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Update showcase notebook - #345
hannahbaumann wants to merge 6 commits into
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View / edit / reply to this conversation on ReviewNB hannahbaumann commented on 2026-10-23T11:43:28Z I added all this background from the openfe demo and the ccp bio sim tutorial, please let me know if you think this is too much for the showcase! jthorton commented on 2026-10-26T15:07:42Z While I do like it maybe we are better of pointing the protocol page in the user guide so we only have a single source to keep up-to-date with how the protocols work? And here assume some knowledge of the calculations and really show off the API and the interchangeable components stuff? IAlibay commented on 2026-10-27T09:08:22Z Since it's the main thing folks usually look at, I'm actuallly pro having "more information". I understand the need for reducing work when doing updates, but it's also the showcase so it's ok to have this be the main place where we have to be vigilant in updating things. |
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View / edit / reply to this conversation on ReviewNB hannahbaumann commented on 2026-10-23T11:43:28Z I thought it would be easier to just create all of them, and put the detailed ChemicalSystem creation and transformation creation into a cookbook? jthorton commented on 2026-10-26T15:42:50Z Yeah I think this looks good we could link to the components user guide as well https://docs.openfree.energy/en/stable/guide/setup/chemical_systems_and_thermodynamic_cycles.html |
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View / edit / reply to this conversation on ReviewNB hannahbaumann commented on 2026-10-23T11:43:29Z I think the full explanation on how to run things in Python should probably be in the RBFE Python API tutorial, but I wasn't sure. jthorton commented on 2026-10-26T15:47:39Z Yeah that makes sense validate and create are probably better suited to this showcase, maybe we should introduce validate here as well with some examples of things it can catch. We should probably show validating a protein component as well? |
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View / edit / reply to this conversation on ReviewNB hannahbaumann commented on 2026-10-23T11:43:30Z Also here I thought maybe the analysis Python API part should be in the RBFE python API tutorial? |
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View / edit / reply to this conversation on ReviewNB hannahbaumann commented on 2026-10-23T11:50:15Z Will need to update this link when the PR is merged (also other links below are still WIP. IAlibay commented on 2026-10-27T09:13:13Z Here and elsewhere, how about using info boxes when linking to other areas - e.g. for the "openfe does not prepare structures". That would make it easier for folks to easily recognise when we're signposting. |
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View / edit / reply to this conversation on ReviewNB atravitz commented on 2026-10-26T12:52:42Z I think this is great, and also makes me that we should maybe be noisier about using duecredit when citing openfe. jthorton commented on 2026-10-26T15:12:15Z Lets pull this into the user guide for the protocol and link to it, having a single source to keep up-to-date would be easier but I agree this is all great info which is missing from the guide. The credit to perses and OpenMM tools should probably go into both though for maximum publicity?
Then I would just have a small details list of the protocol here covering key concepts. IAlibay commented on 2026-10-27T09:11:56Z I don't think I agree with just pulling all this into the user guide and removing it from here. As mentioned above, this quite often the first (and only) place folks look at - I'm pro being very noisy and detailed rather than assuming folks will read the userguide first. In fact, we usually tell folks "if you do anything, look at the showcase". |
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For the analysis parts its probably tied to the simulation health check page we want make which applies to most protocols. We should advertise some of the analysis in the showcase and link to the protocols for more info and then to the health check page. The API tutorials for each protocol should have examples on accessing the data used in the analysis, though. |
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While I do like it maybe we are better of pointing the protocol page in the user guide so we only have a single source to keep up-to-date with how the protocols work? And here assume some knowledge of the calculations and really show off the API and the interchangeable components stuff? View entire conversation on ReviewNB |
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Lets pull this into the user guide for the protocol and link to it, having a single source to keep up-to-date would be easier but I agree this is all great info which is missing from the guide. The credit to perses and OpenMM tools should probably go into both though for maximum publicity?
Then I would just have a small details list of the protocol here covering key concepts. View entire conversation on ReviewNB |
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Yeah I think this looks good we could link to the components user guide as well https://docs.openfree.energy/en/stable/guide/setup/chemical_systems_and_thermodynamic_cycles.html View entire conversation on ReviewNB |
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Yeah that makes sense validate and create are probably better suited to this showcase, maybe we should introduce validate here as well with some examples of things it can catch. We should probably show validating a protein component as well? View entire conversation on ReviewNB |
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View / edit / reply to this conversation on ReviewNB jthorton commented on 2026-10-26T15:58:33Z
Can we put the available protocols back into the grouped list we had? I think it's clearer to see the individual links. IAlibay commented on 2026-10-27T09:05:58Z +1, I would also add back in the link to the tutorials. |
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View / edit / reply to this conversation on ReviewNB jthorton commented on 2026-10-26T15:58:34Z points 10-12 are not in the list. |
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View / edit / reply to this conversation on ReviewNB jthorton commented on 2026-10-26T15:58:35Z I like the figure but maybe it needs updating having alchemiscale is probably confusing at this point, it should have quickrun and task-based execution instead.
The headings in the list should be the same as the figure as well to make mapping them easy for the reader so 1. Plan -> 1. Setup |
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View / edit / reply to this conversation on ReviewNB jthorton commented on 2026-10-26T15:58:36Z How does it look with some binding site side chains shown, you can't really see any interactions from that 3D view IAlibay commented on 2026-10-27T09:13:58Z If this is from the ccpbiosim tutorial - adding the side chains was a real mess / too hard to see anything. |
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View / edit / reply to this conversation on ReviewNB jthorton commented on 2026-10-26T15:58:37Z I think it would be good to keep some of the interop examples with OpenFF. |
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View / edit / reply to this conversation on ReviewNB jthorton commented on 2026-10-26T15:58:38Z This is great! Maybe as the reference for the 2.3.0 AshGC paper, this might be some users first exposure to it. |
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View / edit / reply to this conversation on ReviewNB jthorton commented on 2026-10-26T15:58:39Z This is the default. -> This is the CLI default as we have no API default for the mapping functions? IAlibay commented on 2026-10-27T09:18:44Z Maybe also add the phrase "in our hands this performs the best, especially when you have well aligned ligands"? |
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View / edit / reply to this conversation on ReviewNB jthorton commented on 2026-10-26T15:58:40Z Is this just the notebook issue but for me all the ids are on a single atom? |
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View / edit / reply to this conversation on ReviewNB jthorton commented on 2026-10-26T15:58:41Z Nice these look great! |
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View / edit / reply to this conversation on ReviewNB jthorton commented on 2026-10-26T15:58:42Z Can we add back the to_file demo for the mapping? |
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View / edit / reply to this conversation on ReviewNB jthorton commented on 2026-10-26T15:58:44Z We also have the json method as well now is graphml still the recommended default as thats what the CLI viewer supports? |
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View / edit / reply to this conversation on ReviewNB jthorton commented on 2026-10-26T15:58:45Z Is it time to decide if we are making this public yet before advertising and recomending it here? |
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View / edit / reply to this conversation on ReviewNB jthorton commented on 2026-10-26T15:58:46Z Lets also link the troubleshooting guide here for debugging help. |
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+1, I would also add back in the link to the tutorials. View entire conversation on ReviewNB |
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Since it's the main thing folks usually look at, I'm actuallly pro having "more information". I understand the need for reducing work when doing updates, but it's also the showcase so it's ok to have this be the main place where we have to be vigilant in updating things. View entire conversation on ReviewNB |
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I don't think I agree with just pulling all this into the user guide and removing it from here. As mentioned above, this quite often the first (and only) place folks look at - I'm pro being very noisy and detailed rather than assuming folks will read the userguide first. In fact, we usually tell folks "if you do anything, look at the showcase". View entire conversation on ReviewNB |
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Here and elsewhere, how about using info boxes when linking to other areas - e.g. for the "openfe does not prepare structures". That would make it easier for folks to easily recognise when we're signposting. View entire conversation on ReviewNB |
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If this is from the ccpbiosim tutorial - adding the side chains was a real mess / too hard to see anything. View entire conversation on ReviewNB |
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View / edit / reply to this conversation on ReviewNB IAlibay commented on 2026-10-27T09:16:07Z I wouldn't include the setup/run/gather image (instead I'd vote for some kind of small workflow diagram or similar). Definitely we shouldn't be including alchemiscale in this notebook. |
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View / edit / reply to this conversation on ReviewNB IAlibay commented on 2026-10-27T09:16:08Z [nit] Capital & backticks on "components"? |
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View / edit / reply to this conversation on ReviewNB IAlibay commented on 2026-10-27T09:16:09Z Maybe a little bit more detail about what you're linking to and the info box? |
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Maybe also add the phrase "in our hands this performs the best, especially when you have well aligned ligands"? View entire conversation on ReviewNB |
I added links to different places in our docs in this notebook, however some of those pages are still being written, so we'll need to update the links and make sure they all work later.
There are several open issues here related to the showcase that I think we should decide on here, implement if still desired and close if not: