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Team:SJTU-Software/Project/Tutorial
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Revision as of 20:37, 16 October 2014
Tutorial
“Easy BBK(An Easy Biobrick Blueprint’s pacKage)” has four main function: “search”, “compare”, “present”, and “upload”. This part will guide users about how to use this software tool.
2.2.1 How to start EASY BBK
Software environment: Java SE Development Kit 6 and later version.
1. Download EASY BBK from github
2. Download the latest JDK from http://www.oracle.com/technetwork/java/javase/downloads/index.html
3. Double click the Easybbk.jar and start Easybbk
2.2.2 Home Page
1/2. Click each icon to enter each function
2.2.3 Search
1. Go back to home page
2. Input keyword or sequence
3. Search by keyword
4. Search by sequence
5. Display advanced search conditions
1. Adjust the weight of the 4 properties to make them add up to 100
2. Click “Confirm” before starting search by keyword or sequence
1. Forward or Back to previous or next page
2. Display detail information of the biobrick
3. Click to view the main page of the biobrick on iGEM Registry
4. Check to add the biobrick to “compare”
5. Click to view the result most related to the biobrick on Google Scholar
6. Go to the previous page of search results
7. Go to the next page of search results
8. After biobricks being added from “search”, click to go to “compare” the biobricks
2.2.4 Compare
1. Remove the biobrick below from “Compare”
2. Click to view the main page of the biobrick on iGEM Registry
3. After biobricks being viewed in “compare”, click to go back to “search” results
2.2.5 Present
2.2.5.1 General introduction of Present Page
1. Basic Functions
2. Components on backbone
3. Proteins, plasmid, bacteriophage and chassis
4. Relation between biobricks
5. Backbone
6. Style settings of lines above
7. Bio-system drawing panel
8. Status bar
Basic Functions
1. Discard previous work and create a new bio-system
2. Open previously saved XML file
3. Save the drawn bio-system as an XML file to further edit next time
4. Export the picture of the bio-system as .jpg, .bmp or .png file.
5. Add text to the drawing panel
6. Change the font, size and color of the text
7. Delete components on drawing panel
8. Undo
9. Redo
Components on in bio-systems
1. Promoter
2. Ribosome binding site (RBS)
3. Protein coding sequence
4. Terminator
5. Primer
6. Reporter
7. Protein 1
8. Protein 2
9. Combined protein
10. Plasmid
11. Virus
12. Bacteria
Relation and backbone in bio-systems
1. Inhibit
2. Enhance
3. Other relations (e.g. this could denote a coding sequence code a protein.)
4. Backbone
5. Style settings of lines above
2.2.5.2 Start presenting your bio-system
1st: Draw backbone
Step 1. Click the “Backbone” icon
Step 2. Click anywhere on drawing panel to add a “Backbone”
Step 3. Stretch the “Backbone”
Step 4. Drag the “Backbone” to anywhere on drawing panel
2nd: Add a component to backbone
Step 1. Click the “Promoter” icon
Step 2. Click anywhere on drawing panel to add a “Promoter”
Step 3. Drag the “Promoter” to “Backbone” to automatically become part of the sequence
Step 4. Drag the “Backbone” to anywhere on drawing panel
Upload
Here, users could not only upload their self-created biobricks to our database, but also submit their form filled out in our software to the Registry to upload their self-created biobricks.
Compare
Multiple biobricks can be selected and compared. You can search and get multiple (up to three) biobricks, and compare them side by side.
SJTU-Software
Shanghai Jiao Tong University
800, Dongchuan Road
200240 Shanghai, China
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