Although data analysis has always been an important part of scientific research, the scale has changed in recent years. With the introduction and adoption of High Throughput Sequencing (HTS) methods a different approach to data analysis is now required. Before, most analyses in Life Sciences could be conducted on a personal PC. But the large amounts of data and the requirements of the HTS analysis algorithms call for dedicated servers and an optimized storage solution.
The Applied Bioinformatics & Biostatistics group has been founded with three goals in mind:
- enable wetlab scientists to perform everyday bioinformatic analyses through a user-friendly interface
- provide expertise to tackle custom data and statistical analysis
- offer consultancy and training
This core facility within PSB is also available for industrial collaborations. If you have further questions, get in touch with us!
Bioinformatics
Currently our main focus is in High Throughput Sequencing (HTS) analysis, ranging from RNA-seq, over ChIP-seq, to variant and methylation calling. Next to the data analysis, we also provide expertise in setting up your experiment (see also biostatistics) and identifying the appropriate technology for you research question.
While we develop the analysis pipelines command line, we provide standard workflows through a user-friendly interface in Galaxy. For RNA-seq this workflow involves preprocessing of the raw data, mapping of the reads to the genome and summarize to a count table. By providing a user-friendly graphical environment, instead of command line usage of our high-memory computing cluster (which requires in-depth knowledge of unix), we enable wetlab scientists to perform these analyses themselves. For the statistical correct processing of your data, we offer solutions through consultancy.
Next to HTS analysis, we also provide a broad expertise in bioinformatics analyses. We can offer help in computationally solving systems biology problems such as gene network inference, gene set enrichment, gene annotation, etc. Besides this, our team is also experienced in using modeling approaches to solve a wide range of biological problems. General methodologies typically applied are clustering, regression and classification. With years of experience, we can also provide custom software or scripts to improve and automate your analysis. We apply different programming languages tailored to the analysis: python, java, perl, R, php, javascript, ... If you have further questions, get in touch with us!
Biostatistics
The main task of the statistical consultant is to advise the scientific staff about the design of an experiment and data analysis using modern techniques. The goal is to enable scientists to perform the statistical analyses of their data.
To ensure that your experimental setup is adequate to address the research question, it is desirable to include the statistical consultant from the beginning of the project. He/she will verify that the planned set-up and size of the study will be adequate.
In the Applied Bioinformatics and Biostatistics group, we provide expertise to optimize your experimental setup for your biological questions as well as help with the analysis. We aim to enable scientist to perform the analysis themselves but can also be contacted for custom data analysis projects. If you have further questions, get in touch with us!