WP7 wrap-up

Stian Soiland-Reyes, The University of Manchester

https://orcid.org/0000-0001-9842-9718

 

IBISBA WP6/WP7 workshop, VTT, Espoo

2018-06-15

☑ RetroPath 2.0

☑ RetroPath 2.0-mods-metabolomics

☑ Scope Viewer (with RetroPath)

☑ RP2Path

☑ Selenzyme connector for retropath results

☐ OpenMS

☐ Query Biochemical Rules DataBase (BioRule DB)
     ~December 2018

Initial Workflow nodes for design

https://hub.ibisba.eu/

  • 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

https://hub.ibisba.eu/

Workflow as chain

Workflow nodes to make

Design

Extract sink from strain models (native metabolites)

Machine learning based Enzyme sequence scoring node

Flux balance analysis node

Pathway ranking node

Build

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?)

...

Test

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

...

KNIME to CWL

QuickForm inputs

Workflow parameters

Practical: Wrap RP2Path in CWL

https://hub.ibisba.eu/

Moving from proof of concept to production instance

Single Sign-On for IBISBAHub

Data Storage
by reference

hub.ibisba.eu

...

Data Management Plan

http://autoprotocol.org/



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

Formal language for SOPs