reaches the right audience. They also stress the importance of ensuring a diverse range of voices for accurate information dissemination. However, the challenge remains in convincing researchers to adopt such a new system without being negatively impacted by traditional perceptions of journal quality. Tune in to this thought-provoking episode to learn more about the hosts' vision for a better academic publishing process and join the conversation on how we can work together to create a more efficient, transparent, and inclusive scholarly communication system.

In this episode, the discussion revolves around the rights retention strategy, open access, and the challenges researchers face in the academic publishing landscape. The benefits of green open access and rights retention are emphasized, as they allow authors to retain their rights and share their research more widely. This approach is necessary in light of publishers asserting more rights than they should have for a long time. The conversation delves into the varied stances of publishers on rights retention, with some being more receptive than others. Researchers often face difficulties navigating different publisher policies, leading to confusion and potential issues with sharing their work. To address this, the role of funders in shaping open access policies is considered crucial. Funders like UKRI and the Wellcome Trust have implemented policies to promote open access, which has influenced researchers and institutions to adopt rights retention strategies. The University of Cambridge is conducting a Rights Retention Pilot, inviting researchers to sign up for a non-exclusive CC BY license for their accepted manuscripts published within a year. This pilot aims to provide an additional layer of protection for researchers when dealing with publishers. The open-access team at the university handles any issues with publishers, rather than the authors themselves. The impact of UKRI and Research England policies on open access is also discussed. Research England manages the research excellence framework (REF), which assesses research quality in UK universities. Although the REF requirements have not yet been updated, it is expected that their open access policies will align with those of UKRI. In conclusion, the episode highlights the importance of rights retention and open access in the academic publishing landscape, and how funders and institutions can play a significant role in promoting these practices. Researchers are encouraged to assert their rights and share their work widely, contributing to a more open and accessible research environment.

We are back with Season 2 and chat with Andrew about what hes been up to for the past 2 years. Turns out its been a lot since hes been working on leading a group sequencing SARS-CoV-2. Details of Andrews work: https://quadram.ac.uk/case_studies/genome-sequencing-sars-cov-2-plays-a-critical-role-in-informing-national-and-international-covid-19-public-health-responses/ In this Research Pages podcast, hosts Andrew and Niamh discuss the impact of the COVID-19 pandemic on research and their experiences with COVID-19 research support. Andrew discusses his involvement with the UK COVID-19 Genomics Consortium, a partnership of universities, institutions, public health bodies, and other organizations. The consortium collected samples from hospitals, sequenced and analyzed them, and shared the data with the UK government and public health bodies. Andrew's team worked seven days a week, and the impact of their work was immediate, with reports being sent back to local hospitals about outbreaks, and the information being used to inform government policy. Andrew emphasizes the importance of collaboration and quick action during the pandemic, which led to a shift in traditional research methods towards more immediate action. This resulted in the generation of data that was immediately used to inform government policy and decisions. The conversation also touches on the importance of clear and accurate scientific advice to the government in managing the pandemic. Andrew was involved in one of the Sage working groups, which brought together experts from various fields to answer questions and give clear and accurate advice. Andrew spoke about the importance of answering questions truthfully and giving clear and accurate advice, even when the answer was unknown or more research was needed. Andrew also discussed his involvement in science communication, particularly to the public, acknowledging the importance of communicating clearly and accurately to the public during the pandemic. Finally, Andrew discussed the current situation, with restrictions being dropped in many countries, and how it feels to be moving out of the intense period of the pandemic. He acknowledged that we are now nearly at the point where things are stable, and hopefully, we can get back to a more normal life and a more normal stable system of surveillance. The interviewee discusses how the pandemic has accelerated the adoption of open research practices and collaboration. They are most proud of their work helping other countries set up sequencing capabilities and providing advice to counterparts around the world. The podcast's focus on COVID-19 research and response demonstrates the critical role that research plays in addressing global challenges. The interviewer and interviewee plan to have future conversations about research from the perspectives of a computer scientist and a professional librarian.

We discuss SARS-CoV-2 'new variants' and try to clear up some of the confusion around all the names flying around. Hopefully this helps to give some insights into the various names you hear, but probably by the time you listen the whole thing will have changed again since this field moves so rapidly. Andrew apologises in advance for all the errors that will be found in this podcast! If you want to read a bit more theres an interesting news item on Nature: www.nature.com/articles/d41586-021-00097-w

The process of writing a scientific paper can be complex with lots of little details nobody tells you about. We discuss how it all works practically, from the inception of an idea to getting your paper into review.

We discuss different resources used in research: databases such as free ones like Google Scholar and Pubmed to paid databases, author profiles such as ORCID, and the pros and cons of them. See @research-pages (https://soundcloud.com/research-pages) for all of our other episodes.

Reference managers can save you a lot of time and energy when writing papers, but are an often overlooked tool. We look into what they actually are, why we need them, our own experiences with a variety of different reference managers, and some of the pros and cons. See https://soundcloud.com/research-pages for all of our other episodes.