Difference between revisions of "Workflow"

From metabolic_network
Jump to navigation Jump to search
(Created page with "Category:reaction == Reaction RXN0-4261 == * direction: ** left-to-right * common-name: ** helicase ** putative helicase ** atp-dependent dna helicase ** replicative dna h...")
(Created page with "=Workflow command history= ==Command sequence== * '''Check input''': ''Check the validity, consistency and presence of input files'' * '''Annotation based reconstruction''':...")
 
Line 1: Line 1:
−
[[Category:reaction]]
+
=Workflow command history=
−
== Reaction RXN0-4261 ==
+
 
−
* direction:
+
==Command sequence==
−
** left-to-right
+
* '''Check input''':
−
* common-name:
+
''Check the validity, consistency and presence of input files''
−
** helicase
+
* '''Annotation based reconstruction''':
−
** putative helicase
+
''Extract network data from Pathway Tools annotation output.''
−
** atp-dependent dna helicase
+
* '''Orthology based reconstruction''':
−
** replicative dna helicase
+
''Run the orthology based reconstruction.''
−
** atp-dependent dna helicase pcra
+
* '''SBML mapping''':
−
== Reaction formula ==
+
''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
−
* 1 [[ATP]][c] '''+''' 1 [[Supercoiled-Duplex-DNAs]][c] '''+''' 1 [[WATER]][c] '''=>''' 1 [[ADP]][c] '''+''' 1 [[Pi]][c] '''+''' 1 [[Single-Stranded-DNAs]][c]
+
* '''SBML mapping''':
−
== Gene(s) associated with this reaction  ==
+
''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
−
<div class="toccolours mw-collapsible mw-collapsed" style="width:100%; overflow:auto;">
+
* '''SBML mapping''':
−
* Gene: [[RUMFLAFD1_RS0115545]]
+
''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
−
** Category: [[annotation]]
+
* '''SBML mapping''':
−
*** Source: [[genome_a]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
+
''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
−
* Gene: [[RUMFLAFD1_RS0105995]]
+
* '''SBML mapping''':
−
** Category: [[annotation]]
+
''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
−
*** Source: [[genome_a]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
+
* '''Create draft network''':
−
* Gene: [[RUMFLAFD1_RS0116590]]
+
''Merges all available networks from the /networks directory into one metabolic network.<BR>Merge all data on the studied species.''
−
** Category: [[annotation]]
+
* '''Set medium''':
−
*** Source: [[genome_a]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
+
''Set the growth medium for the studied species.''
−
* Gene: [[RUMFLAFD1_RS0115820]]
+
* '''Run gap-filling''':
−
** Category: [[annotation]]
+
''Calculate the gap-filling solution and generate the metabolic network, completed with the gap-filling solution.''
−
*** Source: [[genome_a]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
+
* '''Manual curation''':
−
* Gene: [[RUMFLAFD1_RS24030]]
+
''Apply the curation described in the form file rumino_rxn_add_gp.csv.''
−
** Category: [[annotation]]
+
* '''Manual curation''':
−
*** Source: [[genome_a]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
+
''Apply the curation described in the form file rxn_to_add_ruminococcus.csv.''
−
* Gene: [[RUMFLAFD1_RS0103985]]
+
* '''Manual curation''':
−
** Category: [[annotation]]
+
''Apply the curation described in the form file rumino_rxn_add_cur.csv.''
−
*** Source: [[genome_a]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
+
* '''Create Wiki pages''':
−
* Gene: [[RUMFLAFD1_RS25000]]
+
''Create Wiki pages to display the metabolic network.''
−
** Category: [[annotation]]
+
==Downloads==
−
*** Source: [[genome_a]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
+
You can download the [[MEDIA:log.txt|command log file here]]
−
* Gene: [[RUMFLAFD1_RS0112705]]
 
−
** Category: [[annotation]]
 
−
*** Source: [[genome_a]], Tool: [[pathwaytools]], Assignment: automated-name-match, Comment: n.a
 
−
</div>
 
−
== Pathway(s)  ==
 
−
== Reconstruction information  ==
 
−
* category: [[annotation]]; source: [[genome_a]]; tool: [[pathwaytools]]; comment: n.a
 
−
== External links  ==
 
−
{{#set: direction=left-to-right}}
 
−
{{#set: common-name=putative helicase|atp-dependent dna helicase|atp-dependent dna helicase pcra|helicase|replicative dna helicase}}
 
−
{{#set: nb gene associated=8}}
 
−
{{#set: nb pathway associated=0}}
 
−
{{#set: reconstruction category=annotation}}
 
−
{{#set: reconstruction tool=pathwaytools}}
 
−
{{#set: reconstruction comment=n.a}}
 
−
{{#set: reconstruction source=genome_a}}
 

Latest revision as of 17:46, 15 January 2021

Workflow command history

Command sequence

  • Check input:

Check the validity, consistency and presence of input files

  • Annotation based reconstruction:

Extract network data from Pathway Tools annotation output.

  • Orthology based reconstruction:

Run the orthology based reconstruction.

  • SBML mapping:

Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).

  • SBML mapping:

Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).

  • SBML mapping:

Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).

  • SBML mapping:

Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).

  • SBML mapping:

Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).

  • Create draft network:

Merges all available networks from the /networks directory into one metabolic network.
Merge all data on the studied species.

  • Set medium:

Set the growth medium for the studied species.

  • Run gap-filling:

Calculate the gap-filling solution and generate the metabolic network, completed with the gap-filling solution.

  • Manual curation:

Apply the curation described in the form file rumino_rxn_add_gp.csv.

  • Manual curation:

Apply the curation described in the form file rxn_to_add_ruminococcus.csv.

  • Manual curation:

Apply the curation described in the form file rumino_rxn_add_cur.csv.

  • Create Wiki pages:

Create Wiki pages to display the metabolic network.

Downloads

You can download the command log file here

Retrieved from "http://gem-aureme.genouest.org//rflavgem/index.php?title=Workflow&oldid=11853"