The Product

We all know the feeling of dealing with a massive dataset in excel. Plotting part of the data is an even greater disaster than only dealing with the data. Not even speaking of combining data from different datasets in one plot. Our final product is the application you need if you struggle with these kinds of problems. For the project we got three different datasets with all their corresponding metadata dataset, related to breast cancer research. These datasets contain data about the Metabolomics, Proteomics and Transcriptomics of breast cancer cells in different cell lines. First you select the type of the dataset, and the dataset. Now you can easily select filters which will adjust the dataset visible on the dataset tab. When you not only want the data but also a visual representation, you can generate different kinds of plots. Choose the type of plot you want and which properties you want to display on the x- and y-axis. Now the plot will be visible under the plot tab. Genes have multiple ways of naming. When you have a different naming of a gene than is used in this application, you can search for another naming of the gene, for example the ENSG symbol, under the Look-up tab. The plots and adjusted datasets can be downloaded together with a log-file which later can again be uploaded to retrieve the same plots and data.

The Customer

Our customer is Hanneke Leeghwater, a Promovendus at the Leiden Academic Centre for Drug Research. She wanted us to program an application which can be used to search for the expression of a specific gene in multiple datasets. The information on the gene expression can then be used to design new experiments. The collaboration went very smoothly. In the first week we got a clear list of requirements for the application with also a few extra requirements which were not mandatory, but useful if implemented. We met almost every week, to give a demo and to check if what we implemented was meeting her expectations.

  • "Software Engineering is expectation management "
  • "The best way to get a project done faster is to start sooner. "
  • "The biggest issue on software teams is making sure everyone understands what everyone else is doing. "
  • “Guys, we still have to do the retrospective.”
The Team

We are a group of six students. Four of us are bioinformatics students and the other two are computer science students. In order to make sure our planning was solid, the decision was made to make one member the Product Owner and one member the Scrum Master. Due to this, working together went smoothly, although it remained a challenging task to keep everybody on the same track. The fact that there were some issues within the team brought the core members of the team closer together and worked as an extra motivation to deliver a result of which we would be immensely proud of. In addition, we focused in this project on our own strengths within coding and generating new strengths for each member. These new strengths, for example, are frontend design, backend interactions and CI/CD with the use of Docker and Github Actions.

The Technologies