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 : Protein's score in cell compartment (One protein)
Figure 2 : Number of Proteins in cell compartment (more than one protein)
Figure 3 : Protein's score in cell compartment (more than one protein)
- 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
DHTML, JavaScript Draw Line, Circle, Ellipse (Oval), Polyline, Polygon, Rectangle
Image 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.
Figure 4 : Text File format
Roadmap
Project progress
Week number
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Completed tasks
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Status
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Week 1
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- 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.
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Week 2
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- 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 (static).
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Week 3
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- Visualization by:
- Grouping proteins based on localization in the cell component.
- Highlighting cell's compartments (dynamic).
- Updating cell’s compartments based on particular protein’s score/Confidence (dynamic).
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Week 4
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- Development of deployable component for reuse by BioJS.
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Week 5
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- Final presentation of project.
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Implementation
Figure 6 : Validation File size
Figure 7 : Validation Cell type
Figure 8 : Validation Use cases 1 & 2
- Highlight cell's compartments following number of proteins and score
Figure 9 : Highlight cell's compartments algorithm
- Showing popup, in case one protein and more than one protein in input file
Figure 10 : Showing popup's algorithm
Figure 12 : Loading of input file.
Figure 13 : 1) Highlighting of eukaryota cell's compartments by number of proteins.
Figure 14 : 2) Highlighting of eukaryota cell's compartments by number of proteins.
Figure 16 : 1) Highlighting of archaea cell's compartments by number of proteins.
Figure 17 : 2) Highlighting of archaea cell's compartments by number of proteins.
Figure 18 : Highlighting of archaea cell's compartments by score.
Figure 19 : 1) Highlighting of bacteria cell's compartments by number of proteins.
Figure 20 : 2) Highlighting of bacteria cell's compartments by number of proteins.
Figure 21 : Highlighting of baceria cell's compartments by score.
Figure 22 : About page which contains information about the project.
GitHub Link
The link to the GitHub account is : GitHub Sub-cellular localization in cell