Your browser has javascript turned off or blocked. This will lead to some parts of our website to not work properly or at all. Turn on javascript for best performance.

The browser you are using is not supported by this website. All versions of Internet Explorer are no longer supported, either by us or Microsoft (read more here: https://www.microsoft.com/en-us/microsoft-365/windows/end-of-ie-support).

Please use a modern browser to fully experience our website, such as the newest versions of Edge, Chrome, Firefox or Safari etc.

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

Marlena Maziarz

  • 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

Mattias Borell, Johan Hultman

  • 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

Jasmina Kravić

  • 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)

Mikael Åkerlund

  • Configuration and maintenance
  • Creating local modules and enhancements to stock system
  • Setup of new data collections