smoretti

Wrong example name

1

Hi on the https://github.com/Oshlack/Lace/wiki/Usage-Documentation page the command *python Lace.py Example/Example_Genome.fasta Example/clusters.txt -t -o Test* does not work because it should be *python3 Lace.py Example/Example_Transcripts.fasta Example/clusters.txt -t -o Test*

Wrong name for cpd00874

1

Hi the stereochemistry of cpd00874 shows it should be named `(3R,5R)` / `D-erythro`. Currently, it has all possible stereo names, i.e. `(3R,5R)` / `D-erythro` and `(3S,5S)` / `L-erythro` What is...

Hi we found several issues with aerobactin compounds in ModelSEED. - cpd26452 SMILES looks to be invalid according to chemaxon and smiles drawer at least. Should be something like `CC(=O)N(O)CCCC[C@H](NC(=O)CC(O)(CC(=O)N[C@@H](CCCCN(O)C(C)=O)C([O-])=O)C([O-])=O)C([O-])=O.[Fe]`...

Hi it looks **cpd27117** and **cpd28855** are fake entries; certainly used in MetaCyc at import time by ModelSEED for testing purposes.

Hi I wonder if (S)-3-Hydroxyisobutyrate (cpd19043) and (S)-3-Hydroxyisobutyric acid (cpd23281) are really what they are supposed to be. - (S)-3-Hydroxyisobutyrate (cpd19043) and (S)-3-Hydroxyisobutyric acid (cpd23281) have different stereochemistry. They look...

General SBML unit question about second multiplier

1

Hi I have a general SBML question about unit tag and the value of multiplier for second. Most models use **mmol_per_gDW_per_hr**, they define **mole**, **gram**, and **second**. They all use...

Is "Biomass_biomass" compound similar to "Biomass" compound?

1

Hi I wonder if "Biomass_biomass" cpd29751 compound and "Biomass" cpd11416 compound are similar?

ChEBI 240 release issues

10

Hi Is ChEBI version 240 officially released? The https://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel240/ folder exists but the https://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel240/ontology/chebi.obo file shows `data-version: 239`. Also, the https://ftp.ebi.ac.uk/pub/databases/chebi/archive/rel240/SDF/ folder is empty. Is the current ChEBI version displayed...

Compilation with -march=native option

4

Hi Do you recommend, or not, to use `-march=native` as compilation option? Instead of simply `-O2 -m64` on Linux

Hi Several Isorhamnetin derived structures cross-linked to Lipid Maps have different stereochemistries compared to Lipid Maps. - [CHEBI:168565](https://www.ebi.ac.uk/chebi/CHEBI:168565) with [LMPK12112336](https://www.lipidmaps.org/databases/lmsd/LMPK12112336) - [CHEBI:197247](https://www.ebi.ac.uk/chebi/CHEBI:197247) with [LMPK12112338](https://www.lipidmaps.org/databases/lmsd/LMPK12112338) - [CHEBI:184521](https://www.ebi.ac.uk/chebi/CHEBI:184521) with [LMPK12112370](https://www.lipidmaps.org/databases/lmsd/LMPK12112370) Could you...