WP7 wrap-up

Stian Soiland-Reyes, The University of Manchester



IBISBA WP6/WP7 workshop, VTT, Espoo


RetroPath 2.0

RetroPath 2.0-mods-metabolomics

Scope Viewer (with RetroPath)


Selenzyme connector for retropath results


Query Biochemical Rules DataBase (BioRule DB)
     ~December 2018

Initial Workflow nodes for design

  • Title

  • Description

  • Workflow type (e.g. KNIME, Galaxy)

  • Diagram

  • License (Apache, GPL, CC-BY)

    • License of workflow

    • license of its dependencies

    • Permission needed to use? (e.g. for commercial users)

  • Compatibility

    • E.g. Windows or Linux

    • WF environment, e.g. plugins

  • Purpose

    • Related to SEEK project structure

Workflow metadata

Workflow as chain

Workflow nodes to make


Extract sink from strain models (native metabolites)

Machine learning based Enzyme sequence scoring node

Flux balance analysis node

Pathway ranking node


Connector node with DNA part repository (promoter, enzyme sequence)

From RP2Path/DNA part connector to SBOL

Translate SBOL to/from vector (SEVA)

Generate combinatorial libraries of SBOL/SEVA varying enzymes sequences, ORI, promoter, RBS for bacteria (strain specific)

Format Build and test SOPs in structured language (AutoProtocol?)



Untargeted/targeted metabolomics connector RetroPath 2.0-mods-metabolomics with OpenMS


Optimize and Scale up

Mixed integer linear program node for gene up/down regulation

DoE for fermentation condition



QuickForm inputs

Workflow parameters

Practical: Wrap RP2Path in CWL

Moving from proof of concept to production instance

Single Sign-On for IBISBAHub

Data Storage
by reference


Data Management Plan

  "op": "oligosynthesize",
  "oligos": [
      "destination": "my_plate/A1",
      "sequence": "CATGGGTAVNNNNGAAB",
      "scale": "25nm" | "100nm" | "250nm" | "1um",
      "purification": "standard" | "page" | "hplc",
        // default: standard
    // ...

Formal language for SOPs

2018-06-15 IBISBA WP7 updates

By Stian Soiland-Reyes

2018-06-15 IBISBA WP7 updates

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