LUDC Bioinformatics unit – areas of expertise
The LUDC Bioinformatics unit provides researchers, students, and technical personnel affiliated with LUDC with bioinformatics, biostatistics, and computational support. The unit also offers access to a high-performance computing environment.
Please contact Dmytro Kryvokhyzha, head of the LUDC Bioinformatics unit, for general questions about support. For specific questions or support requirements, please click the link below for relevant contact information.
Link to webpage with more information about support and contact details
Bioinformatics support
Our bioinformaticians can help you with the following:
- Study design (sample size, sequencing type, sequencing depth, etc.)
- Reproducible and scalable analysis pipeline development
- Programming (Python, R, Bash, Awk, Snakemake)
- Selection of appropriate bioinformatics tools
- Manuscript preparation (methods description, figures, tables, data publishing, etc.)
Bioinformaticians:
Dmytro Kryvokhyzha, head of the LUDC Bioinformatics unit
Dmytro Kryvokhyzha's profile in Lund University's research portal
Mikael Åkerlund
Mikael Åkerlund's profile in Lund University's research portal
Alexandros Karagiannopoulos
Alexandros Karagiannopoulos' profile in Lund University's research portal
Biostatistics
Our biostatistician can help you with the following:
- Study design (prospective, retrospective, cross-sectional, longitudinal, case-control, case-cohort, nested case-control, etc.)
- Selecting the appropriate statistical methods for your study design and scientific question(s)
- Performing statistical analyses in R, SAS, SPSS, and STATA using reproducible research practices
- Results interpretation
- Manuscript preparation (statistical methods and results sections, tables, and figures)
- Responding to reviewers (maximum one hour)
Biostatistician:
Marlena Maziarz
Marlena Maziarz's profile in Lund University's research portal
Servers and high-performance computing
Our systems engineers can help you with the following:
- 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 who work in the HPC cluster environment
Systems engineers:
Johan Hultman, IT coordinator
Johan Hultman's profile in Lund University's research portal
Matthias Jeppsson
Link to Matthias Jeppsson's profile on Lund University's website
Database management
Our database administrator can help you with the following:
- Assisting and developing questionnaires/forms, ensuring they meet the requirements for entering 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
Database administrator:
Jasmina Kravić
Jasmina Kravić's profile in Lund University's research portal
Laboratory information management systems (LIMS)
Our systems engineer can help you with the following:
- Configuration and maintenance
- Setup of new data collections
Systems engineer:
Mikael Åkerlund
Mikael Åkerlund's profile in Lund University's research portal
Contact
Dmytro Kryvokhyzha
Head of the LUDC Bioinformatics unit
dmytro [dot] kryvokhyzha [at] med [dot] lu [dot] se