Team:Amsterdam/Human Outreach/Collaboration/Software Feedback

From 2011.igem.org

Software feedback

Superparts construction software

The Wageningen iGEM 2011 team has been so kind to provide us with the opportunity to beta test their superparts construction software. This tool allows you to plan your part construction using the parts readily available in the registry. The software algorithm calculates the least amount of cloning that is needed to assemble the desired construct. Although the software is still in beta, we’ve tried the software and made a small list of feedback.

GUI

Although the software is still in development, there are a few things that we feel would greatly improve the usability of the program

  • Inserting the several parts is easier if they are separated by spaces.
  • Making double click possible on textbox
  • A graphical representation of the inserted parts/modules. Preferably in the part registry style: . This graphical representation would make it easier to visualize what you’re working with and, in case you forget something, easier to spot.
  • A save/load function for the current modules and settings.
  • Remove the DOS window and make the history box the location where the log is displayed.
  • Also, when making the process threaded, if possible, implement a loading bar/time remaining.

Construct output file

  • Here, spaces would also increase the readability of the program. If you choose to make this also a graphically appealing file you could also export the results as a .pdf file and include the graphical representation mentioned earlier.
  • The addition of a clear indication weither a part is already present in the registry or if certain subparts are only readily available in composites, leading to impossible combinations.

Logarithm

  • Overall, we’re impressed with the output generated by the program. For example, when using the following parts….
    • BBa_R0010BBa_B0034BBa_E0020BBa_B0012BBa_B0011
    • BBa_R0010BBa_B0034BBa_E0040BBa_B0012BBa_B0011
    • BBa_R0010BBa_B0034BBa_K361000BBa_B0012BBa_B0011
  • A very satisfying result is generated. However, these are relatively simple constructs, with the only variable being the protein that is being generated and all parts are in the registry. When changing one of the double terminators around..(BBa_B0012 into BBa_B0011 and vice versa) the program freezes. As such it appears that the program is very “freeze/crash-prone” when giving sequences that it cannot solve. Threading the program and allowing you to see the log file that is being generated seems to be very helpful!

Overall

The program seems like a very useful tool in order to find the quickest way to construct your superpart, even in beta. The program allows you to easily visualize the cloning steps needed to construct your assemblies. At the moment the main improvements that can be made are in the usability of the program, especially when inserting modules, and regarding the graphical representation. A save/load feature would also be greatly appreciated. We are anxious to see what the next versions will bring!

Retrieved from "http://2011.igem.org/Team:Amsterdam/Human_Outreach/Collaboration/Software_Feedback"