Skip to content

Removing option for plant in build_metabolic_model and build_multiple… #101

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
samseaver wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Removing option for plant in build_metabolic_model and build_multiple… #101

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions ui/narrative/methods/build_metabolic_model/display.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,7 @@ parameters :
ui-name : |
Template for reconstruction
short-hint : |
Models are generated based on a default template model in KBase. Template models capture the necessary biochemical information based on user-defined scope. KBase primarily uses four template models: (i) Gram positive microbe, (ii) Gram negative microbe, (iii) Core pathways microbe, and (iv) Plant. These template models differ from each other by biomass composition and biochemical reaction functional associations.
Models are generated based on a default template model in KBase. Template models capture the necessary biochemical information based on user-defined scope. KBase primarily uses four template models: (i) Gram positive microbe, (ii) Gram negative microbe, and (iii) Core pathways microbe. These template models differ from each other by biomass composition and biochemical reaction functional associations.

media_supplement_list :
ui-name : |
Expand Down Expand Up @@ -127,7 +127,7 @@ description : |

<p>Gapfilling is the process by which the App identifies the minimal set of biochemical reactions to add to a draft metabolic model to enable it to produce biomass in a specified media. This step is optional, but it is recommended and runs by default. A radio box in the advanced options of the Build Metabolic Model App can be unchecked to allow model reconstruction without gapfilling. Gapfilling can be done later if desired. To gapfill the draft metabolic model or to perform additional gapfilling analysis please see the <a href="https://narrative.kbase.us/#appcatalog/app/fba_tools/gapfill_metabolic_model/release">Gapfill Metabolic Model App</a>.</p>

<p>The quality of a draft metabolic model depends on the completeness of the annotated genome used for the preliminary reconstruction. Due to the fact that most genomes are not completely annotated, draft metabolic models usually contain gaps preventing the production of some biomass components. In this step, an optimization algorithm identifies the minimal set of reactions that must be added to each model to fill these gaps [3, 4]. The gapfilling algorithm is described in detail in the <a href="https://narrative.kbase.us/#appcatalog/app/fba_tools/gapfill_metabolic_model/release">Gapfill Metabolic Model App page</a>. Reactions to be used by gapfilling are selected from the <a href="https://github.com/ModelSEED/ModelSEEDDatabase/tree/master/Biochemistry">ModelSEED biochemistry database</a>. This curated database contains mass and charge balanced reactions, standardized to aqueous conditions at neutral pH. The ModelSEED reaction database integrates biochemistry contained in KEGG, MetaCyc, EcoCyc, Plant BioCyc, Plant Metabolic Networks, and Gramene. This step is conducted to ensure that every model is capable of simulating cell growth.</p>
<p>The quality of a draft metabolic model depends on the completeness of the annotated genome used for the preliminary reconstruction. Due to the fact that most genomes are not completely annotated, draft metabolic models usually contain gaps preventing the production of some biomass components. In this step, an optimization algorithm identifies the minimal set of reactions that must be added to each model to fill these gaps [3, 4]. The gapfilling algorithm is described in detail in the <a href="https://narrative.kbase.us/#appcatalog/app/fba_tools/gapfill_metabolic_model/release">Gapfill Metabolic Model App page</a>. Reactions to be used by gapfilling are selected from the <a href="https://github.com/ModelSEED/ModelSEEDDatabase/tree/master/Biochemistry">ModelSEED biochemistry database</a>. This curated database contains mass and charge balanced reactions, standardized to aqueous conditions at neutral pH. The ModelSEED reaction database integrates biochemistry contained in KEGG, MetaCyc, EcoCyc, Plant Metabolic Networks, and Gramene. This step is conducted to ensure that every model is capable of simulating cell growth.</p>

<p>Once model reconstruction is complete, <a href="https://narrative.kbase.us/#appcatalog/app/fba_tools/run_flux_balance_analysis/release">Flux Balance Analysis</a> (FBA) can be applied to assess the capacity of reactions to carry flux and reaction essentiality.<p>

Expand Down
6 changes: 0 additions & 6 deletions ui/narrative/methods/build_metabolic_model/spec.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -85,12 +85,6 @@
"ui_name" : "Gram positive",
"display" : "Gram positive"
},
{
"display" : "Plant",
"ui_name" : "Plant",
"value" : "plant",
"id" : "plant"
},
{
"display" : "Core metabolism",
"ui_name" : "Core metabolism",
Expand Down
4 changes: 2 additions & 2 deletions ui/narrative/methods/build_multiple_metabolic_models/display.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ parameters :
ui-name : |
Template for reconstruction
short-hint : |
Models are generated based on a default template model in KBase. Template models capture the necessary biochemical information based on user-defined scope. KBase primarily uses four template models: (i) Gram positive microbe, (ii) Gram negative microbe, (iii) Core pathways microbe, and (iv) Plant. These template models differ from each other by biomass composition and biochemical reaction functional associations.
Models are generated based on a default template model in KBase. Template models capture the necessary biochemical information based on user-defined scope. KBase primarily uses four template models: (i) Gram positive microbe, (ii) Gram negative microbe, and (iii) Core pathways microbe. These template models differ from each other by biomass composition and biochemical reaction functional associations.

media_supplement_list :
ui-name : |
Expand Down Expand Up @@ -102,7 +102,7 @@ description : |

<p>Gapfilling is the process by which the App identifies the minimal set of biochemical reactions to add to a draft metabolic model to enable it to produce biomass in a specified media.This step is optional, but it is recommended and runs by default. A radio box in the advanced options of the Build Multiple Metabolic Models App can be unchecked to allow model reconstruction without gapfilling. Gapfilling can be done later if desired. To gapfill the draft metabolic model or to perform additional gapfilling analysis please see the <a href="https://narrative.kbase.us/#appcatalog/app/fba_tools/gapfill_metabolic_model/release">Gapfill Metabolic Model App</a>.</p>

<p>The quality of each draft metabolic model depends on the completeness of the annotated genomes used for the preliminary reconstruction. Due to the fact that most genomes are not completely annotated, draft metabolic models usually contain gaps preventing the production of some biomass components. In this step, an optimization algorithm identifies the minimal set of reactions that must be added to each model to fill these gaps [3, 4]. The gapfilling algorithm is described in detail in the <a href="https://narrative.kbase.us/#appcatalog/app/fba_tools/gapfill_metabolic_model/release">Gapfill Metabolic Model App page</a>. Reactions to be used by gapfilling are selected from the <a href="https://github.com/ModelSEED/ModelSEEDDatabase/tree/master/Biochemistry">ModelSEED biochemistry database</a>. This curated database contains mass and charge balanced reactions, standardized to aqueous conditions at neutral pH. The ModelSEED reaction database integrates biochemistry contained KEGG, MetaCyc, EcoCyc, Plant BioCyc, Plant Metabolic Networks, and Gramene. This step is conducted to ensure that every model is capable of simulating cell growth.</p>
<p>The quality of each draft metabolic model depends on the completeness of the annotated genomes used for the preliminary reconstruction. Due to the fact that most genomes are not completely annotated, draft metabolic models usually contain gaps preventing the production of some biomass components. In this step, an optimization algorithm identifies the minimal set of reactions that must be added to each model to fill these gaps [3, 4]. The gapfilling algorithm is described in detail in the <a href="https://narrative.kbase.us/#appcatalog/app/fba_tools/gapfill_metabolic_model/release">Gapfill Metabolic Model App page</a>. Reactions to be used by gapfilling are selected from the <a href="https://github.com/ModelSEED/ModelSEEDDatabase/tree/master/Biochemistry">ModelSEED biochemistry database</a>. This curated database contains mass and charge balanced reactions, standardized to aqueous conditions at neutral pH. The ModelSEED reaction database integrates biochemistry contained KEGG, MetaCyc, EcoCyc, Plant Metabolic Networks, and Gramene. This step is conducted to ensure that every model is capable of simulating cell growth.</p>

<p>Once model reconstruction is complete, the <a href="https://narrative.kbase.us/#appcatalog/app/fba_tools/run_flux_balance_analysis/release">Flux Balance Analysis</a> (FBA) can be applied to assess the capacity of reactions to carry flux and reaction essentiality.<p>

Expand Down
6 changes: 0 additions & 6 deletions ui/narrative/methods/build_multiple_metabolic_models/spec.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,12 +79,6 @@
"ui_name" : "Gram positive",
"display" : "Gram positive"
},
{
"display" : "Plant",
"ui_name" : "Plant",
"value" : "plant",
"id" : "plant"
},
{
"display" : "Core metabolism",
"ui_name" : "Core metabolism",
Expand Down