Team:Heidelberg/Collaborations
collaborations
thank you for sticking with us
Collaboration is the key of science. iGEM is not only a huge team-work but also working together in one giant project towards a more convenient synthetic biology. Working together with Co-iGEMers from different scientific backgrounds but also from different countries, continents and cultures opens our eyes and enables the development of new approaches. When we entered iGEM competition we asked ourselves, how we could contribute to this idea and join forces with other excited young scientists.
Collaboration with the Manchester Team
How everything started...
The iGEM Team Manchester and the iGEM Team
Heidelberg first met at the German iGEM Online Meetup, organized by the iGEM Team Marburg-Gießen. The meetup did not only offer us the chance to learn a lot about synthetic biology, but also to meet other teams from all over the world. At the meetup we demonstrated our approach to use web scraping to make the iGEM Registry better accessible. Our idea included searching the iGEM registry for specific parts and filtering entries in the Registry for certain characteristics. Following our presentation, the iGEM Manchester Team asked us if we would be willing to show them how to implement a web scraper for a iGEM Team Wiki study. After a short discussion at the Meetup and several meetings in the week after our plan was born: we will implement a web scraper to quantify specific parameters from different iGEM Team Wiki pages. Using the generated data, the iGEM Manchester Team will write a report with helpful advice for other teams.
How our approach for web scraping works and evolved over the last few months.
Fork us on GitHub!
Figure 1: Data generation
With our know-how, we implemented a web scraper, which accesses the iGEM Wikis and downloads the data, while we are in a constant exchange with iGEM Manchester Team.
To develop the web scraper we used the package BeautifulSoup4 in Python 3.7, which accesses the tags in HTML documents and thereby retrieves the information given. As iGEM teams must use the Standard Pages, we collected data from following links:
Figure 2: Linklist
All links of iGEM Wiki Standard Pages crawled by our web scraper.
In the first meetings in July and August together with the iGEM Manchester team we focussed on accessing the text on iGEM Wiki pages to determine e.g. the sentence length. In August meeting the iGEM Manchester team suggested evaluating even more parameters, such as the number of pictures. Until our meeting in September we implemented a lot more functions to access more parameters. In total the following parameters were determined:
- Number of titles
- Number of subtitles
- Number of subsubtitles
- Number of pictures
- Number of videos
- Mean number of characters per sentence
- Mean number of words per sentence
- Number of internal links
- Number of external links
First, the data is divided by winner or nominee and participants.
Additionally, information about the teams regions, countries, tracks, sections and sizes are provided
and can be used to investigate the differences between the wikis.
In our meeting in October we discussed with the iGEM Manchester team how to provide the data best. We decided together to use a .csv file, as this can easily be accessed and analyzed via the iGEM Manchester team. The .csv file is provided HERE as well. Statistical analysis can easily be undertaken by any other team as well using standard statistical software.
The results
The results are published on the page of the
Manchester Team.
Figure 3: Data delivery
The Manchester Team takes the generated data and will analyze it further.
Postcard Challenge & iGEM Meetup & iJET campaign & iGEM flash mob
One of these collaborations was the postcard challenge from the iGEM Team Düsseldorf. It was awesome to see that this long tradition is being continued and even growing: We received 26 beautiful and interesting postcards from the other iGEM Teams which showed something related to their iGEM project or to synthetic biology in general. This is a sign, that science communication is also growing more important and that young scientists are already aware of it. Talking about science communication: We also showed the postcards to our friends and family which brought up many interesting discussions during dinner.
We contributed with a postcard showing a craftsman' toolbox, which demonstrates our synbio toolbox, including our tools for RNA Linker prediction and making use of Protein-RNA interactions.
The iGEM Meetup initiated by the team from Marburg was another great collaboration. Four people represented our team and enjoyed the fantastic speakers. Most of all we liked the visions of Prof. Tom Ellis who is leading a research team in synthetic genome engineering and synthetic biology in the Department of Bioengineering at the Imperial College London. At this point we would like to thank the iGEM Team Marburg and the German Association of Synthetic Biology (GASB). We were very happy and excited to win the first prize at the video competition!
iGEM Aachen and iGEM Darmstadt joined their forces to organize the iJET campaign. The iJET flew not only over four continents and reached 25+ countries, but brought all iGEM teams participating nearer to each other. - In times, where COVID-19 reigns the minds more important than ever before!
Also, we enjoyed the flash mob organized by iGEM Moscow. Their idea was to create a world map and pin the location of the iGEM teams. It was quite interesting to see where other iGEM teams are located, and a very meaningful gesture for the iGEM community! Especially in times of Corona this project sent a powerful message: We are not alone, we are a united and strong community!
