User: Pablo Carbonell

Name: Pablo Carbonell

Joined: Tuesday 30 May 2017 09:18:11 (UTC)

Last seen: Thursday 26 July 2018 12:58:54 (UTC)

Email (public): pablo.carbonell [at] manchester.ac.uk

Website: http://carbonelllab.org

Location: Manchester, United Kingdom

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Interests:

Engineering biology
Metabolic engineering
Systems biology
Synthetic biology
Control engineering

Field/Industry: Biotechnology

Occupation/Role(s): Senior staff scientist

Organisation(s):

SYNBIOCHEM

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Pathway example for Selenzyme

Created: 2017-08-18 08:35:57 | Last updated: 2017-08-23 11:13:20

Credits: Pablo Carbonell

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example of an input file containing information about a metabolic pathway to query the KNIME workflow for Selenzyme, an enzyme selection tool for pathway design.The file contains a list of reactions or generic reactions expressed in SMILES or SMARTS (SMIRKS) format. In the example, the list of reactions correspond to the different steps of a biosynthetic pathway.

File type: text/csv

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Selenzyme

Created: 2017-08-18 08:23:47 | Last updated: 2017-08-23 11:12:00

Enzyme selection workflow for pathway design

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Workflow

KNIME

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Pablo Carbonell

KNIME Workflow for RetroRules and Selenzyme (4)

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KNIME Workflow for RetroRules and SelenzymeThis worflow provides an examples of retrieving the RetroRules reaction rules for some given reaction and selecting enzyme sequences using the Selenzyme tool.1. Input to the workflow: Chemical reactions expressed using public database identifiers.2. Each reaction queries RetroRules and outputs the corresponding reaction rules.3. Each reaction rule queries Selenzyem and outputs the selected Uniprot sequences for each rule.4. Resulting list of selected...

Created: 2018-07-24 | Last updated: 2018-08-11

Credits: Pablo Carbonell

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KNIME

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Pablo Carbonell

KNIME Workflow for RetroRules and Retropat... (3)

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KNIME Workflow for RetroRules and RetroPath2.0This worflow provides an examples of retrieving the RetroRules reaction rules for some given reaction identifiers.1. Input to the workflow: Chemical reactions expressed using public database identifiers.2. Each reaction queries RetroRules and outputs the corresponding reaction rules.3. Resulting list of rulesenzymes is stored in a csv file in RetroPath2.0 format.Installation notesThe workflow runs a Python scrpt that requires pandas: Python Data A...

Created: 2018-07-26 | Last updated: 2018-08-11

Credits: Pablo Carbonell

Workflow

KNIME

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Pablo Carbonell

Workflow for Selenzyme v 1.0 (2)