From 89986eb1b223130acfa7c3508e0c24c4f358dc7c Mon Sep 17 00:00:00 2001 From: Phil Biggin <51948186+philbiggin@users.noreply.github.com> Date: Fri, 12 Apr 2024 11:19:35 +0100 Subject: [PATCH 01/11] Update docker-publish.yml --- .github/workflows/docker-publish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml index a3aec05..84f4370 100644 --- a/.github/workflows/docker-publish.yml +++ b/.github/workflows/docker-publish.yml @@ -32,7 +32,7 @@ jobs: uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7 with: #images: my-docker-hub-namespace/my-docker-hub-repository - images: davidseiferth/poreanalyser + images: philbiggin/poreanalyser - name: Build and push Docker image uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671 From ba5642ff7855b012b37734720633ed0bb9e35c27 Mon Sep 17 00:00:00 2001 From: Phil Biggin <51948186+philbiggin@users.noreply.github.com> Date: Fri, 12 Apr 2024 11:48:23 +0100 Subject: [PATCH 02/11] Update docker-publish.yml --- .github/workflows/docker-publish.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml index 84f4370..7c435c2 100644 --- a/.github/workflows/docker-publish.yml +++ b/.github/workflows/docker-publish.yml @@ -22,10 +22,10 @@ jobs: uses: actions/checkout@v4 - name: Log in to Docker Hub - uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a + uses: docker/login-action@v3 with: - username: ${{ secrets.DOCKER_USERNAME }} - password: ${{ secrets.DOCKER_PASSWORD }} + username: ${{ secrets.DOCKERHUB_USERNAME }} + password: ${{ secrets.DOCKERHUB_TOKEN }} - name: Extract metadata (tags, labels) for Docker id: meta From b7555eb5b3fa1dbbc3a2a02d8f0ea04ec765806e Mon Sep 17 00:00:00 2001 From: Phil Biggin <51948186+philbiggin@users.noreply.github.com> Date: Fri, 12 Apr 2024 12:28:23 +0100 Subject: [PATCH 03/11] Update python-publish.yml made PyPi action just use release v1. --- .github/workflows/python-publish.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml index 77766db..ba782e8 100644 --- a/.github/workflows/python-publish.yml +++ b/.github/workflows/python-publish.yml @@ -41,7 +41,7 @@ jobs: #echo "Current Version: $(python -c "import PoreAnalyser as pf; print(pf.__version__)")" echo "Current Version: $(python -c "import PoreFinder as pf; print(pf.__version__)")" - name: Publish package - uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29 + uses: pypa/gh-action-pypi-publish@release/v1 with: user: __token__ password: ${{ secrets.PYPI_API_TOKEN }} From 1d486489536851e674f12abad5a3c653570d70d5 Mon Sep 17 00:00:00 2001 From: Phil Biggin <51948186+philbiggin@users.noreply.github.com> Date: Thu, 18 Apr 2024 08:40:33 +0100 Subject: [PATCH 04/11] Update docker-publish.yml added docker hub description for completeness. --- .github/workflows/docker-publish.yml | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml index 7c435c2..3c997c4 100644 --- a/.github/workflows/docker-publish.yml +++ b/.github/workflows/docker-publish.yml @@ -27,6 +27,15 @@ jobs: username: ${{ secrets.DOCKERHUB_USERNAME }} password: ${{ secrets.DOCKERHUB_TOKEN }} + - name: Docker Hub Description + uses: peter-evans/dockerhub-description@v4 + with: + username: ${{ secrets.DOCKERHUB_USERNAME }} + password: ${{ secrets.DOCKERHUB_TOKEN }} + repository: peterevans/dockerhub-description + short-description: ${{ github.event.repository.description }} + + - name: Extract metadata (tags, labels) for Docker id: meta uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7 From d1e43b0f702841cbb972574500a2a7beb3d99968 Mon Sep 17 00:00:00 2001 From: Phil Biggin <51948186+philbiggin@users.noreply.github.com> Date: Thu, 18 Apr 2024 09:52:01 +0100 Subject: [PATCH 05/11] Update app.py reference update --- app.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app.py b/app.py index aabc56d..d739402 100644 --- a/app.py +++ b/app.py @@ -308,4 +308,4 @@ st.subheader("References") st.write("Smart, O.S., Neduvelil, J.G., Wang, X., Wallace, B.A., Sansom, M.S.P., 1996. HOLE: A program for the analysis of the pore dimensions of ion channel structural models. Journal of Molecular Graphics 14, 354–360. https://doi.org/10.1016/S0263-7855(97)00009-X") st.write("Gowers, R., Linke, M., Barnoud, J., Reddy, T., Melo, M., Seyler, S., Domański, J., Dotson, D., Buchoux, S., Kenney, I., Beckstein, O., 2016. MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. Presented at the Python in Science Conference, Austin, Texas, pp. 98–105. https://doi.org/10.25080/Majora-629e541a-00e") -st.write("(preprint) Seiferth, D., Biggin, P., 2024. Exploring the Influence of Pore Shape on Conductance and Permeation.") +st.write("(preprint) Seiferth, D., Biggin, P.C., 2024. Exploring the Influence of Pore Shape on Conductance and Permeation.") From 1b8935333cdf5af623e2b7badc3b74987f94f045 Mon Sep 17 00:00:00 2001 From: Phil Biggin <51948186+philbiggin@users.noreply.github.com> Date: Mon, 22 Apr 2024 13:43:16 +0100 Subject: [PATCH 06/11] Update visualisation.rst --- docs/source/visualisation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/visualisation.rst b/docs/source/visualisation.rst index de6306e..f81e0e1 100644 --- a/docs/source/visualisation.rst +++ b/docs/source/visualisation.rst @@ -1,4 +1,4 @@ -git statVisualisation +Visualisation ============= Visualisation online From 01f6f5ae3c26ed284e46f8aee865cf604738827f Mon Sep 17 00:00:00 2001 From: Phil Biggin <51948186+philbiggin@users.noreply.github.com> Date: Mon, 22 Apr 2024 13:44:31 +0100 Subject: [PATCH 07/11] Update README.md preprint added --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 9e08972..86b60ef 100644 --- a/README.md +++ b/README.md @@ -17,6 +17,8 @@ PoreAnalyser [Try out this software without installing anything](https://poreanalyser.bioch.ox.ac.uk/) +[Read the accompanying preprint](https://doi.org/10.1101/2024.04.18.589791) + Recent advances in structural biology have led to a growing number of ion channel structures featuring heteromeric subunit assembly, exemplified by synaptic Glycine receptors ([GlyRs](https://www.nature.com/articles/s41467-023-37106-7)) and α4β2 nicotinic receptors. These structures exhibit inherent pore asymmetry, which has raised questions about the role of asymmetry in ion channel function. Furthermore, molecular dynamics simulations performed on symmetrical homomeric channels often lead to thermal distortion that means conformations of the resulting ensemble are also asymmetrical. We introduce an algorithm that employs ellipsoidal probe particles, enabling a more comprehensive characterization of pore asymmetries. A constriction is more asymmetric for a larger difference between the smaller and larger radius of the ellipsoidal probe particle. #### Existing tools for pore pathfinding From d41044cbcccc0f2f74c09cc00dda60f5eb2fb870 Mon Sep 17 00:00:00 2001 From: Phil Biggin <51948186+philbiggin@users.noreply.github.com> Date: Mon, 22 Apr 2024 13:45:06 +0100 Subject: [PATCH 08/11] Update README.md --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 86b60ef..dca4f16 100644 --- a/README.md +++ b/README.md @@ -59,7 +59,10 @@ More information about the [output files](https://porefinding.readthedocs.io/en/ To render 3d representations of the pore surface, you can use a variety of software ranging from py3Dmol, VMD to UCSF Chimera. See [Visualisation tools](https://porefinding.readthedocs.io/en/latest/visualisation.html). +### Preprint +![qrcode](https://connect.biorxiv.org/qr/qr_img.php?id=2024.04.18.589791) +Find out more about the influence of pore shape on conductance and permeation in our [preprint](https://doi.org/10.1101/2024.04.18.589791) ## Acknowledgements * Rocco Meli for pointing out streamlit (and hugginface) * SBCB community for discussion From e4a08ce01761213bfe51c9fc46d4e2a773a90ac1 Mon Sep 17 00:00:00 2001 From: Phil Biggin <51948186+philbiggin@users.noreply.github.com> Date: Mon, 22 Apr 2024 13:46:31 +0100 Subject: [PATCH 09/11] Update app.py --- app.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app.py b/app.py index d739402..0f4fb5b 100644 --- a/app.py +++ b/app.py @@ -308,4 +308,4 @@ st.subheader("References") st.write("Smart, O.S., Neduvelil, J.G., Wang, X., Wallace, B.A., Sansom, M.S.P., 1996. HOLE: A program for the analysis of the pore dimensions of ion channel structural models. Journal of Molecular Graphics 14, 354–360. https://doi.org/10.1016/S0263-7855(97)00009-X") st.write("Gowers, R., Linke, M., Barnoud, J., Reddy, T., Melo, M., Seyler, S., Domański, J., Dotson, D., Buchoux, S., Kenney, I., Beckstein, O., 2016. MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. Presented at the Python in Science Conference, Austin, Texas, pp. 98–105. https://doi.org/10.25080/Majora-629e541a-00e") -st.write("(preprint) Seiferth, D., Biggin, P.C., 2024. Exploring the Influence of Pore Shape on Conductance and Permeation.") +st.write("(preprint) Seiferth, D., Biggin, P., 2024. Exploring the Influence of Pore Shape on Conductance and Permeation. https://doi.org/10.1101/2024.04.18.589791") From 32f60740ca3848de01288245cbf2f3b61c708537 Mon Sep 17 00:00:00 2001 From: Phil Biggin <51948186+philbiggin@users.noreply.github.com> Date: Mon, 22 Apr 2024 13:47:20 +0100 Subject: [PATCH 10/11] Update conductance.rst --- docs/source/conductance.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/source/conductance.rst b/docs/source/conductance.rst index 4999621..c3a974c 100644 --- a/docs/source/conductance.rst +++ b/docs/source/conductance.rst @@ -39,3 +39,5 @@ Hence, we can further adapt the model for channel resistance / conductance based :align: center :alt: Fig10_Innexin_6kfg_example_row.png + +Find out more about the conductance model in our `preprint `_ . From 9c6d0bbc340a4fef9abbde76a17664168e345662 Mon Sep 17 00:00:00 2001 From: Phil Biggin <51948186+philbiggin@users.noreply.github.com> Date: Mon, 22 Apr 2024 13:48:08 +0100 Subject: [PATCH 11/11] Update index.rst --- docs/source/index.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/source/index.rst b/docs/source/index.rst index 8e06176..1934d65 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -15,6 +15,8 @@ hosted on a webserver of the Department of Biochemistry (University of Oxford). We introduce an algorithm that employs ellipsoidal probe particles, enabling a more comprehensive characterization of pore asymmetries. A constriction is more asymmetric for a larger difference between the smaller and larger radius of the ellipsoidal probe particle. +In the accompanying `preprint `_ , we explore the influence of pore shape on conductance and permeation. + The package uses the `HOLE `_ programme wrapped by `MDAnalysis `_.