1. Cell Biology
  2. Chromosomes and Gene Expression
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Science Forum: A survey of research quality in core facilities

  1. Isabelle C Kos-Braun  Is a corresponding author
  2. Björn Gerlach
  3. Claudia Pitzer  Is a corresponding author
  1. Interdisciplinary Neurobehavioral Core, Heidelberg University, Germany
  2. PAASP GmbH, Germany
Feature Article
Cite this article as: eLife 2020;9:e62212 doi: 10.7554/eLife.62212
6 figures, 1 table and 3 additional files

Figures

Figure 1 with 4 supplements
Comparison of core facilities by their operating mode and services offered.

(A) Distribution of the surveyed core facilities (CFs) by their operating mode. (B) Fraction [%] of facilities providing different services along the research process. The overall fraction for all CFs, regardless of their operating mode, is depicted in black; different colours represent different operating modes.

Figure 1—figure supplement 1
Distribution of surveyed core facilities according to their type of technology.

NMR, nuclear magnetic resonance.

Figure 1—figure supplement 2
Characteristics of the surveyed core facilities.

Distribution of CFs by number of employees (A), number of users per month (B), and amount of data produced in a month (C).

Figure 1—figure supplement 3
Opinion of core facilities on the importance of training and its aspects.

(A) Facilities were asked to rate the overall importance of training on a scale of 1 to 5. (B) Facilities were asked to list the most important aspects of the training they provide. The results were normalized for each operating mode.

Figure 1—figure supplement 4
Responsibility for raw data analysis.

Facilities were asked who performs the analysis of the raw data generated in the facility. The results were normalized for operating mode.

Figure 2 with 1 supplement
Research quality in core facilities: important factors, challenges and the current situation.

(A) Facilities were asked for the most important factors for achieving research quality (in blue) and the aspects that need to be improved in their facility (in red; open-field question). (B) Challenges faced by core facilities, grouped in three categories (financial, technical and personal/interpersonal). The category “career progression” includes “permanent positions” and “motivation”. (C) Facilities were asked if they agree or not that samples/experiments are replicated at their facility. Facilities were asked to rank on a 5-point scale whether they know what controls are included in experiments (D), and whether users are allowed to proceed with samples of poor quality (E). Facilities were also asked whether they have a quality control for data analysis (F) and, if not, how important such control would be. (G) Facilities were also asked if their involvement in manuscript preparation would improve the quality of published data.

Figure 2—figure supplement 1
Proportion of core facilities having sufficient funding and number of staff.
Figure 3 with 4 supplements
The use of management software and data management in core facilities.

(A) Facilities were asked if they use management software and, if not, whether it would be useful. (B) Proportion of different management software used by core facilities. Software used by only one or two facilities is included under “Other”. In a series of “yes” and “no” questions, facilities were asked if they use data management plans (C), have a system to identify the raw data behind a published figure (D), and have sufficient documentation (E). The results were normalized for operating mode.

Figure 3—figure supplement 1
Core facilities were asked in an open question which tools could be used to improve research quality.

The category “technical aspects” includes instrumentation, robots, automation and improving techniques.

Figure 3—figure supplement 2
Comparison of two categories of management software used in core facilities showing the steps of the experimental process they cover.

CF management software is shown in red, and data management software is shown in blue. The dashed lines indicate that some tasks are not covered or only partially covered by CF management software.

Figure 3—figure supplement 3
Management software used in core facilities by operating mode.

Proportion of the different management software used by core facilities, normalized per operating mode. Software used by only one or two is included under “Other”.

Figure 3—figure supplement 4
Current situation in core facilities regarding different aspects of data management.

Facilities were asked to rate how different aspects of data management are implemented in their facility.

Current state of communication and interaction between core facilities and users.

FFs were asked if the communication between facility staff and users needs to be improved (A), if users use the information provided by facility staff (B), facility staff know how samples have been prepared (C), and if the users contact the facility when they are writing a manuscript (D).

Responsibility for the long-term storage of raw data.

Facilities were asked who is responsible for the long-term storage of raw data. When facilities were not responsible, they were asked if they thought they should be.

Main repercussions of insufficient funding on quality revealed by the survey.

A shortage of funding (left) will have adverse impacts on staff (top), management (middle) and equipment (bottom), each of which will have further repercussions on research quality. This schematic figure shows how the different aspects of quality discussed in this paper are linked together. Additional files.

Tables

Table 1
The proposed four checkpoints to improve quality of research in core facilities.

Based on the current situation in core facilities (CFs) revealed by the survey, four checkpoints were identified, which have the highest potential to improve rigor and reproducibility.

CheckpointsRecommendations
Experimental designCFs should provide information and advice on the experimental design and encourage their users to follow good research practices. They should check the experimental design and reject any ill-designed project.
Sample qualityCFs should control sample quality before starting the experiment and reject samples of poor quality. In case of limiting or rare samples, CFs should discuss with their users what consequences the sample quality will have on data interpretation and if the experiment should continue.
Data analysisCFs and PIs should decide who will be responsible for checking data analysis.
PublicationCFs should be informed before the data produced at the CF are submitted for publication to have the possibility to check them if they wish to.

Additional files

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