Team:SYSU-Software/Medals
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
