Initialising a git repo on an internal server and a local machine
Adding this simple tutorial to my blog for easy retrieval.
PhD in Bioinformatics, Scientist in Antibody Development
Adding this simple tutorial to my blog for easy retrieval.
Our research group went on a retreat (‘OPIGTREAT‘) comprised of presentations made by members of the group, on technical skills and latest research. In light of the booming of data in virtually all areas, my colleague and I decided to run a quick hands-on workshop on distributed computing, integrating the use of protein data.
Recently I had a go at using different libraries to build a web-app with a Python backend, and found out this pretty neat module bokeh. Here is an example of the interaction between pandas and bokeh on some financial data:
In the published Protein Databank (PDB) entries, we recognise that, except for CDRH3, all other CDR loops adopt only a few structural conformations. It could be due to the preference of the original antibody’s germline – consider the fact that the PDB is heavily skewed towards humanised/engineered antibodies which attract pharmaceutical interest, where the CDR loops formed after the antigen exposure and maturation in other species are grafted onto the human antibody framework. Some frameworks may be predisposed to particular structural conformations in their acceptable CDR loops. The limited structural conformations are named “canonical forms” of the CDRs.
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