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
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
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
...
Mixed integer linear program node for gene up/down regulation
DoE for fermentation condition
...
QuickForm inputs
Workflow parameters
Moving from proof of concept to production instance
...
Data Management Plan
{
"op": "oligosynthesize",
"oligos": [
{
"destination": "my_plate/A1",
"sequence": "CATGGGTAVNNNNGAAB",
"scale": "25nm" | "100nm" | "250nm" | "1um",
"purification": "standard" | "page" | "hplc",
// default: standard
},
// ...
]
}
By Stian Soiland-Reyes
