Molecular Biology Extension

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Hi everyone,

I’m a systems / synthetic biologist and I use JupyterLab for most of my experimental design, analysis and note taking. One big limitation, however, is that I can’t display molecular biology objects, such as DNA sequences or annotations, in Jupyter notebooks. So I’ve been toying with the idea of developing an extension to do just that, ideally interactively so you can scroll around sequences, zoom in and out, and turn annotations on and off. But my only background is in programming Python for scientific applications, and from what I understand I’d have to pick up JavaScript and learn how to interface with Jupyter.

I’m very much a novice so would be keen to get your advice on whether this is worthwhile project, how I could go about trying to make it happen, and who else might be interested in chipping in.

Thanks all :slight_smile:

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If you can find a javascript library that already does such things, sometimes it can be much easier to wrap it in a JupyterLab extension. That’s what we did for the FASTA extension, for example: https://github.com/jupyterlab/jupyter-renderers/tree/master/packages/fasta-extension

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So something like https://github.com/josiahseaman/FluentDNA, though that appears to run as a service atm? I also recall NanoDJ: A Dockerized Jupyter Notebook for Interactive Oxford Nanopore MinION Sequence Manipulation and Genome Assembly though never really explored it…

There’s also stuff like https://github.com/arose/nglview which has various Jupyter extensions I think, as well as other extensions built on top of it, such as https://molpx.readthedocs.io/en/latest/ .

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Thanks guys - really helpful suggestions! Though not exactly what I’m looking for, great places to start. I’ll go do some more digging :slight_smile: