Team:Tongji-Software/Collaborations
COLLABORATIONS
Overview
"It is literally true that you can succeed best and quickest by helping others to succeed." –Napolean Hill
We reached out for 3 registered teams this year and achieved mutual benefits in the process of cooperation. As a software team, we use our skills at data processing and front-end visualization to help other teams a lot. Also, they gave lots of practical suggestions on our project from the experimenter's point of view.
SJTU-software
We surprisely found that the project of SJTU-software is also relative to metabolic pathway like us from the website of iGEM. So we contacted with their team leader and held a meeting to communicate on our projects and solve problems we met together.
Mutual Benefits Achieved
Our software contains a function of flux balance analysis with Cobra tool box. Surprisely, some team members of SJTU-software have learnt Cobra tool box in their professional classes. Since our software only evaluated the flux distribution and did not look insight into the results, they showed us some cases and taught us how to choose knockout native genes for more efficient heterologous pathways based on the results of flux balance analysis. We added this to our project and made our software more practical.
Fig.1. Discussing with SJTU-software and Brainstorming.
Fig.2. Example of FBA results in Alpha Ant.
The team of SJTU-software countered some difficulties in visualizing network. During this meetup, we presented beta-version of our software. Since our team also implemented network visualization and master the skill of front-end visualization, we introduced the tutorial of D3.js package which is used for data visualization in detail and help them work it out.
Fig.3. Zhichao Ma from Tongji-Software showed beta-version of our software.
Besides the assistant on project, the team member of SJTU-software Yangzhen Wei who has participated in iGEM twice shared us his experiences in Giant Jamboree and the climate, transportation and accommodation in Boston. Thanks for Wei’s reminder of keeping warm and hydrated due to the dry and cold climate in October in Boston!
Fig.4. Tongji & SJTU.Always good buddy.
Peking
We met Peking in August on the fifth Conference of China iGEMer Community. We communicated a lot during the poster exhibition. After gaining insight into each other’s project, both of us realize that we could have a further collaboration.
Mutual Benefits Achieved
The project of Peking is to construct a ‘synthetic membrane-less organelle’ as a multifunctional toolbox in yeast. They were planning to examine the effect of β-carotene producing in order to verify the feasibility of their project. Theβ-carotene producing consists of several enzymatic reactions.
Fig.5. Visit Peking's poster in CCiC.
Fig.6. Introducing Alpha Ant to Peking.
For purpose of designing rational experiment conditions, they need to know the most efficient pathway of producingβ-carotene and the detail information about enzymes involved in the reactions. Their needs inspire us that we could offer the detail information of enzyme to our users with our software. And then we collected enzyme data from BRENDA and KEGG and integrated them into our web application. Peking got the data they needed from our software and conducted their experiments afterwards.Here is our search result page which includes physiochemical information of compound.
Fig.7. Search result page in Alpha Ant.
Fig.8. Explanation of physiochemical properties.
Copyright ©2003-2018 LIPID MAPS® Lipidomics Gateway
Fudan-CHINA
We reached out for Fudan_CHINA in September and held a meeting to Trouble Shooting in Tongji University. It's a great pleasure to collaborate with dry lab Team. What was exciting that they were really interested in our project.
Mutual Benefits Achieved
Fudan_CHINA planned to develop a web application for visualizing their model this year. However, they got trouble in implementing their software on the web using JavaScript language. We introduced them a high-level Python Web framework which called Django to help them build web app. Similar with Fudan-CHINA, our model is related to Probability Theory. So we instructed Fundan-CHINA to change parameters of their model to make it more reliable. Beyond that, Fudan_CHINA help us edit the wiki. They reminded us to write HTML pages based on the initial code of wiki page otherwise the garbled characters may appear.
Fig.9. We held a meeting with Fudan-CHINA
Fig.10. Trouble shooting with Funda-CHINA on building model and wiki editing.
Thanks a lot to Fudan-CHINA. It is really helpful for both of us among this Trouble Shooting. Hope we all have a great time in Giant Jamboree.
Eurasia Meetup
Thanks to invitation by TU-Delft & BIT-China. We came to attend this Eurasia Meetup on July 24th in Shenzhen, China. We meet a lot of great teams and their excellent projects there. The three-day meetup brought us a full harvest. We introduced our project to teams who attended this meetup and acquire many useful suggestions.What is more,we learnt much about biosafety and bridging bioethics standards between continents.
Fig.11. Tongji-Software in Eurasia Meetup.
Conference of China iGEMer Community
We attended 5th CCiC which was held by ShanghaiTech University in August this summer. During this meeting, we introduced our project to others through presentation and poster exhibition and gained lots of valuable feedbacks.
Fig. 12. Our poster session in CCiC.
Fig. 13. We gave presentation to other teams.Q & A section was really challenging for us.
Collaboration is such a valuable thing to do. We are sincerely grateful to teams the team that gave us help and advice.We hope have further cooperation in the future!
Fig.1. Discussing with SJTU-software and Brainstorming.
Fig.2. Example of FBA results in Alpha Ant.
The team of SJTU-software countered some difficulties in visualizing network. During this meetup, we presented beta-version of our software. Since our team also implemented network visualization and master the skill of front-end visualization, we introduced the tutorial of D3.js package which is used for data visualization in detail and help them work it out.
Fig.3. Zhichao Ma from Tongji-Software showed beta-version of our software.
Besides the assistant on project, the team member of SJTU-software Yangzhen Wei who has participated in iGEM twice shared us his experiences in Giant Jamboree and the climate, transportation and accommodation in Boston. Thanks for Wei’s reminder of keeping warm and hydrated due to the dry and cold climate in October in Boston!
Fig.4. Tongji & SJTU.Always good buddy.
Peking
We met Peking in August on the fifth Conference of China iGEMer Community. We communicated a lot during the poster exhibition. After gaining insight into each other’s project, both of us realize that we could have a further collaboration.
Mutual Benefits Achieved
The project of Peking is to construct a ‘synthetic membrane-less organelle’ as a multifunctional toolbox in yeast. They were planning to examine the effect of β-carotene producing in order to verify the feasibility of their project. Theβ-carotene producing consists of several enzymatic reactions.
Fig.5. Visit Peking's poster in CCiC.
Fig.6. Introducing Alpha Ant to Peking.
For purpose of designing rational experiment conditions, they need to know the most efficient pathway of producingβ-carotene and the detail information about enzymes involved in the reactions. Their needs inspire us that we could offer the detail information of enzyme to our users with our software. And then we collected enzyme data from BRENDA and KEGG and integrated them into our web application. Peking got the data they needed from our software and conducted their experiments afterwards.Here is our search result page which includes physiochemical information of compound.
Fig.7. Search result page in Alpha Ant.
Fig.8. Explanation of physiochemical properties.
Copyright ©2003-2018 LIPID MAPS® Lipidomics Gateway
Fudan-CHINA
We reached out for Fudan_CHINA in September and held a meeting to Trouble Shooting in Tongji University. It's a great pleasure to collaborate with dry lab Team. What was exciting that they were really interested in our project.
Mutual Benefits Achieved
Fudan_CHINA planned to develop a web application for visualizing their model this year. However, they got trouble in implementing their software on the web using JavaScript language. We introduced them a high-level Python Web framework which called Django to help them build web app. Similar with Fudan-CHINA, our model is related to Probability Theory. So we instructed Fundan-CHINA to change parameters of their model to make it more reliable. Beyond that, Fudan_CHINA help us edit the wiki. They reminded us to write HTML pages based on the initial code of wiki page otherwise the garbled characters may appear.
Fig.9. We held a meeting with Fudan-CHINA
Fig.10. Trouble shooting with Funda-CHINA on building model and wiki editing.
Thanks a lot to Fudan-CHINA. It is really helpful for both of us among this Trouble Shooting. Hope we all have a great time in Giant Jamboree.
Eurasia Meetup
Thanks to invitation by TU-Delft & BIT-China. We came to attend this Eurasia Meetup on July 24th in Shenzhen, China. We meet a lot of great teams and their excellent projects there. The three-day meetup brought us a full harvest. We introduced our project to teams who attended this meetup and acquire many useful suggestions.What is more,we learnt much about biosafety and bridging bioethics standards between continents.
Fig.11. Tongji-Software in Eurasia Meetup.
Conference of China iGEMer Community
We attended 5th CCiC which was held by ShanghaiTech University in August this summer. During this meeting, we introduced our project to others through presentation and poster exhibition and gained lots of valuable feedbacks.
Fig. 12. Our poster session in CCiC.
Fig. 13. We gave presentation to other teams.Q & A section was really challenging for us.
Collaboration is such a valuable thing to do. We are sincerely grateful to teams the team that gave us help and advice.We hope have further cooperation in the future!
