Intermine Web Services available in a Jupyter environment running via the Binder service.
Click any launch binder badge on this page to run code that takes advantage of Intermine Web Services inside your browser.
IMPORTANT: As of July 1st 2024, Yeastmine is scehduled to be shut down July 15, 2024. https://x.com/yeastgenome/status/1807832546027491641 July 2024
"YeastMine is closing July 15 due to ongoing funding cuts. For more info: https://community.alliancegenome.org/t/yeastmine-shutting-down-july-15/7720 #yeast"
That linked note says:
"We are working to move the YeastMine data into AllianceMine, hosted by the Alliance of Genome Resources, of which SGD is a founding member." SOURCE
The content of this repo has not yet been updated to take into account any aspect of this new & still developing situation as I am looking for the dust to settle and to see what changes to programmatic access there is. I do note that the AllianceMine where the YeastMine data is going is listed on the main InterMine page and so maybe things won't be that different.
Click the link below to open a guide to getting started with using Intermine sites and Jupyter using MyBinder-served Jupyter notebooks. It starts out with a step-by-step guide to get you up and running code fast. From there, it offers options of what to do next, including work through an advanced effort:
InterMine provides programmatic access to its features via web services. This repository is set up to make use of the Intermine web services via active Jupyter sessions served from MyBinder.org.
Clarifying Attribution: I, Wayne, am not involved in the Intermine web services or Binder system software at all. Those listed among the resources noted here are the respective developers. See their materials. I simply set up this repository to make the Intermine web services useable without installation/Python 2 vs 3 headaches.
This repository is set up to make use of the binder service offered by MyBinder.org. See their site or the end of the section here for more information about Binder.
Chances are good that this repository I have set up is enough to get you started if you want to use Python and Intermine. The requirements.txt file has some of the main popular modules and you can always use !pip install followed by the module name in a cell within an active notebook to install additional modules into that session. Advanced users will most likely to set up their own Binder repository to specify certain modules to already be there upon launch. See here for more on adapting repositories to your needs. You may wish to start with a 'fork' of this one.
Click this button below to begin using Intermine web services via Binder: