Maria Heitmeier

Package 'qt5-default' has no installation candidate

2

Hi, I'm trying to build a container on Mac OS Catalina 10.15.4 but run into the following error: ``` import SimpleContainerGenerator mkpath("my_image_name") cd("my_image_name") pkgs = [ "DataFrames" ] julia_version =...

Hi, I was wondering whether it might be possible to add [Wikipedia2Vec](https://wikipedia2vec.github.io/wikipedia2vec/pretrained/) embeddings? That would extend the list of languages for which word2vec embeddings are available by 11 languages.

Conversion from JSON to SBML stays at Reading input file

4

Converting some json files to SBML leads to the conversion getting stuck at `reading input file` in the gui or to a `NullPointerException` in the command line: `java -jar -Xms8G...

Conversion SBML -> Escher creates mistake in file

7

Apparently, something goes wrong in the conversion from SBML to Escher. Converting from SBML to Escher works: `java -jar -Xms8G -Xmx8G -Duser.language=en EscherConverter-1.2.1.jar --input=GlycolysisLayout_small.sbml.xml --format=Escher --output=glycolysis.json --gui=false` But going back...

NullPointerException when inferring compartment boundaries

3

When trying to open `e_coli_core_metabolism.escher.json` with inferring compartment boundaries set to true, a NullPointerException occurs:  ``` 26.07.2019 16:02:30 de.zbit.gui.GUITools showErrorMessage --- WARNUNG: java.lang.NullPointerException java.util.concurrent.ExecutionException: java.lang.NullPointerException at java.util.concurrent.FutureTask.report(Unknown Source) at...

Conversion stops at CreateMultiMarkers if neither BoundingBox nor Curve are set

1

When converting the file `GlycolysisLayout_small.sbml.xml` from `data` the conversion stops at `edu.ucsd.sbrg.escher.converter.SBML2Escher createMultiMarkers --- INFORMATION: creating multi-markers from species reference glyph (SpeciesReferenceGlyph_01)`. This is probably because in this `SpeciesReferenceGlyph` `BoundingBox`...

Setting --gui=false returns JsonParseException

1

When using the command line with normal `input` and `output` options and independent of the `--format` option, setting `gui=false` returns the following error: ``` com.fasterxml.jackson.core.JsonParseException: Unexpected character ('

ReconMap returns NullPointerException

1

When trying to convert the ReconMap SBML file to Escher, there is a NullPointerException. Options were all set to default:  Stack trace: >12:52:16 edu.ucsd.sbrg.escher.gui.SBMLLayoutViewPanel lambda$0 --- WARNUNG: java.lang.NullPointerException java.util.concurrent.ExecutionException:...

Hi @AdarshKumar712 , it's awesome that you are developing this package! I run into the following problem when trying to use report_stats with a binary classification task: (borrowing from your...