Difference between revisions of "Sub Cellular Localization"
From Protein Prediction 2 Winter Semester 2014
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[[File:eukaryota2.png|thumb|center|500px|500px|Figure 14 : 2) Highlighting of eukaryota cell's compartments by number of proteins.]] |
[[File:eukaryota2.png|thumb|center|500px|500px|Figure 14 : 2) Highlighting of eukaryota cell's compartments by number of proteins.]] |
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+ | [[File:Eukatyota3.png|thumb|center|500px|500px|Figure 15 : Highlighting of eukaryota cell's compartments by score.]] |
Revision as of 17:36, 5 January 2015
Sub Cellular Localization in Cell
Contents
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
- 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)
- Good color scheme to highlight :
Application design
- Expected technical difficulties
- Wrong file input format
- Correct identification of localization
- Libraries
DHTML, JavaScript Draw Line, Circle, Ellipse (Oval), Polyline, Polygon, RectangleImage map generator- D3 Data-Driven Documents - http://d3js.org/
Data
- Remarks about input format
- Text file must contain proteins of only one type of cell
- Text file format :
- Input data file should be either a ".txt" or ".csv" file.
- File’s first line should contain cell type (i.e: eukaryota, archea, bacteria).
- File's second line should contain Score (i.e: 0-100). Note: Minimum score should be zero.
- File's third line should contain columns description (i.e: Protein Id, Score, Localization).
- User’s file can have more than 3 columns but additional columns will not be executed.
Roadmap
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Implementation
- Parsing input file
- Highlight cell's compartments following number of proteins and score
- Showing popup, in case one protein and more than one protein in input file
- Output
GitHub Link
The link to the GitHub account is : GitHub Sub-cellular localization in cell