# Our Contribution
2021 iGEM Team Fudan has made great contributions to the iGEM community, which can be useful to future teams. Here, we would like to stress our software tool: Part Camera -- A new Search Engine specially designed for iGEM registered parts which not only expels more usable details when do searching but also shows both the direct and potential links and relations between parts in a direct way. See more on our Software page
Figure 1. Icon of our software tool-- Part Camera
our software tools can be a capable helper when future teams are faced with the following situations:
- In need of a part that shares a similar function with the known part, so as to have a better effect in a bio-circuit designed by future teams.
- In need of a regulatory part that can regulate the known part with testing data, to save time for testing
- In need of searching for the relationships between parts.
- In need of checking the repetition situation of your new part from all iGEM registered parts.
Our software tool contains two major pillars: the database containing whole parts info (updated on the date push to GitHub) and the functional functions ready to be called by an interface.
# Database
Our database is set by a crawler using selenium, containing the original and potential info of all iGEM registered after being processed. Our database is saved in three formats: .fasta, .xlsx, and .json, enabling both direct reading or program processing for future teams. These data are helpful for both software teams focusing on iGEM part repository and experiments designers. Moreover, the links between parts, which is also a result of our data processing, help the optimization of distribution kits.
| Part properties | Example (BBa_I14044) |
|---|---|
| Part number | BBa_I14044 |
| Part name | weak RBS . LacI |
| Part url | http://parts.igem.org/wiki/index.php?title=Part:BBa_I14044 |
| Short description | weak RBS . LacI |
| Part type | Translational_UnitT |
| Team | Princeton |
| Registered year | 2004 |
| Part sequence | tcacacaggaaacctactagatggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtct...(see full sequence in our database ) |
| Part Page Contents | weak RBS . LacI BBa_B0031 BBa_C0012 Sequence and Features R |
| Release status | Released HQ 2013 |
| Sample status | Sample In stock |
| Stars | 1 |
| Twins | BBa_I14044 BBa_S0112 BBa_J09340 BBa_J24683 |
| Assembling standards | 1 1 0 1 1 1 |
| Part used | BBa_S05370 |
| Using parts | self |
| Length | 1173 |
| Cits | BBa_0031 BBa_0012 |
| Whether in distribution kits | 1 |
| Cited by | None |
| Cited times | 0 |
| Scores | 18 |
Table 1: our data format with an example
# Function 1: Searching Engine
We develop a searching engine supporting fuzzy search not only for part's id but also short keywords and sequence thanks to Participle Method. And the searching results are sorted by relevance, so future teams may find their most desired results in the shortest time. Moreover, we carefully designed an abstract block, which is helpful for the future to get usable part details only with fast scanning.
Figure 2. searching results of 'gp2' as an example
# Function 2: BLAST
We also allow future teams to BLAST their sequence in the iGEM registered parts database. With this function, you may find more info than the official BLAST tool and find similar parts in the parts repository, helping you to recheck your parts' repetition when registering and uploading.
Figure 3. BLAST result of 'BBa_K3790086' as an example
# Function 3: Treemap
TreeMap can fully expose the relationships between parts in an intuitive way. With a clickable treemap set by Pyecharts with our data, users can grab all the relationships at a glance. You may continue your exploration or brainstorming according to this map.
# Future and Meaning
- Our data may help the optimization of distribution kits.
The design of distribution kits may refer to our data about part relationships. For example, linking frequently used pairs in one plasmid to save wells of plates, adding a new useable twin into distribution kits, making distribution kits more useful, multi-optional, and less expensive in the manufacturing process.
- Seqr formats and multi-format databases enable the extension to other bioinformatic modules, making easy DIY functions possible.
In our database, parts data are transformed into three modules including .fasta, which is a commonly used format in sequence processing, helping other bioinformatic modules can easily access the database.
Meanwhile, in our data stream, every part is transformed into Seqr format, a universal format for BioPython. So you may add your desired functions and modules with a few lines of codes and integrate this new function into our PartCam.
- Better searching engine, better ideas
Inspiring and sparking ideas by links is what PratCam most concerns. Just like how Fudan2021 iGEM teams get their ideas, we believe that more and more teams will draw their sparks from Part Camera along with the linkings between parts Part Camera set, and making their sparks into great meaningful projects.
# Other Contributions
- A complex Model to simulate T7 expression in bacteria
- The first σS promoter in the Registry
- A composite part that produce enzyme for isothermal amplification without the need to purify
- A collection of DNA binding domains to improve polymerases
- Genelizable conclusions and approaches for Education, Inclusivty and Sustainable development in resource-limited regions