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Notebook

BioBrick Creator

Aída Moreno and José Gutiérrez

• Week 1

Defining our program

We met up with the wet lab to get a general idea about what should be the functionalities of the BioBrickCreator. We tried to define some key features and what standards our program should met.

• Week 2

Jose: My firsts contacts with biological terminology. I started to understand the basics of synthetic biology and how the BioBricks system worked. I had to decide about which language of programming I would use to develop the tool. Finally I chose to use JAVA because it's a multiplatform way to run the application.

Aída: I made a long searching process in the iGEM parts registry website. I tried to familiarize with all iGEM terminology due to this was my first year in the iGEM.

• Week 3

Jose: I got a general idea about how should be the whole design of our program. I also started to work in and develop the independent modules before start designing biological algorithms. Like for example the best way to process string sequences to be modified.

Aída: Once I perfectly understood how the iGEM parts registry worked, I tried to think about how we could implement all those standards in one single program. I thought that the best could be to divide the program into three main modules and I thought about how each module should work.

• Week 4

Genetic algorithms design

Jose: I worked in the design of the first’s module main genetic algorithms. I designed a specific algorithm for each type of genetic input. I learned and understood the process of genes translation. I made the first draft of the codifying sequences algorithm for which I had to implement the genetic code table into the program.

Aída: I tried to explain Jose how all the genetic algorithms should work in order to meet the BioBricks standards. I also downloaded from the NCBI the genetic code table and the codon frequencies tables for the main model organisms in synthetic biology.

• Week 5

Testing and debugging genetic algorithms

Jose: I continued working on the writing process of all the module 1 genetic algorithms. The codon optimisation algorithm was pretty challenging but finally, it worked.

Aída: I tried to assist Jose with the biological part of the algorithms and I also tested the designed algorithms.

• Week 6

Group meeting

We met up with the team to show them the BioBrick Creator first draft and also, how the genetic algorithms worked. From this meeting we got interesting advices and conclusions, in which we worked on the rest of the week.

• Week 7

Module 1 finished

Jose: I finished the module 1 and I started to work on module 2. I wrote the composite parts algorithm. In addition, during this week I worked in managing output files and the formatting process. At the beginning I was sure to use only text files for output format files, but the FASTA format files were more easy to work with. Moreover, I decided what program features couldn’t be done due to time restrictions (future versions of the BioBrick Creator will implement them!).

Aída: I explained Jose how the output files should look like and what information should they contain. I also finished designing the Module 2 and I started working on the design of the Module 3. I looked in iGEM parts registry for the most interesting and well characterised plasmid backbones and I downloaded their sequences and main information.

• Week 8

Jose: Hard work week. I implemented all plasmids information into the program. I finished the design of the module 3. I worked in the interface design and to complete the user experience I added helping buttons to guide during the execution, this would help confused users to navigate through the application.

Aída: I wrote help pop-ups and I tested each independent module. After the testing process I suggest Jose some minor changes.

• Week 9

Last week!!

Jose: Almost done with it but still a lot of work to be done! I spent most of time testing, listening to other’s people opinions and finishing the program in order to upload it in time. I also designed and wrote with Aida the BioBrick Creator wiki page. Furthermore I made a video tour showing the functionalities of our program. Work done, the BioBrick Creator can be downloaded from our wiki!!

Aída: I worked with Jose in the design and writing process of the wiki BioBrick page. Thanks to Jose the BioBrickCreator is now a reality!! Good job! :D