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 10 professional edition with 8GB RAM and Intel(R) Xeon(R) CPU E5-2620 v3 @ 2.40GHz, 64-bit operating system.


  • The installation on Windows system is relatively easy and it will finish soon as the images.



  • Alex-ThinkPad-SL410 with ubuntu 15.10, 3.7G RAM and Pentium(R) Dual-Core CPU T4400 @ 2.20GHz * 2, 64-bit operating system.


Mac OS X


  • 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.


  • 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


  • 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.


  • 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.