Sub Cellular Localization

Sub Cellular Localization in Cell

Objective

"To visualize biological cells and highlight by a user selected sub-cellular compartments in a way that they stand out from the un-selected ones"

GUI mockups

Figure 1 : Number of Proteins in cell compartment

Figure 2 : Protein's score in cell compartment

• User experience
  • Interactivity
  • Easy identification of the number of proteins in cell compartment
  • Good visualization of data
• Functionality
  • Parsing the user input “txt” file
  • Mapping the file content into visualization
• Features
  • Good color scheme to highlight :
    • Number of proteins in a compartment
    • Score of each protein (confidence)

Application design

• Expected technical difficulties
  • Wrong file input format
  • Correct identification of localization
• Libraries
  • D3 - Zoomdata
    • https://live.zoomdata.com/zoomdata/visualization#51db7ad4e4b04caf9ab346db-51db7ad4e4b04caf9ab346d5

Data

• Remarks about input format
  • Each text file must contain proteins of only one type of cell
  • Text file format:
    • Protein id
    • Score (certainty of existence of particular protein within a cell compartment)
    • Localization (component)
    • Cell type

Figure 3 : Text File format

Roadmap

Figure 4 : Roadmap

The table's caption

Week number	Completed tasks
Week 1	*Researching Biology literature in order to identify proteins belonging to different cells (Archaea / Bacteria / Eukaryota) Identify existing tools or libraries which can help us in visualizing input data. Identification of importance of protein localization in cell's compartments. Obtaining images of Archea, Bacteria and Eukaryota. Creation of repository in github. Definition of input file format.
Week 2	*Coding for uploading file. Parsing input file. Counting number of proteins in cell's compartments.