2024-04-04

This is PMAS's COMMONS Lab daily Open Notebook.

Today is 2024.04.04

Todo today

Have a look at the COMMONS research discussion forum

- https://github.com/orgs/commons-research/discussions

Daily work on the Open Science for natural products research Viewpoint

See Viewpoint

Doing

sirius -i /home/allardpm/git_repos/mapp-metabolomics/laure-weisskopf-group/docs/mapp_project_00016/mapp_batch_00060/results/mzmine/mapp_batch_00060_sirius.mgf --output /home/allardpm/git_repos/mapp-metabolomics/laure-weisskopf-group/docs/mapp_project_00016/mapp_batch_00060/results/sirius/mapp_batch_00060 --maxmz 800 config --IsotopeSettings.filter=true --FormulaSearchDB=BIO --Timeout.secondsPerTree=0 --FormulaSettings.enforced=HCNOP --Timeout.secondsPerInstance=0 --AdductSettings.detectable=[[M+H3N+H]+,[M+Na]+,[M-H4O2+H]+,[M+K]+,[M-H2O+H]+,[M+H]+] --UseHeuristic.mzToUseHeuristicOnly=650 --AlgorithmProfile=orbitrap --IsotopeMs2Settings=IGNORE --MS2MassDeviation.allowedMassDeviation=5.0ppm --NumberOfCandidatesPerIon=1 --UseHeuristic.mzToUseHeuristic=300 --FormulaSettings.detectable=Cl,Br,S --NumberOfCandidates=10 --ZodiacNumberOfConsideredCandidatesAt300Mz=10 --ZodiacRunInTwoSteps=true --ZodiacEdgeFilterThresholds.minLocalConnections=10 --ZodiacEdgeFilterThresholds.thresholdFilter=0.95 --ZodiacEpochs.burnInPeriod=2000 --ZodiacEpochs.numberOfMarkovChains=10 --ZodiacNumberOfConsideredCandidatesAt800Mz=50 --ZodiacEpochs.iterations=20000 --AdductSettings.enforced=, --AdductSettings.fallback=[[M+Na]+,[M+K]+,[M-H2O+H]+,[M+H]+] --FormulaResultThreshold=true --InjectElGordoCompounds=true --StructureSearchDB=BIO --RecomputeResults=false formula zodiac fingerprint structure canopus write-summaries

Relaunching with