If you want to speed up processing and identification of target gRNA sequences for introduction to Candida species via CRISPR techniques, this Jupyter notebook can help. After the user fills in a sequence of forms and selects Run all, the code will;
The nice thing about this is that the notebook does all of the waiting for the different servers for you. If, for example, the EuPaGDT generates a lot of results that need to be submitted to the RNA Fold Server, you don't have to manually process them one by one. The notebook does that for you, consolidating the information from both servers into one table. And if you get the process started then walk away only to return after Google Colab has disconnected you, the notebook as already downloaded the results to your local Downloads directory.
This Jupyter Notebook uses features that are only available in Google Colaboratory. For example, we can easily hide code to avoid distraction by using forms. For this reason, you are encouraged to use the notebook from there.
[We assume that you are familiar with using Jupyter Notebooks.]
The first few times you use this, it is best to step through each of the steps in the notebook in sequence. If there are fields to fill in, ensure that the default values are what you need, or change them to meet your needs before you click on the Run button.
After you are familiar with the steps, and the various options you have at each point, you can easily fill in the fields for all of the forms in the notebook, then select to "Run all".
If you use this notebook as part of work that is to be published, please add the following citations for the underlying tools to your published work:
The software in this project is licensed under the MIT License. Refer to the LICENSE file. The services that this software uses may be protected by their own copyright. Refer to the web sites linked above for their respective copyright or license.