User Experience Project Structure Design
In this section, we describe the user experience project structure design of the PHYLOViZ Web Platform. We describe the vision of what the user will be able to do within the app's project structure and what features are to be available.
- Creating a Project
- Computing and Visualizing
- Multiple Views and Algorithms
- What's new - Main differences from PHYLOViZ ONLINE and PHYLOViZ (desktop version)
Firstly, the user must create a project, give it a name, and upload the necessary files, like the profiles dataset.
A project file structure is shown to the user, first only having the initial uploaded files (profiles dataset).
Clicking on the dataset box will show a list of options:
- Launch Tree - Go through all the computational steps (calculate distance matrix, calculate inference tree, calculate coordinates) and show the tree at the end.
- Calculate Distance Matrix - Calculates the distance matrix, which is the next step.
- View - View the dataset as a table.
- Download - Download the dataset as a file.
When choosing the launch tree or calculate distance tree options, the project file structure will update as shown in the below images.
Just like the dataset box, clicking in any of the intermediate step boxes will show a list of options:
- View - View the distance matrix. Multiple view options may be available (table view, heatmap view).
- Calculate inference tree - Calculates the inference tree, which is the next step.
- Launch tree - Go through the rest of the computational steps (calculate inference tree, calculate coordinates) and show the tree at the end.
- Download - Download the distance matrix as a file.
- View - View the inference tree. Multiple view options may be available.
- Calculate tree coordinates - Calculates the tree coordinates, which is the next step.
- Launch tree - Go through the rest of the computational steps (calculate coordinates) and show the graph tree at the end.
- Download - Download the inference tree as a file.
- View - View the tree. Multiple view options and layouts may be available.
Whenever an option that calculates the tree coordinates is selected (this includes the launch tree options), a new Tree View box is created, possibly resulting in multiple views, even if the same algorithms were used.
Each step is identified with the specific algorithm that was used. Provided the option to choose what algorithm is to be used for each step, this may result in multiple algorithms being used, and being appropriately organized in the project structure.
In the online version, it's already possible to view the distance matrix as a heatmap, but the limitation is that it's necessary to compute all the steps and launch the tree, and only after that the possibility of generating a heatmap based on selected nodes is given. In this new version, the aim is to provide an easy way to compute and visualize only what the user deems as necessary.
In the desktop version, it's already possible to to generate multiple tree views for a same project. However, these views encompass all the intermediate steps. In this new version, it is important for the intermediate steps to be shown and carefully organized, providing a way for multiple algorithms to be used in different combinations.