List view
- No due date
- No due date
- No due date•0/4 issues closed
- Overdue by 1 year(s)•Due by April 1, 2024•0/5 issues closed
- No due date
- No due date
- No due date
- No due date
- Overdue by 2 year(s)•Due by January 1, 2024•0/1 issues closed
- Overdue by 2 year(s)•Due by November 1, 2023
Should be compatible with EDD experimental data description
Overdue by 1 year(s)•Due by March 1, 2024a placeholder for various tasks
Overdue by 2 year(s)•Due by October 1, 2023•1/4 issues closed**Description** Address the inconsistencies between the simulated data and the actual growth phenotypes for the ternary consortium. **Deliverable** Model that is consistent the experimental data based on the test from the milestone 3b
Overdue by 2 year(s)•Due by September 24, 2023•1/2 issues closed**Description** Design a nutrient media or genetic modifications that will enforce the cross-organism feedback dependency and thus stabilize consortia. The preferred way to ensure stable growth is media design. Genetic modifications is a back up approach. Pass a few candidate media for ternary consortia to experimental team for validation. (April, 2023) **Deliverable** Media specifications designed for sustained rhodo/syn co-culture growth
Overdue by 2 year(s)•Due by September 15, 2023•1/2 issues closedBased on validation, we will prioritize which modifications to the individual and joint models are needed to support the binary consortium. Note, the refinement of the microbial consortia models does not have a routine protocol. Therefore, we will explore multiple approaches once we have better understanding of the problem. **Deliverable** Updated model that scores higher for the test developed in milestone [2b](https://github.com/PNNL-CompBio/CONCERTO/milestone/7)
Overdue by 2 year(s)•Due by August 24, 2023•0/6 issues closed**old description** We'll fit the individual species growth curves with biomass fluxes. For those binary consortia that have measured external metabolites, we can test secretions. **Description** *Get experimental data:* * growth curves of the individual species in co-culture * secreted metabolites in co-culture *Test model:* * Simulate the model in MICOM environment for the proper media * Compare against the experimental data (growth/no growth) * (OPTIONAL) Fitting growth curves **Deliverables** * Conclusion(s) on the agreement of the simulation and the data * (OPTIONAL) code for quantitative evaluation of the goodness-of-fit of the predictions to the experimental data
Overdue by 2 year(s)•Due by April 28, 2023•2/7 issues closed**Description** The models will be tested against 3 types of data. There are 2 types of outcomes for each type of data. **First**, is when model predicts growth or secretion, but experimental data tells otherwise. This situation is considered as false positive prediction. Generally, this requires a removal of a reaction to make the model consistent with the data. **Second**, is the opposite, when model does not predict growth or secretion, but it does happen. This is considered false negative. To address this it typically requires adding a reaction. In summary: false positive -> removing reaction false negative -> adding reaction A *special case* is when a metabolite is a *byproduct of growth*. If it must be produced (according to the model), but not present in the experimental data of the secreted metabolites. It may be missing (false positive) for two reasons. First - metabolomics experimental platform can't detect it (e.g. ethanol or ammonia). In this case we can't make any conclusions. Second - it is detectable, but missing. In this situation, the model requires more complicated update, rather than removing a reaction. Approaches for adding/removing reactions: * gapfill * crop The probabilistic approaches take together 1) experimental, 2) computational, 3) pathway context and 4) thermodynamic evidences to come up with a probability for a given reaction that could be added. **Deliverable** Refined models pass more tests (less FP and FN) than previously.
Overdue by 2 year(s)•Due by October 1, 2023•4/12 issues closed**old description** If a ternary consortia is known not to be stable, then the models should reflect that fact **Description** If any new experimental data isn't available, we'll be testing for the stability of growth. It is known that ternary consortium is unstable and quickly stops growing. We will simulate the ternary model in MICOM and test for confirmation of the growth instability. **Deliverables** Confirmation of the unstable growth
Overdue by 2 year(s)•Due by April 28, 2023•0/1 issues closed**Description** Deliverable: Design a nutrient media or genetic modifications that will enforce the cross-organism feedback dependency and thus stabilize consortia. The preferred way to ensure stable growth is media design. Genetic modifications is a back up approach. Pass a few candidate media for ternary consortia to experimental team for validation. (April, 2023) **Deliverable** Media composition that is predicted to sustain the growth of the ternary consortium.
Overdue by 2 year(s)•Due by October 1, 2023•0/2 issues closed