Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities

Abstract

Over the last decade, the cost of -omics data creation has decreased 10-fold, whereas the need for analytical support for those data has increased exponentially. Consequently, bioinformaticians face a second wave of challenges: novel applications of existing approaches (e.g., single-cell RNA sequencing), integration of -omics data sets of differing size and scale (e.g., spatial transcriptomics), as well as novel computational and statistical methods, all of which require more sophisticated pipelines and data management. Nonetheless, bioinformatics cores are often asked to operate under primarily a cost-recovery model, with limited institutional support. Seeing the need to assess bioinformatics core operations, the Association of Biomolecular Resource Facilities Genomics Bioinformatics Research Group conducted a survey to answer questions about staffing, services, financial models, and challenges to better understand the challenges bioinformatics core facilities are currently faced with and will need to address going forward. Of the respondent groups, we chose to focus on the survey data from smaller cores, which made up the majority. Although all cores indicated similar challenges in terms of changing technologies and analysis needs, small cores tended to have the added challenge of funding their operations largely through cost-recovery models with heavy administrative burdens.

Keywords: ABRF; funding model; institutional support; omics.

FIGURE 1.

Technologies supported by small bioinformatics cores. A) Bioinformatics technologies. Response to survey question: Which kinds of bioinformatics do you support? B) Next generation (nextgen) sequencing technologies. Response to survey question: What kinds of nextgen sequencing do you support? ATAC-seq, assay for transposase-accessibly chromatin sequencing; ChIP-seq, chromatin immunoprecipitation sequencing; CRISPR, clustered regularly interspaced short palindromic repeats; CyTOF, mass cytometry; DNA-seq, DNA sequencing; FACS, fluorescence activated cell sorting; HiC/3C/4C, chromatin conformation capture techniques; MethylSeq, methylation sequencing.

FIGURE 2.

Financial support models for small bioinformatics cores. A) Institutional support to cores. Response to survey question: What form does institutional financial support to the core take? B) Other sources of funding. Response to survey question: What other sources of funding are part of your core’s funding model? C) Charging mechanisms. Response to survey question: How do you charge for your work? $/h, dollars per hour; $/FTE/mo, dollars per full-time equivalent per month.

FIGURE 3.

Development and support of custom software by small bioinformatics facilities. A) Reasons for development of custom software. Response to survey question: If developing custom software for investigators, why? B) Cost recovery for custom software. Response to survey question: If you develop custom software, how is your time paid for?

FIGURE 4.

Data storage models at small bioinformatics cores. Response to survey question: How do you store investigator data files?

FIGURE 5.

Reporting and accreditation practices at small bioinformatics cores. A) Reporting practices for grants and papers. Response to survey questions: Are you required to report on grant submissions you have helped with? If yes, are you required to report on which were funded? Are you required to report on manuscripts you have assisted with? If yes, are you required to report on which were accepted for publication? B) Recording and notification for grants. Response to survey question: How do you track which grants are funded? C) Recording and notification for papers. Response to survey question: How do you track which manuscripts were published? PI, primary investigator.