S-Din (Search engine and Design platform for inspiration with Network analysis) is an integrated Search Engine and Design Platform, developped specifically for Synthetic Biology. Due to the exponential growth of published researches, many of them have never been fully exploited of their values. S-Din has been designed to integrate searching and designing seamlessly, finding exactly what users need and enabling users to edit simultaneously. What's more exciting about S-Din is that tree of words and various analyses were developed to inspire the user to generate a better idea. A simulation model was developed to help ensure the robustness of user’s design and wet-lab validation was conducted to validate its reliability. Our Github repo can be access from here.
Team:SYSU-Software/Demonstrate
Synbio is just a S-Din away!
SYSU-Software 2017
Overview
Installability test
we successfully installed S-Din on Windows and Linux system.
We recommend users to follow the installation tutor on out github repository
Hardware requirement
| Basic Requirements | Highly Recommended | |
| Storage | 20G | 20G SSD |
| Memory | 4G | 6G |
| CPU | Intel I5-2500k or better |
Windows
Environment
Windows 10 Enterprise edition with 8GB RAM and Intel(R) Core(TM) i7-4720HQ CPU @ 2.60GHz, 64-bit operating system
Result
The installation on Windows system is relatively easy. You just need to click initial.bat and runserver.bat and it will finish soon as the images
Linux
Environment
GNOME ver 3.26.1 with 15.6G RAM and Intel Core i7-4720HQ CPU @ 2.60GHZ x8, 64-bit operating system
Result
Mac OS Sierra
Environment
MacBook Air(13-inch, Early 2015) with maxOS Sierra (Version 10.12.6), 2.2GHz Intel Core i7 and 8GB 1600 MHz DDR3.
Result
Successful installation results
After you follow our installation tutor and successfully install S-Din, you can open our software in browser.
Demo
In this part，we will illustrate how to operate S-Din to search Synthetic biology projects and desin a circuit.
1
If you want to use the design function, you should register for an account firstly, but if you just want to search something, you don't need to sign in.
2
Search for projects, you can type in some keywords in search bar, and we will recommend some projects according to the keywords.
3
When we show you the search results, you can choose one you are insterested in, and then will see details about this project. You can see what this work has done and may get inspiration from that circuit and the decription for this work.
4
Click ”Design“ to switch to desgin function, here you can start you design.
5
You can search for part and add them to the design paper, and you can see the description for the parts you search to help you make a good choice.
6
If you don't know what is the best match between two parts, we privoide parts interaction information to help you make a choice.
7
After add parts to the design pages, you can add relationship between them.
8
When you finish your work, we provide a simulation function to help you check your work whether it is good or not.
9
Finally you can download your work to your PC!
User studies
The best user experience makes the best software, even though we've done enough preparation and investigation before initiation of this project. User study is also important because help us adjust the details in our software to make it more user-friendly.
It's pity that we can't expand the scale of our user study due to the long development period and lack of coders. But we're happy that they offer their precious time to help us test out software and give us positive feedbacks.
Shen Dong
research assistent who help us on our wet-lab validation
study in molecular mechanism of interaction between pathogen and host.
"It's considerable that you add safety surveillance system in your design platform. I wonder how many High-risk parts are there in your database? Yeah, may not many, but this is still necessary right?"
"From a researcher's point of view, I would say that the software still needs to improve to be more fit in the need of expertise. Though the current version is good enough."
Haoquan Zhao
Ph.D. Student of bioinformatics , Columbia University
"The engagement of search and design is designed in an elegant way, I have to say I like this design"
"The design platform is fluent and easy to use indeed but I think it can be more professional or more biology? There are lots of processes need to reflect on a circuit of pathway sketch."
"Beautiful UI, how much money your team pay for the designer?"
Jiajin Li
PhD student, University of California, Los Angeles
"You make a great attempt at solving problems like avoiding simply repeating the work that's already been done."
"There are things you need to consider like the updating of your database and how to make others use your software. Well done but keep on!"
Future works
1. Expand the scale of our database.
Projects in iGEM and literature field are grow at a remarkable speed, thus it's a responsible for us to update the data in our database regularly so that our users can catch the latest ideas and utilize into reproduction and testing. In next year, every team and publisher will be invited to redraw their genetic circuit on our design platform for seamless reutilization in future works, which is the most fastest and accurate way we can imagine for expanding the database. For display aspect, a wiki plug-in tool of S-Din will be developed so that all the teams next year can using the same editable tools in their wiki so that no more PS will be needed and also benefit us for gathering data from the first hand.
2. Evaluating an uncarried-on project by Artificial Intelligence.
In the future, we are going to adding a crowdsourcing feature in our software. To evaluate the project, a reliable auto-judging system will be created. The evaluation system will not only consist of simulation results but also variety of aspects that may affect the reliability of a project to function well (not only for Competition Awards but also for TRUE scientific & social effect it has). Machine learning and other method in big data mining area will definitely be used in the coming feature.
3. More validation experiments and feedbacks.
According to basic principles of engineering, iteration of the design-test-redesign circle for a product could never be enough. More efficient and user friendly features will be added during our further human practice in Synthetic Biology field. In our human practice section, we have demonstrate how we gain the idea of S-Din and how we enhanced it during the summer. We will do the same job for future improvement of S-Din, to make S-Din more popular and well-featured.
4. Dynamic data flow for synthetic biology.
During the brain storm, we want to add the feature that can provide dynamic data (news, latest paper) which can automatically upgraded everyday. Due to the limitation of time, we didn't merge this function into our software. In the future, these feature will be also added.
5. System optimization of the whole genome with the inserted circuits.
As a software team in synthetic biology, we felt responsible to build a software that can truly utilize the power of computer and algorithm to manage synthetic biologists to accomplish important and complexed tasks. After circuits getting used seamlessly from search results, an consideration of the genome level are going into our sight. As the electronic system, performance and connection can be optimized to a most efficient or robustest way.
S-Din is the first step of our ambition to solve real synthetic biology problem based on which further project will have a ground foundation of data collection.
And more
Sun Yat-sen University, Guangzhou, China
