Team:SYSU-Software/Demonstrate
DEMONSTRATE
Installability test
Following the frame of previous installability test in CORE, project of 2015 SYSU-Software team, we successfully installed
CRAFT on Windows, Linux and Mac OS X system, and Satellite on Linux system.
Windows
Environment
Windows 10 professional edition with 8GB RAM and Intel(R) Xeon(R) CPU E5-2620 v3 @ 2.40GHz, 64-bit operating system.
Result
The installation on Windows system is relatively easy and it will finish soon as the images.
Linux
Environment
Alex-ThinkPad-SL410 with ubuntu 15.10, 3.7G RAM and Pentium(R) Dual-Core CPU T4400 @ 2.20GHz * 2, 64-bit operating system.
Result
Installation on linux system is complex. We recommend the users to follow the installation tutor on our GitHub
https://github.com/igemsoftware2016/SYSU-Software-2016. We have proved that installation on linux system works well.
Mac OS X
Environment
MacBook (Retina, 12-inch, Early 2016) with OS X EI Capitan (Version 10.11.4), 1.2 GHz Intel Core m5 and 8GB 1867 MHz LPDDR3.
Result
We have also proved that the installation on Mac OS X system performs well. But we also recommend the users to follow the
tutor on our GitHub because it is also relatively complex.
Plug-in Satellite
Installation Result
Satellite can only be installed on linux system but its installation performs stably and correctly.
Operation Result
We also test if satellite will work in CRAFT with our demo. The result indicates that Satellite is really useful and practical.
Hardware Requirement
Hardisk: 20G ** Highly recommended **
Memory: 4G Memory: 6G memory or better
CPU: Intel I5-2500k / AMD Phenom II Storage: 20G SSD
Demo
In this part, we will illustrate how to operate CRAFT to solve our real problems with a demo, synthesizing violacein,
which is also our validation experiment target. In Proof, more messages about its effciency will be shown.
Step 1
Enter CRAFT Designer, choose a system mode: synthesis mode, and give a new design name, Vio. Then we can begin our
design.
Step 2
Choose the targets product of our system, violacein, and set restrictions for this system, including minimum and
maximum concentration, reaction time, medium and background bacteria.
Step 3
Here is the pending page, submitted design needs to be calculated. To test our distributed computing plug-in,
satellite, we had installed it in another computer.
Step 4
About 30 minutes later, the results will be shown as the image below, with chassis species and plasmid messages,
in which the strength of promoter and RBS can be freely change.
Step 5
Waiting for another calculation for several minutes, a simulation curve of violacein will be shown on the screen,
which expresses the change of concentration along with time.
Step 6
Confirming the simulation curve, the protocol will be then given, in which operation of every step of experiment
and base sequence of plasmid will also be provided.
Step 7
Finally, the system will provide a new dataframe for experiemnt data feedback. These data will be applied to
modify the parameters in the model
User Studies
As good practices in software engineering, user studies can help us do some research on how users interact with our project,
and where we can improve.
Due to limited time period for software development, we could only do user studies covering only a limited number of
people. It is a great honor for us to invite Yu Zhou (team leader of 2015 NJU-China and instructor of 2016 NJU-China), Jinyu
Li (team member of 2013 and 2014 SYSU-Software, and now PhD at Yale University), and Jiajing Li(team member of 2013
SYSU-Software, and now PhD at University of California, Los Angeles campus) to help us find out the user experience of
CRAFT.
Our user studies invited them to try out our software (with the help of the easy user guide or some guidance given by us).
Then give some feedbacks on the three parts (i.e., CRAFT Designer, CRAFT Square and plug-in Satellite) of CRAFT.
Yu Zhou, team instructor of 2016 NJU-China
Background Information: 2016 NJU-China is doing a project on building a transplantable drug system targeting a specific
molecule to treat cancer.
Feedbacks:
“We’re doing the project on shRNA this year, but the system designed in CRAFT dose not contain parts of shRNA. To make
it universal, is it possible to add shRNA in your graph and your system can be regulated by ncRNAs?”
“CRAFT Square should allow other users to duplicate other design and modify to suit for their own demands.”
“Satellite is a creative design, and relatively easy to use.”
Inspiration:
In wet-lab teams, it seems that more and more teams have included ncRNAs into their synthetic system, but few of our
software have taken this into consideration. This year, however, even though the original data contained ncRNA regulation
data, we failed to find reference models for evaluating these regulations, so we eliminate these in CRAFT at last to ensure our
accuracy.
Most of users in CRAFT Square won’t design their system from scratch, but refer to other design and modify them, so it is
necessary for Square to show the settings of existed design.
Jinyu Li, PhD student at Yale
Background Information: Jinyu Li is a PhD student at Yale University. She is a biomedical student and also a wet-lab practitioner.
Some Feedbacks:
“The concept in generating protocols is really cool! And it really work! I just wonder what will the protocol like if I have input
hundreds of targets in the first step of CRAFT Designer?”
“Satellite? This name is appropriate and it is easy to use it. But how can I ask others to help me calculate my design?”
Inspiration:
We are delight to find the protocol generated in this way can correctly guide users’ experiment, but we can not ensure what
will happen if the number of targets have raised to hundred. So we develop a channel of feedback and made the protocol
scalable. Users who have found more effective protocols can contact us and we will add them into our system. Of course, it must be
very kind for those who really make an experiment with hundreds species of bacteria.
How to ask other users calculate my design? This question really inspired us to add some parts in Designer and Square: in
designer the users will have a number related to their design and their help request will be shown on the Square. With this
number, other users can help calculation in their computer with Satellite on their computers.
Jiajing Li, PhD student at UCLA
Background Information: Jiajing Li is a PhD student at University of California, Los Angeles campus. He is now a student on
human genetics.
Some Feedbacks:
“The adjustable promoter and RBS in CRAFT Designer is a very smart design, but you should ensure that the recommended
promoter and RBS is the most appropriate.”
“CRAFT Designer have done well on biosafety problems, but you should consider the situation when someone use the
designed system, whose targets are safe on your catalog, to produce other dangerous products.”
“How many photo do you have on earth in your icon setting?!!”
Inspiration:
To prove the combination recommended by our system is the most appropriate, we design a validation experiment to
measure the efficiency of recommended promoter, RBS and other combinations, and the results indicated that CRAFT
Designer have successfully provided the appropriate combination.
Jiajin Li’s biosafety concern also reminded us to add a report system in our Square, with which other users can report to us if
they find someone try to design systems and use their products for dangerous motivation.
As for the photos in icon setting, just try or you might find something interesting!
Future Works
Distributed Computing Plug-in
Recently, our distributed computing plug-in Satellite have only been tested on voluntary computers, and it can only run on
linux system and is complex when installing. Therefore, we need to spread Satellite, improving the calculation ability of CRAFT
main server and simplify the installation in the future.
User Data
CRAFT is a newly designed software, with a few users and insufficient experiment data, thus the self-revised algorithm, which
largely depends on experiment data, can’t work in this newly released version. Therefore, with more users and more data, our
software can modify the parameters in the models, ensuring the results more practical.
Application
CRAFT aims at designing solutions in real and complex environments. We will transfer data in real problems into our software
and craft a synthetic biological system in solving these problems.
