Merging in main branch

RJ3 · Apr 9, 2023 · 39a6d0e · 39a6d0e
2 parents d8ee9c5 + 84659c9
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diff --git a/CITATION.cff b/CITATION.cff
@@ -1,22 +1,91 @@
 cff-version: 1.2.0
-message: "For now, cite OpenFold with its DOI."
-authors:
-- family-names: "Ahdritz"
-  given-names: "Gustaf"
-  orcid: https://orcid.org/0000-0001-8283-5324
-- family-names: "Bouatta"
-  given-names: "Nazim"
-  orcid: https://orcid.org/0000-0002-6524-874X
-- family-names: "Kadyan"
-  given-names: "Sachin"
-- family-names: "Xia"
-  given-names: "Qinghui"
-- family-names: "Gerecke"
-  given-names: "William"
-- family-names: "AlQuraishi"
-  given-names: "Mohammed"
-  orcid: https://orcid.org/0000-0001-6817-1322
-title: "OpenFold"
-doi: 10.5281/zenodo.5709539
+preferred-citation:
+    authors:
+    - family-names: "Ahdritz"
+      given-names: "Gustaf"
+      orcid: https://orcid.org/0000-0001-8283-5324
+    - family-names: "Bouatta"
+      given-names: "Nazim"
+      orcid: https://orcid.org/0000-0002-6524-874X
+    - family-names: "Kadyan"
+      given-names: "Sachin"
+      orcid: https://orcid.org/0000-0002-6079-7627
+    - family-names: "Xia"
+      given-names: "Qinghui"
+    - family-names: "Gerecke"
+      given-names: "William"
+      orcid: https://orcid.org/0000-0002-9777-6192
+    - family-names: "O'Donnell"
+      given-names: "Timothy J"
+      orcid: https://orcid.org/0000-0002-9949-069X
+    - family-names: "Berenberg"
+      given-names: "Daniel"
+      orcid: https://orcid.org/0000-0003-4631-0947
+    - family-names: "Fisk"
+      given-names: "Ian"
+    - family-names: "Zanichelli"
+      given-names: "Niccolò"
+      orcid: https://orcid.org/0000-0002-3093-3587
+    - family-names: "Zhang"
+      given-names: "Bo"
+      orcid: https://orcid.org/0000-0002-9714-2827
+    - family-names: "Nowaczynski"
+      given-names: "Arkadiusz"
+      orcid: https://orcid.org/0000-0002-3351-9584
+    - family-names: "Wang"
+      given-names: "Bei"
+      orcid: https://orcid.org/0000-0003-4942-9652
+    - family-names: "Stepniewska-Dziubinska"
+      given-names: "Marta M"
+      orcid: https://orcid.org/0000-0003-4942-9652
+    - family-names: "Zhang"
+      given-names: "Shang"
+      orcid: https://orcid.org/0000-0003-0759-2080
+    - family-names: "Ojewole"
+      given-names: "Adegoke"
+      orcid: https://orcid.org/0000-0003-2661-4388
+    - family-names: "Guney"
+      given-names: "Murat Efe"
+    - family-names: "Biderman"
+      given-names: "Stella"
+      orcid: https://orcid.org/0000-0001-8228-1042
+    - family-names: "Watkins"
+      given-names: "Andrew M"
+      orcid: https://orcid.org/0000-0003-1617-1720
+    - family-names: "Ra"
+      given-names: "Stephen"
+      orcid: https://orcid.org/0000-0002-2820-0050
+    - family-names: "Lorenzo"
+      given-names: "Pablo Ribalta"
+      orcid: https://orcid.org/0000-0002-3657-8053
+    - family-names: "Nivon"
+      given-names: "Lucas"
+    - family-names: "Weitzner"
+      given-names: "Brian"
+      orcid: https://orcid.org/0000-0002-1909-0961
+    - family-names: "Ban"
+      given-names: "Yih-En"
+      orcid: https://orcid.org/0000-0003-3698-3574
+    - family-names: "Ban"
+      given-names: "Yih-En Andrew"
+      orcid: https://orcid.org/0000-0003-3698-3574
+    - family-names: "Sorger"
+      given-names: "Peter K"
+      orcid: https://orcid.org/0000-0002-3364-1838
+    - family-names: "Mostaque"
+      given-names: "Emad"
+    - family-names: "Zhang"
+      given-names: "Zhao"
+      orcid: https://orcid.org/0000-0001-5921-0035
+    - family-names: "Bonneau"
+      given-names: "Richard"
+      orcid: https://orcid.org/0000-0003-4354-7906
+    - family-names: "AlQuraishi"
+      given-names: "Mohammed"
+      orcid: https://orcid.org/0000-0001-6817-1322
+    title: "OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization"
+    type: article
+    doi: 10.1101/2022.11.20.517210
+doi: 10.1101/2022.11.20.517210
 date-released: 2021-11-12
-url: "https://github.com/aqlaboratory/openfold"
+url: "https://doi.org/10.1101/2022.11.20.517210"
diff --git a/Dockerfile b/Dockerfile
@@ -1,6 +1,17 @@
-FROM nvidia/cuda:10.2-cudnn8-runtime-ubuntu18.04
+FROM nvidia/cuda:11.3.1-cudnn8-runtime-ubuntu18.04
 
-RUN apt-get update && apt-get install -y wget cuda-minimal-build-10-2 git
+# metainformation
+LABEL org.opencontainers.image.version = "1.0.0"
+LABEL org.opencontainers.image.authors = "Gustaf Ahdritz"
+LABEL org.opencontainers.image.source = "https://github.com/aqlaboratory/openfold"
+LABEL org.opencontainers.image.licenses = "Apache License 2.0"
+LABEL org.opencontainers.image.base.name="docker.io/nvidia/cuda:10.2-cudnn8-runtime-ubuntu18.04"
+
+RUN apt-key del 7fa2af80
+RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub
+RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
+
+RUN apt-get update && apt-get install -y wget libxml2 cuda-minimal-build-11-3 libcusparse-dev-11-3 libcublas-dev-11-3 libcusolver-dev-11-3 git
 RUN wget -P /tmp \
     "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" \
     && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \