Click a launch binder badge anywhere on this page to begin.
Seeing if this can be binderized?
Simple script for automatically annotating SDS-PAGE gel images.
Go beyond the built-in demonstration by adding your own gel image.
To upload your own data, drag and drop into the file browser panel on the left.
Then change gel_file assignment to specify your gel name.
(If you prefer the classic notebook interface, you can change the end of the url from lab to tree to switch to classic. See here for more about that.)
The interactive plots made by the demonstration will not render as output when you first launch the active notebook via MyBinder.org. You must run the cells in the notebook again, and then they will show up in the output cell area. This is a security feature to block abuse.
The interactive versions of the plots do not get rendered when viewing the static notebooks in Github; however, if you view the static notebook page via nbviewer here, the interactive Plotly plots will render and be interactive.
Next planned is to make the script into one that takes command line arguments and also is callable as a function, with the demonstration related items removed to just be in the accompanying demonstration notebook.
Anything that gets altered will need to be incorporated into the demo notebook.
Things I hope to alter are adding an option for specifying what lane contains the protein standards and if any marker bands were run off.
Add a setting for the number of lanes with a default being the one used in example(?).
It would also be nice to be able to somewhere have some commonly used protein marker sets defined. (I have yet to determine the source in the example.)
Add tiff handling for the image, if it won't automatically work already(?).
Following that, I want to make a new landing point notebook . This will offer a link to the demonstration notebook in the header. And in the footer. The one in the footer being suggested as if you want to see what is behind the code.
The notebook is meant to run the new processing script on any images (png, jpg, [and I hope tiff is possible]) dropped in the file navigation panel. It will avoid the demo one unless some setting is adjusted. That will also offer a place to refer user to demo notebook which is meant to actually serve that purpose.
Following that, it would be nice to convert that notebook over to a widget based app. There would be instructions detailing how to drag-and-drop the gel images into the panel on the left. There could be drop downs for setting the number of gel lanes, choosing the marker set, or a place to input it still, choosing the number of bands run off the gel, etc. And then a button to press to process all the images dropped in. Then report back after to encourage users to grab the results. Probably best to zip them up for easy grabbing as one file.
Many thanks to mathieuboudreau for working out using Plotly's orca with the MyBinder.org service. See here for more on that. Keeping the Dockerfile here for now, but as a hidden file, since it may be useful for future efforts by myself or others. Especially since quite different approach for the last steps dealing with getting orca ready. In particular, I couldn't find a way to work with usr/bin in postBuild (or terminal) without permissions problems even though it seems to work for the Dockerfile.
Click the launch binder badge below to begin: