Synthetic Biology — Editorial Board Home
This is a new, experimental "Editorial Board Home" for a given topic. It is intended to provide a single place for maintainers and editorial board members to find out key information about their topic and identify action items.Editorial Board
Joan Hérisson Thomas Duigou Kenza Bazi-Kabbaj Guillaume GricourtAction Items
Item | Status | Why you should do this |
---|---|---|
Summary | Done ✅ | Provide a sufficiently detailed summary of the topic to let learners know what they're learning about in this topic. |
Sufficient Editorial Board Members | Done ✅ (4 members) | Having multiple people sharing the burden of being responsible for a specific topic can reduce board member burn-out in the long term. |
Enable Subtopics | Pending ❌ | Subtopics help organize the content and make it easier to navigate. |
Annotate Funders | Pending ❌ | By annotating the funders of your topic's materials, you make it easier to write your grant reports later |
Learning Pathway CTA | Pending ❌ | By providing a Learning Pathway CTA, we can help guide learners to the best resources for learning about this topic. |
Topic Materials
Material | Contributions v2 help | Pre-requisites help | Follow up trainings | Data on Zenodo | Notebook | Server Compatibility |
---|---|---|---|---|---|---|
Designing plasmids encoding predicted pathways by using the BASIC assembly method | ❌ | ❌ | ❌ | ✅ | ❌ | |
Evaluating and ranking a set of pathways based on multiple metrics | ❌ | ❌ | ❌ | ✅ | ❌ | |
Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools | ❌ | ❌ | ❌ | ❌ | ❌ |
Topic Workflows
Material | Workflow | Updated | Version | Tests | Reports | Comments |
---|---|---|---|---|---|---|
Designing plasmids encoding predicted pathways by using the BASIC assembly method | Genetic Design (BASIC Assembly) | Dec 22, 2024 | 1 | ❌ | ❌ | ❌ |
Evaluating and ranking a set of pathways based on multiple metrics | Pathway Analysis | Dec 22, 2024 | 1 | ❌ | ❌ | ❌ |
Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools | RetroSynthesis | Dec 22, 2024 | 1 | ❌ | ❌ | ❌ |
Current Server Compatibility table for "Designing plasmids encoding predicted pathways by using the BASIC assembly method"
Data as of 2024-12-22 00:12:55 +0000
Tool | APOSTL | ARGs-OAP | CIRM-CFBP | ChemFlow | Coloc-stats | CorGAT | CoralSNP | CropGalaxy | Dintor | FreeBioinfo | GASLINI | Galaxy@AuBi | Galaxy@Pasteur | GalaxyTrakr | Genomic Hyperbrowser | GigaGalaxy | IPK Galaxy Blast Suite | ImmPort Galaxy | InteractoMIX | MISSISSIPPI | Mandoiu Lab | MiModD NacreousMap | Oqtans | Palfinder | PepSimili | PhagePromotor | UseGalaxy.be | UseGalaxy.cz | UseGalaxy.eu | UseGalaxy.fr | UseGalaxy.no | UseGalaxy.org (Main) | UseGalaxy.org.au | Viral Variant Visualizer (VVV) |
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toolshed.g2.bx.psu.edu/repos/tduigou/dnabot/dnabot/3.1.0 | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing |
toolshed.g2.bx.psu.edu/repos/tduigou/rpbasicdesign/rpbasicdesign/0.3.4 | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing |
toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.2.0 | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing |
Current Server Compatibility table for "Evaluating and ranking a set of pathways based on multiple metrics"
Data as of 2024-12-22 00:12:55 +0000
Tool | APOSTL | ARGs-OAP | CIRM-CFBP | ChemFlow | Coloc-stats | CorGAT | CoralSNP | CropGalaxy | Dintor | FreeBioinfo | GASLINI | Galaxy@AuBi | Galaxy@Pasteur | GalaxyTrakr | Genomic Hyperbrowser | GigaGalaxy | IPK Galaxy Blast Suite | ImmPort Galaxy | InteractoMIX | MISSISSIPPI | Mandoiu Lab | MiModD NacreousMap | Oqtans | Palfinder | PepSimili | PhagePromotor | UseGalaxy.be | UseGalaxy.cz | UseGalaxy.eu | UseGalaxy.fr | UseGalaxy.no | UseGalaxy.org (Main) | UseGalaxy.org.au | Viral Variant Visualizer (VVV) |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/rpfba/rpfba/5.12.1 | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing |
toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.12.1 | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing |
toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.12.1 | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing |
toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpthermo/5.12.1 | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing |
Current Server Compatibility table for "Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools"
Data as of 2024-12-22 00:12:55 +0000
Tool | APOSTL | ARGs-OAP | CIRM-CFBP | ChemFlow | Coloc-stats | CorGAT | CoralSNP | CropGalaxy | Dintor | FreeBioinfo | GASLINI | Galaxy@AuBi | Galaxy@Pasteur | GalaxyTrakr | Genomic Hyperbrowser | GigaGalaxy | IPK Galaxy Blast Suite | ImmPort Galaxy | InteractoMIX | MISSISSIPPI | Mandoiu Lab | MiModD NacreousMap | Oqtans | Palfinder | PepSimili | PhagePromotor | UseGalaxy.be | UseGalaxy.cz | UseGalaxy.eu | UseGalaxy.fr | UseGalaxy.no | UseGalaxy.org (Main) | UseGalaxy.org.au | Viral Variant Visualizer (VVV) |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
toolshed.g2.bx.psu.edu/repos/tduigou/get_sbml_model/get_sbml_model/0.0.1 | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing |
toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.3.0 | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing |
toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/1.5.0 | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing |
toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpcompletion/5.12.2 | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing |
toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpextractsink/5.12.1 | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing |
toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6 | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing | Missing |
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TODO once this is merged: https://github.com/galaxyproject/training-material/pull/4963Statistics For Your Materials
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