Wikipathways
Most likely THE place to start learning about Wikipathways https://wikipathways.org/academy/
Ran into the following issues
ā pathvisio-3.3.0 sh pathvisio.sh Problem creating boot delegation class loader: java.lang.reflect.InaccessibleObjectException: Unable to make protected java.security.SecureClassLoader(java.lang.ClassLoader) accessible: module java.base does not "opens java.security" to unnamed module @49b70bc7 (Private) Installing bundles that are embedded in the jar. Detected embedded bundle: org.apache.batik.svggen_1.7.0.v201011041433.jar Loading jar:file:/Applications/pathvisio-3.3.0/pathvisio.jar!/org.apache.batik.svggen_1.7.0.v201011041433.jar ^C^C% ā pathvisio-3.3.0 java --version openjdk 17.0.1 2021-10-19 OpenJDK Runtime Environment (build 17.0.1+12-39) OpenJDK 64-Bit Server VM (build 17.0.1+12-39, mixed mode, sharing)
Pathvisio aparently only supports java 8 https://github.com/PathVisio/pathvisio/issues/155
https://medium.com/@brunofrascino/working-with-multiple-java-versions-in-macos-9a9c4f15615a
Adapted line for java8 to
https://stackoverflow.com/a/28635465
Needed to echo eval "$(jenv init -)" >> /Users/pma/.zshrc
Documented here https://github.com/PathVisio/pathvisio/issues/155#issuecomment-1059946761
Stopped here https://wikipathways.org/academy/stages/wp-publish/index.html Now waiting for an auth from Wikipathways to upload
https://wikipathways.org/academy/path.html
The last part (QA protocol) could give some inspiration regarding a curation interface for lotus data
Was having a look at BioCyc when ... oh surprise
(#amoeba) <<< will use this tag when I know amoeba splitting will be required later on
http://ambit.sourceforge.net/ https://apps.ideaconsult.net/data/demo/reaction?search=C%5BS%2B%5D%28C%5BC%40%40H%5D3%28%5BC%40%40H%5D%28O%29%5BC%40%40H%5D%28O%29%5BC%40H%5D%28N1%28C2%28%5CN%3DC%2FN%3DC%28C%28%5CN%3DC%2F1%29%3D2%29%2FN%29%29%29O3%29%29CC%5BC%40%40H%5D%28C%28%5BO-%5D%29%3DO%29%5BNH3%2B%5D&smirks=%5BC%3A1%5D%28%5BH%5D%29%5BO%3A2%5D%5BH%5D%3E%3E%5BC%3A1%5D%3D%5BO%3A2%5D
http://ideaconsult.github.io/Toxtree.js/
https://github.com/ideaconsult/notebooks-ambit
Looks like arabit hole afternoon to me ... https://github.com/twosigma/beakerx Now installing java kernel for jupyter nb
Since https://github.com/twosigma/beakerx/issues/8317
I
conda create --name ambit -c beakerx -c conda-forge python=3.7 beakerx_kernel_java
Could not run the notebooks. Filed an issue at https://github.com/ideaconsult/notebooks-ambit/issues/2
https://onlinelibrary.wiley.com/doi/abs/10.1002/minf.202100027