biopython UI?

Question

[tada]

Hello,

Is there any UI for this library? I looked for it and I cannot find it. If there is none, are there any current plans to create one?

Thank you, Adrian

Answer 1

[Joe]

There is certainly nothing "official".

I'm not sure there ever could be either, as the whole point of biopython is for it to be a programming "API" for biology, and therefore having a UI would kind of defeat the object (not to mention I don't know what it could look like).

The closest thing you could find would be something like https://galaxyproject.org/ - this is a UI of sorts, and has some more point-and-click functionality but is still about coding at its core.

The next best option would be a good development environment ("IDE") which can assist with things like object models, variable management, inbuilt help etc.

[Wayne]

I'd suggest along the lines of the next best option Joe proposes also would be the current JupyterLab and the document-centric Jupyter Notebook (versions 7 and up). Several of these you can use now without installing anything on your own system via MyBinder-served sessions, JupyterLite, py.cafe, or Anaconda Cloud. The first three listed don't necessarily involve you even signing up for anything or logging in. You can easily build in fancier UI's with ipywidgets, solarar, and anywidgets and use interactive dashboards/app providers already in the ecosystem, like Voila and Voici along with other. While I am mentioning interactive dashboards/ online apps, I'll add that py.cafe is targeted at this type of use and because Biopython is built in Pyodide, beyond use in JupyterLite, it should also be useful on py.cafe. Here is an example on Py.cafe where Biopython is used in support of a macromolecular visualization tool Molstar. (You can get to the editor to see the code by clicking the button in the upper right corner, or go directly to the page here.) That example isn't exactly what the original poster seeks because no UI elements are interacting with Biopython, but the expanded example here using two-way hover/highlight between ipymolstar and altair starts to give you an idea of what could be easily possible in a shareable form.
As for my first suggestion of Jupyter Notebook, I don't have an amazing example to point out off the top of my head but I do note that David Bikard's genome browser project. And I pointed out to the developer David Bikard that you could use it easily without installing anything of logging in because I forked the project and configured things so it launches via MyBinder-served sessions. You can see this in action by going here and clicking on the 'launch binder' badge you see here. If you are patient, you should get a session in your browser where 00_Examples.ipynb comes up and you can step through running the cells or just do Run > Run All Cells to really get a sense of what is possible.
(Oh yes, there was an effort to have a set of Jupyter .ipynb files for an introductory tutorial offered via MyBinder service here ; however, it hasn't been updated in five years. Sadly.)

Hopefully, adding some concrete-ish examples will provide a sense of the vast scope of options and possbilities already present and back up some of what Joe said in his first couple of paragraphs.

[tada]

Thank you for the very detailed and documented answers. I was not specific enough in my question. Any person doing molecular bio uses one of these three applications: Geneious, SnapGene or Benchling. All are based on APIs and all are proprietary. All are based on public domain algorithms. Geneious is the best as it can be extended however the full license is quite expensive. Benchling is the least flexible, cannot be extended and requires stable Internet connection.

That Application was what I meant when I said UI.

So I guess the answer is no for BioPython.