biojs-sub-cellular-localization-in-cell v0.2.0

Sub-cellular-localization-in-cell

Description

"Sub-cellular-localization-in-cell" is a component 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.

Documentation

Input data:

• Input data file should be either a ".txt" or ".csv" file.
• Text file must contain proteins of only one type of cell.
• 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.

Supported Web browsers:

• Google Chrome

Click here to see this component in action.

Implementation:

• 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 and matched to a color.
• We included 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.

Description of color scale for localization and score:

Localization: The lightest color represents the minimum number of proteins in a cell compartment, in contrast, the darkest color represents the maximum number of proteins within a cell compartment. These values are also expressed in percentages where the lightest color matches with 0% and the darkest color with 100%.

Score(confidence): The color scale for score (confidence) is based on percentages from 0 to 100 % where 0 means low confidence and 100 means accurate confidence.

Contributing

All contributions are welcome.

Support

If you have any problem or suggestion please open an issue here.

License

This software is licensed under the Apache 2 license, quoted below.

Copyright (c) 2015, 3Biogirls.

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.