LUDC Bioinformatics Unit
We provide bioinformatics, biostatistics and computational support to anyone affiliated with LUDC, as well as access to a high-performance computing environment. Our fields of expertise cover a wide range of areas.
Bioinformatics
Dmytro Kryvokhyzha (Head of the LUDC Bioinformatics Unit), Mikael Åkerlund
- Designing a study (sample size, sequencing type, sequencing depth, etc.)
- Developing reproducible and scalable analysis pipelines
- Programming (Python, R, Bash, Awk, Snakemake)
- Selecting appropriate bioinformatics programs
- Manuscript preparation (methods description, figures, tables, data publishing, etc.)
Biostatistics
- Designing a study (prospective, retrospective, cross-sectional, longitudinal, case-control, case-cohort, nested case-control, among others)
- Selecting the appropriate statistical methods to use for your study design and your scientific question(s)
- Performing statistical analyses in R, SAS, SPSS, or STATA using reproducible research practices
- Interpreting results
- Manuscript preparation (statistical methods and results sections, tables, and figures)
- Responding to reviewers
Servers and High Performance Computing
- Creating tools, webapps and scripts for users and groups / studies
- Programming (PHP, Perl, JavaScript, Bash)
- Databases (PostgreSQL, MySQL, MariaDB, DB2, SQLite)
- System administration of our server systems
- General Linux knowledge
- Installation and maintenance of a software repository for our HPC cluster
- Maintaining backups of servers, databases, and all data stored in GPFS, our storage for the HPC cluster
- Guiding and helping users working in the HPC cluster environment
Database management
- Assisting and developing questionnaires/forms, ensuring they meet requirements for the entry and reporting of clinical data of varying complexity
- Defining and creating datasets in the database for receiving, processing, and tracking data
- Transforming/coding, cleaning, and uploading the collected data from different studies/sources
- Controlling access to the database, setting data privacy and ensuring data integrity
- Generating data retrievals and summaries for national and international projects
- Providing statistical summaries of data
Laboratory information management systems (LIMS)
- Configuration and maintenance
- Creating local modules and enhancements to stock system
- Setup of new data collections
