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BioTransformer's README


This is version 1.0.8 of BioTransformer. BioTransformer is a software tool that predicts small molecule metabolism in mammals, their gut microbiota, as well as the soil/aquatic microbiota. BioTransformer also assists scientists in metabolite identification, based on the metabolism prediction. Please make sure to download the folders database and supportfiles, and save them in the same folder as the .jar file.

BioTransformer is offered to the public as a freely acessible software package under the GNU License GPL v2.1.

Users are free to copy and redistribute the material in any medium or format. Moreover, they could modify, and build upon the material unfer the condition that they must give appropriate credit, provide links to the license, and indicate if changes were made. Furthermore, the above copyright notice and this permission notice must be included. Use and re-distribution of the these resources, in whole or in part, for commercial purposes requires explicit permission of the authors. We ask that all users of the BioTransformer software tool, the BioTransformer web server, or BioTransformerDB to cite the BioTransformer reference in any resulting publications, and to acknowledge the authors.

Cite: Djoumbou-Feunang Y, Fiamoncini J, de la Fuente AG, Manach C, Greiner R, and Wishart DS; BioTransformer: A Comprehensive Computational Tool for Small Molecule Metabolism Prediction and Metabolite Identification; Journal of Cheminformatics 201911:2; DOI: 10.1186/s13321-018-0324-5.

To report issues, provide feedback, or ask questions, please send an e-mail the following address: djoumbou@ualberta.ca


Usage: java -jar biotransformer-1.0.8 -k <BioTransformer Task> -b <BioTransformer Option> [-ismi, -imol, or -isdf <Input file>] [-imol, or -isdf <Output>] [-s <Number of steps>] [-a <Annotate>] [-m <Masses>] [-r <Masses>] [-f <Formulas>]

This is the version 1.0.8 of BioTransformer. BioTransformer is a software tool that predicts small molecule metabolism in mammals, their gut microbiota, as well as the soil/aquatic microbiota. BioTransformer also assists scientists in metabolite identification, based on the metabolism prediction.

-a,--annotate Search PuChem for each product, and annotate with CID and synonyms

-b,--btType <BioTransformer Option> The type of description: Type of biotransformer - EC-based (ecbased), CYP450 (cyp450), Phase II (phaseII), Human gut microbial (hgut), human super transformer* (superbio, or allHuman), Environmental microbial (envimicro).

-h,--help Prints the usage.

-ismi, --ismiles <Input> Read the input as a single molecule in SMILES format

-imol, --molinput <Input file> Read the input as a single molecule in the specified MOL format

-isdf, --sdfinput <Input file> Read the input from the specified SDF format

-k, --task <BioTransformer Task> The task to be permed: pred for prediction, or cid for compound identification

-m,--mList Given the starting comound(s), Find all their metabolites with the specified masses, and show a metabolism pathway. A whitespace-separated list of masses is expected.

-ocsv, --csvoutput <Output file> Save the results into the specified CSV file

-osdf, --sdfoutput <Output file> Save the results into the specified SDF file

-f,--formulas <formulas> Semicolon-separated list of formulas of compounds to identify
-s,--nsteps <Number of steps> The number of steps for the prediction. This option can be set by the user for the EC-based, CYP450, Phase II, and Environmental microbial biotransformers. The default value is 1.

-t,--mTolerance Mass tolerance for metabolite identification (default is 0.01).
(* ) While the 'superbio' option runs a set number of transformation steps in a pre-defined order (e.g. deconjugation first, then Oxidation/reduction, etc.), the 'allHuman' option predicts all possible metabolites from any applicable reaction(Oxidation, reduction, (de-)conjugation) at each step.

(** ) For the environmental microbial biodegradation, all reactions (aerobic and anaerobic) are reported, and not only the aerobic biotransformations (as per default in the EAWAG BBD/PPS system).


Examples:


1) To predict the biotransformation of a molecule from an SDF input using the human super transformer (option superbio) and annotate the metabolites with names and database IDs (from PubChem), run

  java -jar biotransformer-1-0-8.jar -k pred -b superbio -isdf -i #{input file name} -osdf #{output file} -a.

2) To predict the 2-step biotransformation of Thymol (a monoterpene) using the human super transformer (option allHuman) using the SMILES input and saving to a CSV file, run

  java -jar biotransformer-1-0-8.jar  -k pred -b allHuman -ismi "CC(C)C1=CC=C(C)C=C1O" -ocsv #{replace with output file name} -s 2

Currently, the outputfile is SDF per default.

3) Identify all human metabolites (max depth = 2) of Epicatechin ("O[C@@H]1CC2=C(O)C=C(O)C=C2O[C@@H]1C1=CC=C(O)C(O)=C1") with masses 292.0946 Da and 304.0946 Da, with a mass tolerance of 0.01 Da. Provide an annotation (Common name, synonyms, and PubChem CID), when available.

  java -jar biotransformer-1-0-8.jar  -k cid -b allHuman -ismi "O[C@@H]1CC2=C(O)C=C(O)C=C2O[C@@H]1C1=CC=C(O)C(O)=C1" -osdf #{replace with output file name} -s 2 -m "292.0946;304.0946" -t 0.01 -a

- DO NOT forget the quotes around the SMILES string or the list of masses.