UAB Biological Data Sciences (U-BDS) Core
The UAB Computational Biology Core provides researchers with access to appropriate computational resources, as well as education and training on the use of bioinformatics software. Dr. Liz Worthey is the Core Director, and Dr. Lara Ianov is the Co-Director. U-BDS provides consultation service to faculty, staff, and trainees within UAB and data analysis services through percent effort and fee-for-service. Our team of computational biologists and bioinformaticians have performed analysis and interpretation of data for a variety of omics-based projects. Our team is also experienced in the development of robust and reproducible pipelines and analysis tools for use in these applications of computational biology as well as with data visualization. We have access to all of the necessary computational tools and methods needed for complex computational biology and bioinformatics projects.
Currently, supported use cases include 1. Identification and interpretation of whole-genome sequence or whole-exome sequence derived variation including chromosomal abnormalities. 2. Polygenic risk score (PRS) generation for traits in individuals with common complex and rare disease. 3. RNA sequencing including differential expression (total RNA/mRNA/miRNA), single-cell/single-nuclei (RNA, ATAC, multimodal, CITE-seq), spatial transcriptomics (10x Visium and 10x Xenium), and subsequent pattern/pathway matching analyses. 5. Variant impact prediction on protein structure including with the introduction of multiple variants. 6. Whole-genome and reduced representation bisulfite sequencing 7. Integrative analyses spanning the above use cases and including network analyses like cell-cell signaling, etc. U-BDS follows best practices in reusable tool and method development and we 1. Define the appropriate standardized set of analytical tools necessary to meet the needs across the biological research programs and grants at UAB. 2. Deliver a toolkit by building or integrating existing algorithms, pipelines, tools, and infrastructure. 3. Where applicable, deliver centralized data repositories necessary for biological data. 4. Work with Research Computing to source and size the necessary computer infrastructure. 5. Provide training to our institutional researchers, students, or collaborators so that they can be maximally efficient and effective in their analyses based on the appropriate framework, tools, and data and 6. Continuously monitor and evaluate cutting edge data science approaches to ensure UAB researchers are using the most appropriate and up-to-date tools, pipelines, and methods.
A critical function of the U-BDS is also to provide opportunities across the UAB departments to learn and access data science materials. To expand on this critical topic, U-BDS provides bi-annual two-day Software and Data Carpentry courses, which teach foundational coding and data science skills to researchers including R and Python programming, the unix shell, version control with git, reproducible scientific analysis and data visualization. U-BDS also provides annual workshops on a special topic which includes analysis such as bulk RNA-seq analysis, nf-core pipelines and Nextflow with current plans to expand into other areas. U-BDS also offers weekly drop-in office hour sessions where community members can meet with U-BDS staff without a prior appointment and for free to get advice concerning their data science questions, projects, and study design. Community members across departments access office hours through Zoom and Slack.