A survey of research quality in core facilities

Best practices for user consultation in flow cytometry shared resource laboratories

This "Best Practices in User Consultation" article is the result of a 2022 International Society for the Advancement of Cytometry (ISAC) membership survey that collected valuable insights from the shared research laboratory (SRL) community and of a group discussion at the CYTO 2022 workshop of the same name. One key takeaway is the importance of initiating a consultation at the outset of a flow cytometry project, particularly for trainees. This approach enables the improvement and standardization of every step, from planning experiments to interpreting data. This proactive approach effectively mitigates experimental bias and avoids superfluous trial and error, thereby conserving valuable time and resources. In addition to guidelines, the optimal approaches for user consultation specify communication channels, methods, and critical information, thereby establishing a structure for productive correspondence between SRL and users. This framework functions as an exemplar for establishing robust and autonomous collaborative relationships. User consultation adds value by providing researchers with the necessary information to conduct reproducible flow cytometry experiments that adhere to scientific rigor. By following the steps, instructions, and strategies outlined in these best practices, an SRL can readily tailor them to its own setting, establishing a personalized workflow and formalizing user consultation services. This article provides a pragmatic guide for improving the caliber and efficacy of flow cytometry research and aggregates the flow cytometry SRL community's collective knowledge regarding user consultation.

Future proofing core facilities with a seven-pillar model

Centralised core facilities have evolved into vital components of life science research, transitioning from a primary focus on centralising equipment to ensuring access to technology experts across all facets of an experimental workflow. Herein, we put forward a seven-pillar model to define what a core facility needs to meet its overarching goal of facilitating research. The seven equally weighted pillars are Technology, Core Facility Team, Training, Career Tracks, Technical Support, Community and Transparency. These seven pillars stand on a solid foundation of cultural, operational and framework policies including the elements of transparent and stable funding strategies, modern human resources support, progressive facility leadership and management as well as clear institute strategies and policies. This foundation, among other things, ensures a tight alignment of the core facilities to the vision and mission of the institute. To future-proof core facilities, it is crucial to foster all seven of these pillars, particularly focusing on newly identified pillars such as career tracks, thus enabling core facilities to continue supporting research and catalysing scientific advancement. Lay abstract: In research, there is a growing trend to bring advanced, high-performance equipment together into a centralised location. This is done to streamline how the equipment purchase is financed, how the equipment is maintained, and to enable an easier approach for research scientists to access these tools in a location that is supported by a team of technology experts who can help scientists use the equipment. These centralised equipment centres are called Core Facilities. The core facility model is relatively new in science and it requires an adapted approach to how core facilities are built and managed. In this paper, we put forward a seven-pillar model of the important supporting elements of core facilities. These supporting elements are: Technology (the instruments themselves), Core Facility Team (the technology experts who operate the instruments), Training (of the staff and research community), Career Tracks (for the core facility staff), Technical Support (the process of providing help to apply the technology to a scientific question), Community (of research scientist, technology experts and developers) and Transparency (of how the core facility works and the costs associated with using the service). These pillars stand on the bigger foundation of clear policies, guidelines, and leadership approaches at the institutional level. With a focus on these elements, the authors feel core facilities will be well positioned to support scientific discovery in the future.

A practical guide to bioimaging research data management in core facilities

Bioimage data are generated in diverse research fields throughout the life and biomedical sciences. Its potential for advancing scientific progress via modern, data-driven discovery approaches reaches beyond disciplinary borders. To fully exploit this potential, it is necessary to make bioimaging data, in general, multidimensional microscopy images and image series, FAIR, that is, findable, accessible, interoperable and reusable. These FAIR principles for research data management are now widely accepted in the scientific community and have been adopted by funding agencies, policymakers and publishers. To remain competitive and at the forefront of research, implementing the FAIR principles into daily routines is an essential but challenging task for researchers and research infrastructures. Imaging core facilities, well-established providers of access to imaging equipment and expertise, are in an excellent position to lead this transformation in bioimaging research data management. They are positioned at the intersection of research groups, IT infrastructure providers, the institution´s administration, and microscope vendors. In the frame of German BioImaging - Society for Microscopy and Image Analysis (GerBI-GMB), cross-institutional working groups and third-party funded projects were initiated in recent years to advance the bioimaging community's capability and capacity for FAIR bioimage data management. Here, we provide an imaging-core-facility-centric perspective outlining the experience and current strategies in Germany to facilitate the practical adoption of the FAIR principles closely aligned with the international bioimaging community. We highlight which tools and services are ready to be implemented and what the future directions for FAIR bioimage data have to offer.

Improving light microscopy training routines with evidence-based education

The low reproducibility of scientific data published in articles has recently become a cause of concern in many scientific fields. Data involving light microscopy is no exception. The low awareness of researchers of the technologies they use in their research has been identified as one of the main causes of the problem. Potential solutions have hinted at the need to improve technological and methodological education within research. Despite the pivotal role of microscopy core facilities in the education of researchers being well documented, facility staff (FS) often learn their trade on the job, without receiving themselves any structured education about the technology they teach others to use. Additionally, despite endorsing an important role at the highest level of education, most FS never receive any training in pedagogy, the field of research on teaching and learning methods. In this article, we argue that the low level of awareness that researchers have of microscopy stems from a knowledge gap formed between them and microscopy FS during training routines. On the one hand, FS consider that their teaching task is to explain what is needed to produce reliable data. On the other, despite understanding what is being taught, researchers fail to learn the most challenging aspects of microscopy, those involving their judgement and reasoning. We suggest that the misunderstanding between FS and researchers is due to FS not being educated in pedagogy and thus often confusing understanding and learning. To bridge this knowledge gap and improve the quality of the microscopy education available to researchers, we propose a paradigm shift where training staff at technological core facilities be acknowledged as full-fledged teachers and offered structured education not only in the technology they teach but also in pedagogy. We then suggest that training routines at facilities be upgraded to follow the principles of the Constructive Alignment pedagogical method. We give an example of how this can be applied to existing microscopy training routines. We also describe a model to define where the responsibility of FS in training researchers begins and ends. This involves a major structural change where university staff involved in teaching research technologies themselves receive appropriate education. For this to be achieved, we advocate that funding agencies, universities, microscopy and core facility organisations mobilise resources of time and funding. Such changes may involve funding the creation and development of 'Train-the-trainer' type of courses and giving incentives for FS to upgrade their technological and pedagogical knowledge, for example by including them in career paths. We believe that this paradigm shift is necessary to improve the level of microscopy education and ultimately the reproducibility of published data.

Elevating the Educational Mission of "Full-Service" Core Facilities through Formal Biotechnology Workshops

Core facility laboratories are an essential part of the successful research enterprise of many universities around the world. Core facilities provide state-of-the-art instrumentation and technologies to support research of all faculty, postdocs, and students on a fee-for-service basis. Academic next-generation sequencing cores are typically "full service" facilities, and access to and training on their instrumentation is limited to core staff. To address these limitations, we provided graduate students with technical training at our core facility. We developed a 1-week noncredit-bearing workshop and recruited 6 graduate students (N = 6) as part of a pilot program. The program involved online teaching, classroom-based teaching, and hands-on training in next-generation sequencing library preparation and sequencer operation. A post-participation survey revealed highly positive outcomes in terms of skill development and increased awareness of technologies offered by the core facility. A workshop of this scale could be incorporated into the graduate curriculum and extended to core facilities that focus on other technologies. We believe that introducing formal standardized teaching spearheaded by core facilities would improve the graduate student curriculum and hope that this study can provide guidance on curriculum design for similar workshops.

Approaches for single-cell RNA sequencing across tissues and cell types

Single-cell sequencing of RNA (scRNA-seq) has advanced our understanding of cellular heterogeneity and signaling in developmental biology and disease. A large number of complementary assays have been developed to profile transcriptomes of individual cells, also in combination with other readouts, such as chromatin accessibility or antibody-based analysis of protein surface markers. As scRNA-seq technologies are advancing fast, it is challenging to establish robust workflows and up-to-date protocols that are best suited to address the large range of research questions. Here, we review scRNA-seq techniques from mRNA end-counting to total RNA in relation to their specific features and outline the necessary sample preparation steps and quality control measures. Based on our experience in dealing with the continuously growing portfolio from the perspective of a central single-cell facility, we aim to provide guidance on how workflows can be best automatized and share our experience in coping with the continuous expansion of scRNA-seq techniques.

Strategies for Shared Research Resources for Enhancing Research Sustainability: Communicating Between Stakeholders and Managing Expectations to Maximize Value and Impact

Shared research resources occupy a unique role in the scientific research landscape. Sometimes called core facilities, shared research resources provide instrumentation, services, and expertise to a wide range of researchers. With dedicated staff maintaining instruments, training users, and supporting collaborations, these resources are well situated to churn out reproducible high-quality data, lead research innovation, create efficiencies, and stimulate economic development all while driving down capital costs for institutions. That being said, in the high-paced disciplines of science with limited resources and competing priorities, these resources are often obligated to demonstrate their worth, especially beyond traditional service delivery models. How can shared research resources quantify and communicate their value and impact to stakeholders for optimal support and sustainability? For best approaches towards value proposition, it is important to understand the various stakeholders in the shared research resource ecosystem, including their needs, expectations, and value systems. This will in turn inform models of support and best approaches for planning, positioning, managing, evaluating, and improving shared research resource output to return the most value to all stakeholders involved. It is imperative that communication is tailored for each unique group of stakeholders, and terminology and expectations are managed accordingly. This work attempts to curate and share approaches and best practices toward this effort, gathered through available literature and focused engagement with various shared research resource stakeholders.

Research Infrastructure Core Facilities at Research Centers in Minority Institutions: Part I-Research Resources Management, Operation, and Best Practices

Funded by the National Institutes of Health (NIH), the Research Centers in Minority Institutions (RCMI) Program fosters the development and implementation of innovative research aimed at improving minority health and reducing or eliminating health disparities. Currently, there are 21 RCMI Specialized (U54) Centers that share the same framework, comprising four required core components, namely the Administrative, Research Infrastructure, Investigator Development, and Community Engagement Cores. The Research Infrastructure Core (RIC) is fundamentally important for biomedical and health disparities research as a critical function domain. This paper aims to assess the research resources and services provided and evaluate the best practices in research resources management and networking across the RCMI Consortium. We conducted a REDCap-based survey and collected responses from 57 RIC Directors and Co-Directors from 98 core leaders. Our findings indicated that the RIC facilities across the 21 RCMI Centers provide access to major research equipment and are managed by experienced faculty and staff who provide expert consultative and technical services. However, several impediments to RIC facilities operation and management have been identified, and these are currently being addressed through implementation of cost-effective strategies and best practices of laboratory management and operation.

Rigor, Reproducibility, and Transparency in Shared Research Resources: Follow-Up Survey and Recommendations for Improvements

Rigor, reproducibility, and transparency (RR&T) are essential components of all scientific pursuits. Shared research resources, also known as core facilities, are on the frontlines of ensuring robust RR&T practices. The Association of Biomolecular Resource Facilities Committee on Core Rigor and Reproducibility conducted a follow-up survey 4 years after the initial 2017 survey to determine if core facilities have seen a positive impact of new RR&T initiatives (including guidance from the National Institutes of Health, new scientific journal requirements on transparency and data provenance, and educational tools from professional organizations). While there were fewer participants in the most recent survey, the respondents' opinions on the role of core facilities and level of best practices adoption remained the same. Overall, the respondents agreed that procedures should be implemented by core facilities to ensure scientific RR&T. They also indicated that there is a strong correlation between institutions that emphasize RR&T and core customers using this expertise in grant applications and publications. The survey also assessed the impact of the COVID-19 pandemic on core operations and RR&T. The answers to these pandemic-related questions revealed that many of the strategies aimed at increasing efficiencies are also best practices related to RR&T, including the development of standard operating procedures, supply chain management, and cross training. Given the consistent and compelling awareness of the importance of RR&T expressed by core directors in 2017 and 2021 contrasted with the lack of apparent improvements over this time period, the authors recommend an adoption of RR&T statements by all core laboratories. Adhering to the RR&T guidelines will result in more efficient training, better compliance, and improved experimental approaches empowering cores to become "rigor champions."

Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey

Background:  Knowing the needs of the bioimaging community with respect to research data management (RDM) is essential for identifying measures that enable adoption of the FAIR (findable, accessible, interoperable, reusable) principles for microscopy and bioimage analysis data across disciplines. As an initiative within Germany's National Research Data Infrastructure, we conducted this community survey in summer 2021 to assess the state of the art of bioimaging RDM and the community needs. Methods: An online survey was conducted with a mixed question-type design. We created a questionnaire tailored to relevant topics of the bioimaging community, including specific questions on bioimaging methods and bioimage analysis, as well as more general questions on RDM principles and tools. 203 survey entries were included in the analysis covering the perspectives from various life and biomedical science disciplines and from participants at different career levels. Results: The results highlight the importance and value of bioimaging RDM and data sharing. However, the practical implementation of FAIR practices is impeded by technical hurdles, lack of knowledge, and insecurity about the legal aspects of data sharing. The survey participants request metadata guidelines and annotation tools and endorse the usage of image data management platforms. At present, OMERO (Open Microscopy Environment Remote Objects) is the best known and most widely used platform. Most respondents rely on image processing and analysis, which they regard as the most time-consuming step of the bioimage data workflow. While knowledge about and implementation of electronic lab notebooks and data management plans is limited, respondents acknowledge their potential value for data handling and publication. Conclusion: The bioimaging community acknowledges and endorses the value of RDM and data sharing. Still, there is a need for information, guidance, and standardization to foster the adoption of FAIR data handling. This survey may help inspiring targeted measures to close this gap.

Assessing and Improving Research Quality in Core Facilities

Core facilities allow scientists to perform experiments needing specialized technologies in a time- and cost-efficient way. They became increasingly important and now produce a significant amount of research data. Experiments carried out in core facilities are typically shared between the facility staff and the users. However, sharing experiments brings additional challenges to ensure data rigor and reproducibility-for example, in communication, trust, and accountability. We present here an interactive website developed especially for core facilities that offers tools to help them assess, improve, and ensure research quality.

Do German university medical centres promote robust and transparent research? A cross-sectional study of institutional policies

Background

In light of replication and translational failures, biomedical research practices have recently come under scrutiny. Experts have pointed out that the current incentive structures at research institutions do not sufficiently incentivise researchers to invest in robustness and transparency and instead incentivise them to optimize their fitness in the struggle for publications and grants. This cross-sectional study aimed to describe whether and how relevant policies of university medical centres in Germany support the robust and transparent conduct of research and how prevalent traditional metrics are.

Methods

For 38 German university medical centres, we searched for institutional policies for academic degrees and academic appointments as well as websites for their core facilities and research in general between December 2020 and February 2021. We screened the documents for mentions of indicators of robust and transparent research (study registration; reporting of results; sharing of research data, code and protocols; open access; and measures to increase robustness) and for mentions of more traditional metrics of career progression (number of publications; number and value of awarded grants; impact factors; and authorship order).

Results

While open access was mentioned in 16% of PhD regulations, other indicators of robust and transparent research were mentioned in less than 10% of institutional policies for academic degrees and academic appointments. These indicators were more frequently mentioned on the core facility and general research websites. Institutional policies for academic degrees and academic appointments had frequent mentions of traditional metrics.

Conclusions

References to robust and transparent research practices are, with a few exceptions, generally uncommon in institutional policies at German university medical centres, while traditional criteria for academic promotion and tenure still prevail.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12961-022-00841-2.