Bartłomiej Wilkowski

Leading an IT group responsible for:
- administration, maintanence and further development of the existing internal biobank's IT systems and infrastructure (e.g. LIMS, automated freezers, laboratory robots, data analytics etc.);
- maintanence and further developments of the national system: Danish Biobank Register;
- design and development of the Danish National Biobank's databank in collaboration with Danish supercomputing provider (Computerome) and the Nordic e-Infrastructure Collaboration (NeIC);
- research related data extractions;
- design of ETL processes supporting efficient data management and flow between heterogeneous biobank related systems and databases;

Lead designer and developer of the Danish National Biobank Register (www.biobanks.dk). This project integrates huge amounts of patient data (person information, health-related (diagnosis) information, and sample information) from various data repositories in Denmark (person registers, hospital registers, biobanks). The Biobank Register provides efficient search service for biomedical researchers and MDs.

Involved and responsible for:
- Determining system requirements (organizing meeting with the target users, mockups, presentations, etc.)
- Database and system design
- Database implementation and administration
- Implementation of web services
- Efficient integration of the data sources (registers)
- Development of automatic update mechanism for the system database
- Testing
- Documentation

Recently, I am responsible for expanding the coverage of the Danish Biobank Register to other Nordic countries and creating the Nordic Biobank Register.

Member (representative of the Nordic Biobank Network) of the reference group in the Tryggve project (Nordic IT infrastructure project administered by NeIC and funded by NordForsk).

IT environment: MS SQL, .NET, Java, Spring Framework, Python, MS Office Suite, JIRA.

This external research training is carried out on the National Institutes of Health, Bethesda, MD, USA.

Scope of the research:

- Literature-based knowledge discovery in the medical domain - employing graph theory for automated discovery of the unknown links and relations of various medical concepts using UMLS ontology and semantic predicates.

- Improving an indexing process for medical publications from the PubMed database using machine learning techniques.

3-year PhD studies period. Topic: Knowledge Discovery for Neuroinformatics.

Content: Involved in the Cimbi.org project, neuroscientific database integration, automatic keyword extraction from abstracts, prospective searching, Matlab toolbox development, ontological engineering.

Employed in the medical project Cimbi.org (Center for molecular brain imaging). Matlab toolbox and plugin development. Java programming. Database administration and modelling.

Participation in the cycle of the workshops about the web applications programming in Java and JSP. Participation in the project CGM ERA made for the polish mobile network provider Era PTC. Usage of the Eclipse platform with Hibernate and Spring frameworks, XML & Ant, JSP. The internship was concurrent with attending the classes at the university.

Collaboration in the project www.velocimetro.org. Pivotal aim of this project is to measure and demonstrate to the web users the Quality of Service and effectiveness of the transfers through the Internet. Java programmer work - preparing the application
for automatic generation of graphics, image objects and HTML pages in dependence with the database data. Technical reports writer (in English and Spanish).

3-tier architecture designer and programmer. "Atena" web project for high school management.