When working with medical data, in this case NGS data, quality control (QC) is essential. To be able to gather and compile quality control data from NGS runs and put it in a nocoBD table in structured format, I created an ETL procedure. In order to obtain an in-depth understanding of a sample's performance in the sequencing run as well as the secondary and tertiary analyses, this data can be utilized to aggregate several QC metrics. From bcl2fastq to CollectHsMetrics.
2024-11-29
As NGS analysis becomes more advanced, different meaningful results can be obtained. In the case of a Whole Exome Sequencing (WES) Pipeline, complex biomarkers, Single Nucleotide Polymorphisms (SNPs), small InDel Mutations, Copy Number Alterations (CNAs), and mutation profiles, for example. I developed a Technical Report Generator in R utilising knitr, CRAN, and bioconductor packages. That report comprises information retrieved from a nocoDB via API snippets.
2024-07-07
Away from paper and towards more digital processes. The use of nocoDB as an "interactive database" for dockets, tracking and searches has been successfully established. In addition, further features have been added to nocoDB, which enable highlighting in the table views, customizable for each user and use case.
2024-03-08
Digitization has transformed medical health and pathology, leading to better patient care and diagnosis precision. Digitalization has automated and streamlined procedures, resulting in faster and more accurate workflows. Digital pathology systems allow pathologists to analyse digital slides, making information more accessible and shareable. This also allowes for remote consultations and communication among pathologists. We are currently modernising procedures and systems, pushing pathology's digitalization to the next level.
2024-01-20
Using MRBS, I setup a web based room booking and reservation system. No more booking collisions and more missed meetings. Another nice improvement on our way to digitalization.
2023-04-29
Using nocodb and adding some custom code, I built a sample tracking system for the lab. That way we can switch from paper to digital data. Another plus: Data can now be search, exported, imported and customized workflows are supported. I really love the simple setup and huge potential of this solution.
2023-04-26
The Open Cases Tracker became the Open Cases Checker - OCC and is now in productive setting. Based on the feedback of users, I added different features and cron jobs to keep all information updated and display recent cases automatically. Some auto filters and some more complex regular expressions keep the page clean and makes data import much more robust.
2023-04-08
To streamline data analysis processes, I implemented different micro services. An ETL process to collect new cases and transform them into database entries. As interactive frontend a bootstrap5 UI to check and change status of a case. jQuery and AJAX API components to update interface and database. This is still unter development.
2023-03-10
I developed a dockerized verion of redmine (based on Vladimir Afinello's github repository) with additional plugins, themes and some other improvements. I really enjoyed this.
2023-02-16
Started my new job as head of bioinformatcs in a molecular pathology department.
2023-02-01
Finally a new Version of my homepage and my sites. It took quite a while to change the design and also the main focus.
2022-10-10
Site might be offline for a while. Redesign, new focus, and structural changes.
2022-10-01