Difference between revisions of "Sub Cellular Localization"
From Protein Prediction 2 Winter Semester 2014
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! Week 2 |
! Week 2 |
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* Highlighting cell's compartments (static). |
* Highlighting cell's compartments (static). |
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** Updating cell’s compartments based on particular protein’s score/Confidence (dynamic). |
** Updating cell’s compartments based on particular protein’s score/Confidence (dynamic). |
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* Bug fixing |
* Bug fixing |
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* Final presentation of project. |
* Final presentation of project. |
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* Development of deployable component for reuse by BioJS. |
* Development of deployable component for reuse by BioJS. |
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* The images of the different cell compartments were saved in svg file format. |
* The images of the different cell compartments were saved in svg file format. |
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* Using the information from the user's input file, the number of proteins present in each compartment were determined. |
* Using the information from the user's input file, the number of proteins present in each compartment were determined. |
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− | * Each compartment was highlighted using a localization color scale, which was obtained by converting the number of proteins present in each localization into a percentage and matched to a color. |
+ | * Each compartment was highlighted using a localization color scale, which was obtained by converting the number of proteins present in each localization into a percentage of the total number of proteins and matched to a color. |
* A table to display all the proteins present in each cell compartment and their scores. |
* A table to display all the proteins present in each cell compartment and their scores. |
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* Upon 'mouseover' over a compartment, a tooltip was displayed, which shows the proteins present in that cell compartment, and the score (confidence) of the protein. |
* Upon 'mouseover' over a compartment, a tooltip was displayed, which shows the proteins present in that cell compartment, and the score (confidence) of the protein. |
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*Output |
*Output |
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− | [[File: |
+ | [[File:Loc0.png|thumb|center|500px|500px|Figure 12 : Home page]] |
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+ | [[File:Loc1.png|thumb|center|500px|500px|Figure 13 : Loading of input file.]] |
− | [[File: |
+ | [[File:Loc2.png|thumb|center|500px|500px|Figure 14 : 1) Highlighting of eukaryota cell's compartments by percentage of proteins number.]] |
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+ | [[File:Loc3.png|thumb|center|500px|500px|Figure 15 : 2) Highlighting of eukaryota cell's compartments by percentage of proteins number.]] |
− | [[File: |
+ | [[File:Loc4.png|thumb|center|500px|500px|Figure 16 : Highlighting of eukaryota cell's compartments by protein score.]] |
− | [[File: |
+ | [[File:Loc5.png|thumb|center|500px|500px|Figure 17 : 1) Highlighting of bacteria cell's compartments by percentage of proteins number.]] |
− | [[File: |
+ | [[File:Loc6.png|thumb|center|500px|500px|Figure 18 : 2) Highlighting of bacteria cell's compartments by percentage of proteins number.]] |
− | [[File: |
+ | [[File:Loc7.png|thumb|center|500px|500px|Figure 19 : Highlighting of bacteria cell's compartments by protein score.]] |
− | [[File: |
+ | [[File:Loc8.png|thumb|center|500px|500px|Figure 20 : 1) Highlighting of archaea cell's compartments by percentage of proteins number.]] |
− | [[File: |
+ | [[File:Loc9.png|thumb|center|500px|500px|Figure 21 : 2) Highlighting of archaea cell's compartments by percentage of proteins number.]] |
− | [[File: |
+ | [[File:Loc10.png|thumb|center|500px|500px|Figure 22 : Highlighting of archaea cell's compartments by protein score.]] |
− | [[File: |
+ | [[File:Loc11.png|thumb|center|500px|500px|Figure 23 : About page which contains information about the project.]] |
= GitHub Link = |
= GitHub Link = |
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− | The link to the GitHub account is : [ |
+ | The link to the GitHub account is : [http://3biogirls.github.io/Sub-cellular-localization-in-cell/index.html GitHub Sub-cellular localization in cell] |
− | The link to presetation is : |
+ | The link to presetation is : [[:File:Sub-cellular-localization-in-cell.pdf]] |
=Related components= |
=Related components= |
Latest revision as of 12:12, 29 January 2015
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
Case 1
One protein, one localization:
Case 2
Multiple proteins, multiple localizations:
Requirements
- 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
- D3 Data-Driven Documents - http://d3js.org/
- Tools
- GIMP Image editor
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
Week number | Completed tasks | Status |
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Week 1 |
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Week 2 |
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Week 3 |
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Week 4 |
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Week 5 |
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Week 6 |
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Implementation
What we did
- First, all the cell compartments were identified by the paths that were marked using the GIMP image editor.
- The images of the different cell compartments were saved in svg file format.
- Using the information from the user's input file, the number of proteins present in each compartment were determined.
- Each compartment was highlighted using a localization color scale, which was obtained by converting the number of proteins present in each localization into a percentage of the total number of proteins and matched to a color.
- A table to display all the proteins present in each cell compartment and their scores.
- Upon 'mouseover' over a compartment, a tooltip was displayed, which shows the proteins present in that cell compartment, and the score (confidence) of the protein.
- The proteins displayed in the tooltip were made clickable so that the cell image could be updated to reflect the scores of the protein in all the cell compartments.
- Finally, the cell compartments were highlighted using a score color scale, which was obtained by mapping the score of a protein in each cell compartment to a color.
Screenshots
- Marking cell compartments using GIMP image editor
- 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
The link to presetation is : File:Sub-cellular-localization-in-cell.pdf
Related components
The Compartments database The Compartments database