Michael Blinov
Michael Blinov
BMDB and Pathway Commons imports are broken on Rel and Alpha due to MalformedURLException BMDB error (when retrieving a model) MalformedURLException-no protocol: nullBIOMD0000000355 Pathway Commons error (when trying to search):...
The annotations branch has search for annotations in multiple databases and automatic retrieval and adding of annotations, eliminating the need to go to external databases and search/enter external ids. The...
Two emails from vcellserver 9:55am and 10:07am are about this issue, ending in java.lang.Thread.run(Thread.java:748)\njava.lang.ArrayIndexOutOfBoundsException: 0\n\tat cbit.vcell.mapping.SimulationContext.getSimulations(SimulationContext.java:1777)\n\tat org.vcell.util.gui.exporter.NfsimExtensionFilter.writeBioModel(NfsimExtensionFilter.java:35)\n\tat cbit.vcell.client.task.ExportDocument.run(ExportDocument.java:134)\n\tat cbit.vcell.client.task.ClientTaskDispatcher.runTask(ClientTaskDispatcher.java:675)\n\tat cbit.vcell.client.task.ClientTaskDispatcher.access$600(ClientTaskDispatcher.java:55)\n\tat cbit.vcell.client.task.ClientTaskDispatcher$1.construct(ClientTaskDispatcher.java:382)\n\tat swingthreads.SwingWorker$2.run(SwingWorker.java:109)\n\tat java.lang.Thread.run(Thread.java:748)\n","softwareVersion":"Rel_Version_7.5.0_build_62","platform":"Running under Java 1.8.0_141, published by Oracle Corporation,...
New links autogenerated in html help are dead https://vcell.org/webstart/VCell_Tutorials/VCell_Help/topics/ch_3/BioModelApplications/Simulations/Results/Spatial/OpenHDF5ImageJ.html https://vcell.org/webstart/VCell_Tutorials/VCell_Help/topics/ch_9/Appendix/AnnotationProviders.html All pages for kinematics are dead https://vcell.org/webstart/VCell_Tutorials/VCell_Help/topics/ch_8/PropertiesPanes/PP_KinematicsVolumeProcess.html https://vcell.org/webstart/VCell_Tutorials/VCell_Help/topics/ch_8/PropertiesPanes/PP_KinematicsSurfaceProcess.html
Set z coordinate of membrane-bound site to 0
Pass values from Edit Simulation -> Mesh at VCell to SpringSalad solver. Input the default SpringSalad values into Mesh.
Time step is now set to be 0.1. In SpringSalad it is 1e-8 (System Information -> System Times). Need to check if it is passed to SpringSalad solver and fix.
SpringSalad version in Help-> About is not updated - it's difficult to track which version we're using. Need to update automatically with the version and build number for each new...
Parallel simulations in stand-alone SpringSalad latest version do not work on Windows and Mac
Create a fake single state0, initial state in UI will be empty.