Data visualization and UI
Data visualization is an important aspect of bioinformatics. A first glance at a histogram of protein expression values in a sample can already tell us about the distribution and quality of our data. A heatmap including clustering can reveal groups of proteins that behave in the same way across samples. Visualizations can range from single scatter plots to complex multi-dimensional plots with different levels of annotation. However, not everyone has the resources or the knowledge to programmatically produce high-quality and high-detail plots for their data. We implement and provide generic visualization tools or platforms that researchers can use to visualize but also explore in-house or their data.
The implemented visualization tools can either be standalone web-applications or part of existing platforms. This comes with the additional goal of providing an easy-to-use and navigate user interface. ProteomicsDB is an online resource for the exploration and visualization of quantitative omics expression data. It is constantly expanded with visualization and analysis tools to allow scientists to explore the stored data in various ways. Developing on such a platform requires proper data modeling as the underlying data are stored in a relational database (SAP HANA) as well as web development skills (frontend and backend).
Plots and visualization tools for ProteomicsDB are implemented using the D3JS programming language while the rest of the user interface will be developed in VueJS. For the database, SQL is used, while more database management systems are starting to get embedded/connected to the SAP HANA database, such as Neo4J, etc. For standalone applications, visualization can be done using R and R/shiny or Python and Django. It is highly recommended even in standalone applications to avoid the usage of R plots and use, instead, plots implemented in D3JS, as it will allow easier embedding of the application to other frameworks.
- Pathway visualization - BA, Internship
- VueJS plotting components - BA, Internship