Team:SYSU-Software/Medals

SYSU-Software:Project

OVERVIEW

  • We have developed our project for nearly a year and tried our best to follow the criteria on the web-

  • site. We are confident that our project will meet all requirements of medals.

BRONZE

  • Register the team, have a great summer, and plan to have fun at the Giant Jamboree.

  • SYSU-Software had registered in 2016 iGEM competition, and all members had prepared well for the coming Giant

  • Jamboree for one year.

  • Meet all deliverables on the Requirements page (section 3), except those that specifically mention parts.

  • We had finished all tasks on the Requirements page. Our designers and programmers constructed an excellent wiki, in

  • which Attributions are thoroughly described. We also finished our Judging Form and Safety Forms.

  • As a software team, we had no new parts for submission to the Registry and did not create a part page.

  • Create a page on your team wiki with clear attribution of each aspect of your project.

  • This page must clearly attribute work done by the students and distinguish it from

  • work done by others, including host labs, advisors, instructors, sponsors, professional

  • website designers, artists, and commercial services.

  • We created an attribution page in our wiki, clearly demonstrated our work and acknowledged help from other people

  • and organizations.

  • Document at least one new substantial contribution to the iGEM community that

  • showcases a project made with BioBricks. This contribution should be equivalent in

  • difficulty to making and submitting a BioBrick part.

  • Our software used Biobricks of promoters and RBSs in iGEM Registry to construct our circuits, and the selected CDS

  • sequences will also be combined with restriction sites to form standard Biobricks. Details please see Human Practices.

SILVER

  • Validate that something you created (art & design, hardware, software, etc) per-

  • forms its intended function. Provide thorough documentation of this validation on

  • your team wiki.

  • We have tested our software with several demoes, including synthesize and decompose target materials, small chemi-

  • cals or proteins. We also installed our software on different system, including Windows, Linux and MAC OS X, to test if

  • all the three parts in our software would work well on different computers.

  • We also validated our software in experiment, and found it work well in solving real problems.

  • For more details see Demonstrate, and Proof.

  • Convince the judges you have helped any registered iGEM team from a high-school,

  • different track, another university, or institution in a significant way by, for example,

  • mentoring a new team, characterizing a part, debugging a construct, modeling/simu-

  • lating their system or helping validate a software/hardware solution to a synthetic

  • biology problem.

  • We collaborated with NJU-China, programming a small tool for them to generate siRNAs and select the most appro-

  • priate following the principles of siRNA design. We also collaborated with SYSU-China, hosting Central China iGEM

  • Consortium (CCiC), with more than 30 teams attending. For more details see Collaborations.

  • iGEM projects involve important questions beyond the bench, for example relating

  • to (but not limited to) ethics, sustainability, social justice, safety, security, and intel-

  • lectual property rights. We refer to these activities as Human Practices in iGEM.

  • Demonstrate how your team has identified, investigated and addressed one or more

  • of these issues in the context of your project.

  • During our projects, we not only focused on our main project, but held or attended other activities to spread our pro-

  • ject ideas and synthetic biology to the society, or integrated our project with what we noticed in these activities. Our

  • Human Practices activities covered three aspects, including social and scientific thinking, project assessment as well as

  • public engagement. For more details see Human Practice Silver.

GOLD

  • Expand on your silver medal activity by demonstrating how you have integrated the

  • investigated issues into the design and/or execution of your project.

  • During our Human Practice activities, we found some of our previous design was not appropriate for the users, had

  • some potential safety problems. Moreover, some data were found insufficient to realize the intended function of our

  • software. So we redesigned the function and user interface of our software, making it accessible to a wider range of

  • users and eliminating the biosafety problems. We also developed a model to calculate data rather than purely retrieved

  • data from various databases.

  • For more detail see Human Practices Gold.

  • Improve the function OR characterization of an existing iGEM project (that your

  • team did not originally create) and display your achievement on your wiki.

  • Our software improved from SYSU-Software project in 2015 iGEM competition on model and data, safety, and

  • strengthened the linkage between software simulation and experiment.

  • In previous SYSU-Software project CORE, data were retrieved from precursor research and other iGEM projects.

  • CORE used ODEs as their main model with many parameters to be estimated from various sources, making the results

  • imprecise in a way. This year we have developed five new models to calculate the data required in our software such

  • as promoters and RBSs strength, keeping the consistence in the results of different steps. For more details in our model

  • please see Model.

  • For safety, CORE took parts and chassis species into consideration but missed potential biosafety problems in prod-

  • ucts. This year, our project not only discussed much deeper in parts and species, searching all parts in registry,

  • and pairing Risk Group list from NIH Guidelines with species in our software, deleting those in Group 3 and 4,

  • but also constructing a chemical ban list from Catalogue of Hazardous Chemicals, deleting the circuit containing

  • these chemicals and stopping the users who input dangerous chemicals.

  • For more details on what we have done on safety. Please see Safety.

  • CORE helped the user construct the plasmids for experiment when results shown. Besides the plasmids, our software

  • will provide a protocol for realizing the circuit with chosen plasmid and chassis species, and a record frame

  • for uploaded experiment data, which will be saved in our software for future usage. For more about this system,

  • please see Design.

  • Michigan_Software Team have developed a useful tools, Protocol Cat for protocol collection and established

  • a large protocol database. Our project improved their work from collection to generate a standard protocol

  • for a specific plasmid and species. For more details can also see Design.

  • We continued to use the frame of installability test applied by 2015 SYSU-Software team and finished our test of

  • CRAFT on three systems. With this frame, we also operated installability test for our distributed computing plug-in,

  • Satellite, on linux. For more about our installability test, please see Demonstrate.

  • Demonstrate a functional proof of concept of your project.

  • We use experiment to validate that the circuit from our software is available in real experiment. We use violacein as

  • the target product, and construct the plasmid consisting of the promoters and RBSs recommended by the software. Ex-

  • periment with other three combinations of promoter and RBS showed the recommend combination performed best.

  • The system also recommended us to transduce two plasmid into two bacteria, co-culturing, and the result, compared

  • with standard violacein, showed by HPLC, also performed well. For more details of our proof, please see Proof.

  • Bring your prototype or other work to the Giant Jamboree and demonstrate it to

  • iGEMers and judges in your track showcase.

  • We thoroughly demonstrate our results on our wiki, describing what we have achieved, where we improved and our

  • user studies. We also briefly indicate what our software will accomplish in the future. We will bring our software and

  • well-designed poster to Giant Jamboree, presenting our achievement and discussing with other iGEMers. For our

  • demonstration, please see Demonstration.

  • You can use our software in various ways:

  • Starting from source code --- GitHub: https://github.com/igemsoftware2016/SYSU-Software-2016

  • Install on your computer: download the install package of CRAFT in the GitHub repository, and install CRAFT

  • on Windows, Mac OS X and Linux (CentOS 7 - x86_64, Ubuntu - x86_64). You can also download Satellite, a distri-

  • bution plug-in, on Linux system.

  • Use CRAFT online: http://craft.sysusoftware.info