Difference between revisions of "Team:IIT-Madras/Design"
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<h1>User Experience Design</h1> | <h1>User Experience Design</h1> | ||
<h2>Home page</h2> | <h2>Home page</h2> | ||
| − | When the user hits on the home page, (s)he can either search for organisms, browse through the index or choose to contribute data for an organism that are not yet in the database. | + | When the user hits on the home page, (s)he can either search for organisms, browse through the index or choose to contribute data for an organism that are not yet in the database. |
| + | <br><img src="https://static.igem.org/mediawiki/2017/b/b2/T--IIT-Madras--ss1.png" style="width: 100%;"> | ||
<h2>Add/edit page</h2> | <h2>Add/edit page</h2> | ||
The add new organism page and edit organism data page have a similar design, carefully designed to provide the user with the description of the data that is expected to be entered. | The add new organism page and edit organism data page have a similar design, carefully designed to provide the user with the description of the data that is expected to be entered. | ||
| + | <br><img src="https://static.igem.org/mediawiki/2017/d/da/T--IIT-Madras--ss2.png" style="width: 100%;"> | ||
<h2>View page</h2> | <h2>View page</h2> | ||
The details about each organism can be viewed on the view page. The page is designed for easy navigation to different sections of the entry. This page also contains a link to edit the entry | The details about each organism can be viewed on the view page. The page is designed for easy navigation to different sections of the entry. This page also contains a link to edit the entry | ||
| + | <br><img src="https://static.igem.org/mediawiki/2017/5/53/T--IIT-Madras--ss3.png" style="width: 100%;"> | ||
<h1>Chassis tools</h1> | <h1>Chassis tools</h1> | ||
| Line 48: | Line 51: | ||
<h2>Codon optimization tool</h2> | <h2>Codon optimization tool</h2> | ||
We have designed and integrated a highly interactive tool for codon optimization. The optimized sequence can be manually edited to remove restriction sites or reduce GC content, using a drop-down menu that shows codons that can be used to replace the current codon without changing the amino acid. | We have designed and integrated a highly interactive tool for codon optimization. The optimized sequence can be manually edited to remove restriction sites or reduce GC content, using a drop-down menu that shows codons that can be used to replace the current codon without changing the amino acid. | ||
| + | <br><img src="https://static.igem.org/mediawiki/2017/a/a0/T--IIT-Madras--ss4.png" style="width: 100%;"> | ||
<h2>Future work</h2> | <h2>Future work</h2> | ||
Revision as of 16:46, 30 October 2017
Design
An easy access platform with a database of various host organisms and a collection of tools to work with them.
The blueprint of an organism
To create the database of host organisms, we first started by defining a template/blueprint of the data that needs to be collected about each organism. Our proposed blueprint consists of the following:- Scientific name (genus, species and strain) and taxonomy
- Biosafety level
- A description of what makes the host special for synthetic biology applications
- Genotype
- Growth characteristics
- Culture sources for obtaining the organism
- Maintenance protocols
- Transformation protocols
- Other protocols
- Biobrick parts for this organism
- Vectors for the organism
- Metabolic models
- Genome sequence
Building the database
A database site design consists of two essential components: a backend that is responsible, storing data on the server and serve the data when requested, and a front-end that is responsible for creating a visual interface between the back-end and the user.Back-end
Our backend is powered by Flask, a framework for Python. All the data about different organisms are stored as .json (JavaScript Object Notation) files on the server.Front-end
The front-end was done using HTML, CSS and JavaScript.User Experience Design
Home page
When the user hits on the home page, (s)he can either search for organisms, browse through the index or choose to contribute data for an organism that are not yet in the database.
Add/edit page
The add new organism page and edit organism data page have a similar design, carefully designed to provide the user with the description of the data that is expected to be entered.
View page
The details about each organism can be viewed on the view page. The page is designed for easy navigation to different sections of the entry. This page also contains a link to edit the entry
Chassis tools
We decided to make ChassiDex the one-stop solution for dealing with your host. Hence, we intended to integrate some chassis tools which can be used on the different chassis within the database. These are tools that are vital to molecular biology work on the chassis and such an assembly of tools at one place eases the process of working with them.Codon optimization tool
We have designed and integrated a highly interactive tool for codon optimization. The optimized sequence can be manually edited to remove restriction sites or reduce GC content, using a drop-down menu that shows codons that can be used to replace the current codon without changing the amino acid.
Future work
We plan to similarly integrate more such chassis tools such as those for genome analysis and metabolic simulations.
Contact Us
igemiitmadras@gmail.com
Department of Biotechnology
Indian Institute of Technology Madras
Sardar Patel Road
Chennai, India - 600036
igemiitmadras@gmail.com
Department of Biotechnology
Indian Institute of Technology Madras
Sardar Patel Road
Chennai, India - 600036
