DLBPointon / APSB-coursework

Advanced Programming for Systems Biology and Visualisation

This repo contains the files used in completing the coursework component of APSB.

Repo Structure:

• 1836811-APSB coursework.pdf - Coursework file in PDF.

• 1836811-APSB coursework.html - Coursework file in HTML.

• 1836811-APSB coursework.ipynb - Coursework file - This has been run in VisualStudio.

• bertozzi_model.py - Model from BioModels

• leloup_model.py - Model from BioModels

• data_model

  • The XML model files downloaded from BioModels (26th July 2022).

• data_networkx

  • Two FASTA files used as input to BLASTN.
  • Two TSV summerising the data taken from BLASTN and used in producing the networkx graphs.

• MarkdownCoursework

  • Due to errors with converting to PDF, a markdown copy of the coursework has been included
  • 16 png images for the graphs produced.

Above is a graph produced using networkx for this coursework. It shows the scaffolds of 9 bees (Bombus sp. and Apis sp. )

Change Log

 30@27-07-2022

BioModels website has crashed and notes added to the IPYNB to alert the user.

 30@28-07-2022

• BioModels website is still down.

• Removed TSV dumps to local files for end user assessment, due to the size of these files it wasn't possible.

31@01-08-2022

• BioModels is back up, modifying coursework to reflect it.

• Added HTML copy of coursework - better than the PDF.