Team:SJTU-Software/Requirement/Notebook

Introduction

This is our time table;

2. Silver

EASY BBK:

An EASY Biobrick Blueprint’s
pacKage

Digging into the current biobrick database maintained by the iGEM foundation, we have found the current biobrick database is difficult for users to interpret and find biobricks of good quality. In addition, different types of biobricks which were presented in the previous biosystems varied from each other so greatly that even the most experienced synthetic biologists might find it difficult to interpret the biosystem the teams had created.
Given the above reasons, we have constructed an Easy Biobrick Blueprint’s pacKage (EASY BBK) to solve the problems. Its functions are listed as follows.

Search

This function is provide to users to search and evaluate the candidate biobricks based on keywords or part names. It can help users to decide if an existing biobrick meets their requirements before they start their experiments.
The searching engine is based on a database converted from the iGEM biobrick database (Date, or version number). There are 27,093 biobricks in the database If the input are one or more keywords, the biobricks related to the keywords will be listed, sorted and displayed to the users. Advanced search mode is also provided to refine or sort the search results based. Besides, users can search the biobrick database based on sequence similarity. If users input a DNA sequence, the hit sequences in the database by NCBI Blastn will be returned, sorted by their E-values and displayed.

3.Gold

In addition to the Bronze and Silver Medal requirements, two additional goals must be achieved:

1. Provide a convincing validation, testing the performance of the development -- experimentally (can be outsourced) or by other teams and users. Note, even if the algorithm or tool turns out not to work that well, the Gold requirement is fulfilled if the test is good and the analysis convincing. Validation may include: preferably experiments, informatics analysis (complexity, run time) of an algorithm, or user studies.

And the second goal can be any one of the following:

1. Make your software interact / interface with the Registry.

2. Re-use and further develop previous iGEM software projects (or parts thereof) or use and/or improvement of existing synthetic biology tools or frameworks.

3. Develop a well documented library or API for other developers (rather than “only” a stand-alone app for end users.)

4. iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, or intellectual property rights. Describe an approach that your team used to address at least one of these questions. Evaluate your approach, including whether it allowed you to answer your question(s), how it influenced the team’s scientific project, and how it might be adapted for others to use (within and beyond iGEM). We encourage thoughtful and creative approaches, and those that draw on past Policy & Practice (formerly Human Practices) activities.