Difference between revisions of "Sub Cellular Localization"
From Protein Prediction 2 Winter Semester 2014
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! Week 1 |
! Week 1 |
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− | *Researching Biology literature in order to identify proteins belonging to different cells (Archaea / Bacteria / Eukaryota) |
+ | * 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. |
+ | * Identify existing tools or libraries which can help us in visualizing input data. |
− | *Identification of importance of protein localization in cell's compartments. |
+ | * Identification of importance of protein localization in cell's compartments. |
− | *Obtaining images of Archea, Bacteria and Eukaryota. |
+ | * Obtaining images of Archea, Bacteria and Eukaryota. |
− | *Creation of repository in github. |
+ | * Creation of repository in github. |
− | *Definition of input file format. |
+ | * Definition of input file format. |
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! Week 2 |
! Week 2 |
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− | *Coding for uploading file. |
+ | * Coding for uploading file. |
− | *Parsing input file. |
+ | * Parsing input file. |
** Counting number of proteins in cell's compartments. |
** Counting number of proteins in cell's compartments. |
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− | ** Storing protein's score |
+ | ** Storing protein's score. |
− | * Writing functions for identifiying "x" and "y" positions of cell's compartments |
+ | * Writing functions for identifiying "x" and "y" positions of cell's compartments. |
+ | * Highlighting cell's compartments upon "mouse-over" event. |
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! Week 3 |
! Week 3 |
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+ | * Visualization by : |
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+ | ** Grouping proteins based on localization in the cell component |
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+ | ** Updating cell’s compartments based on particular protein’s score (Confidence) |
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! Week 4 |
! Week 4 |
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+ | * Development of deployable component for reuse by BioJS. |
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+ | * Final presentation of project. |
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Revision as of 21:14, 26 November 2014
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
- 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
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
Roadmap
Week number | Completed tasks |
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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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