Sub Cellular Localization

From Protein Prediction 2 Winter Semester 2014
Revision as of 21:00, 26 November 2014 by Ppwikiuser (talk | contribs) (Roadmap)

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

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
Week number Completed tasks Status
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. Template:Check mark








Project progress
Week number Completed tasks Status
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.
Check.jpg
Week 2
  • Coding for uploading file.
  • Parsing input file.
    • Counting number of proteins in cell's compartments.
    • Storing protein's score.
  • Writing functions for identifiying "x" and "y" positions of cell's compartments.
  • Highlighting cell's compartments upon "mouse-over" event.
Week 3
  • Visualization by:
    • Grouping proteins based on localization in the cell component.
    • Updating cell’s compartments based on particular protein’s score (Confidence).
Week 4
  • Development of deployable component for reuse by BioJS.
Week 5
  • Final presentation of project.