Difference between revisions of "Workflow"

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(Created page with "Category:Reaction == Reaction [http://metacyc.org/META/NEW-IMAGE?object=RXN0-5462 RXN0-5462] == * direction: ** LEFT-TO-RIGHT * common name: ** at1g33290 ** uridine_kinase...")
(Created page with "=Workflow command history= ==Command sequence== * '''Check input''': ''Check the validity, consistency and presence of input files'' * '''Orthology based reconstruction''': '...")
 
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[[Category:Reaction]]
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=Workflow command history=
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== Reaction [http://metacyc.org/META/NEW-IMAGE?object=RXN0-5462 RXN0-5462] ==
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* direction:
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** LEFT-TO-RIGHT
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* common name:
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** at1g33290
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** uridine_kinase
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** ORF
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** atp-dependent_metalloprotease
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** member_of_the_hsp104_clp_superfamily
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** katanin_p60_atpase-containing_subunit_a-like_2
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** helicase_mov-10-_-like
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** replication_factor_c_subunit_5
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** e3_ubiquitin-protein_ligase_rnf213-like
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** replication_factor_c_subunit_2
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** atpase_family_aaa_domain-containing_protein_2b-_partial
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** adenylate_guanylate
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** replication_factor_c_subunit_3
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−
** adenylate_kinase_domain-containing_protein_1
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−
** replication_control_protein_1_like
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−
** aaa_family_cdc48_subfamily
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−
** fidgetin-like_protein1
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−
** dna-binding_protein_smubp-2
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−
** atp-dependent_zinc_metalloprotease
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−
** gtpase
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−
** cytosolic_fe-s_cluster_assembly_factor_nubp1_homolog
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−
** uncharacterized_transmembrane_protein_ddb_g0290641
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** isoform_m_of_dna_helicase_mcm9
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** replication_factor_c_subunit_1
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** 26s_proteaseregulatorysubunit6bhomolog
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** atpase_family_associated_with_various_cellular_activities
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** nfx1-type_zinc_finger-containing_protein_1
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** gtpase_der
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** origin_recognition_complex_subunit_4
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−
** hsp104
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** atpase_afg2_protein
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** trna-splicing_endonuclease_positive_effector
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** sh2_domain_containing_protein
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** atp-dependent_proteaseatpasesubunit
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** atpase_aaa
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* ec number:
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** [http://enzyme.expasy.org/EC/3.6.5.1 EC-3.6.5.1]
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** [http://enzyme.expasy.org/EC/3.6.5.2 EC-3.6.5.2]
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** [http://enzyme.expasy.org/EC/3.6.5.3 EC-3.6.5.3]
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** [http://enzyme.expasy.org/EC/3.6.5.4 EC-3.6.5.4]
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** [http://enzyme.expasy.org/EC/3.6.5.5 EC-3.6.5.5]
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** [http://enzyme.expasy.org/EC/3.6.5.6 EC-3.6.5.6]
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** [http://enzyme.expasy.org/EC/3.6.1.15 EC-3.6.1.15]
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* Synonym(s):
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== Reaction Formula ==
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==Command sequence==
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* With identifiers:
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* '''Check input''':
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** 1 [[WATER]][c] '''+''' 1 [[GTP]][c] '''=>''' 1 [[PROTON]][c] '''+''' 1 [[Pi]][c] '''+''' 1 [[GDP]][c]
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''Check the validity, consistency and presence of input files''
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* With common name(s):
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* '''Orthology based reconstruction''':
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** 1 H2O[c] '''+''' 1 GTP[c] '''=>''' 1 H+[c] '''+''' 1 phosphate[c] '''+''' 1 GDP[c]
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''Run the orthology based reconstruction.''
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* '''Annotation based reconstruction''':
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== Genes associated with this reaction  ==
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''Extract network data from Pathway Tools annotation output.''
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Genes have been associated with this reaction based on different elements listed below.
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* '''SBML mapping''':
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* Gene: [[Tiso_gene_19350]]
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''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
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** Source: [[annotation-in-silico_annotation]]
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* '''SBML mapping''':
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*** Assignment: EC-NUMBER
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''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
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* Gene: [[Tiso_gene_826]]
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* '''SBML mapping''':
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** Source: [[annotation-in-silico_annotation]]
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''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
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*** Assignment: AUTOMATED-NAME-MATCH
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* '''Create draft network''':
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* Gene: [[Tiso_gene_13653]]
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''Merges all available networks from the /networks directory into one metabolic network.<BR>Merge all data on the studied species.''
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** Source: [[annotation-experimental_annotation]]
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* '''Get compartments''':
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*** Assignment: AUTOMATED-NAME-MATCH
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''Display all the compartments of the metabolic network.''
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* Gene: [[Tiso_gene_1984]]
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* '''Change compartment''':
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** Source: [[orthology-esiliculosus]]
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''Modify a compartment in the metabolic network.''
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* Gene: [[Tiso_gene_1959]]
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* '''Change compartment''':
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** Source: [[annotation-in-silico_annotation]]
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''Modify a compartment in the metabolic network.''
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*** Assignment: EC-NUMBER
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* '''Change compartment''':
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* Gene: [[Tiso_gene_8859]]
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''Modify a compartment in the metabolic network.''
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** Source: [[annotation-in-silico_annotation]]
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* '''Change compartment''':
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*** Assignment: EC-NUMBER
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''Modify a compartment in the metabolic network.''
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* Gene: [[Tiso_gene_15500]]
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* '''Change compartment''':
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** Source: [[orthology-esiliculosus]]
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''Modify a compartment in the metabolic network.''
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* Gene: [[Tiso_gene_9423]]
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* '''Change compartment''':
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** Source: [[annotation-in-silico_annotation]]
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''Modify a compartment in the metabolic network.''
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*** Assignment: EC-NUMBER
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* '''Get compartments''':
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* Gene: [[Tiso_gene_4155]]
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''Display all the compartments of the metabolic network.''
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** Source: [[orthology-esiliculosus]]
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* '''Set medium''':
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* Gene: [[Tiso_gene_20327]]
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''Set the growth medium for the studied species.''
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** Source: [[annotation-in-silico_annotation]]
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* '''Run gap-filling''':
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*** Assignment: EC-NUMBER
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''Calculate the gap-filling solution and generate the metabolic network, completed with the gap-filling solution.''
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* Gene: [[Tiso_gene_546]]
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* '''Manual curation''':
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** Source: [[orthology-esiliculosus]]
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''Apply the curation described in the form file export_biomass_rxn.csv.''
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* Gene: [[Tiso_gene_8950]]
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* '''Manual curation''':
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** Source: [[annotation-in-silico_annotation]]
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''Apply the curation described in the form file reactions_PWY-6475_tiso_add.csv.''
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*** Assignment: EC-NUMBER
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* '''Set FBA''':
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* Gene: [[Tiso_gene_12149]]
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''Set the biomass reaction to run flux balance analysis on the network.''
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** Source: [[annotation-in-silico_annotation]]
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* '''Test FBA''':
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*** Assignment: EC-NUMBER
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''Run flux balance analysis on the network.''
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* Gene: [[Tiso_gene_4596]]
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* '''Create Wiki pages''':
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** Source: [[orthology-esiliculosus]]
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''Create Wiki pages to display the metabolic network.''
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* Gene: [[Tiso_gene_4092]]
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==Downloads==
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** Source: [[orthology-esiliculosus]]
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You can download the [[MEDIA:log.txt|command log file here]]
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* Gene: [[Tiso_gene_195]]
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−
** Source: [[annotation-in-silico_annotation]]
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*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_2452]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_20353]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_250]]
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−
** Source: [[orthology-esiliculosus]]
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−
* Gene: [[Tiso_gene_873]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_16252]]
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−
** Source: [[orthology-esiliculosus]]
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−
* Gene: [[Tiso_gene_12148]]
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−
** Source: [[annotation-in-silico_annotation]]
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*** Assignment: EC-NUMBER
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* Gene: [[Tiso_gene_674]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_10221]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_2449]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_4726]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_5166]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_2068]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
** Source: [[annotation-experimental_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_199]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
** Source: [[orthology-esiliculosus]]
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−
* Gene: [[Tiso_gene_8949]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_1611]]
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−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_1541]]
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−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_2447]]
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−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_14239]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_11098]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_14474]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_6614]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_5525]]
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−
** Source: [[orthology-esiliculosus]]
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−
* Gene: [[Tiso_gene_14227]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
** Source: [[orthology-esiliculosus]]
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−
* Gene: [[Tiso_gene_14646]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_17449]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_9659]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_1610]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_8860]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_38]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_13738]]
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−
** Source: [[orthology-esiliculosus]]
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−
* Gene: [[Tiso_gene_13264]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_1291]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_2889]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_623]]
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−
** Source: [[orthology-esiliculosus]]
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−
* Gene: [[Tiso_gene_829]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_7387]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_4192]]
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−
** Source: [[orthology-esiliculosus]]
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−
* Gene: [[Tiso_gene_2631]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_2924]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_17616]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_5529]]
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−
** Source: [[orthology-esiliculosus]]
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−
* Gene: [[Tiso_gene_9926]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_7734]]
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−
** Source: [[orthology-esiliculosus]]
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−
* Gene: [[Tiso_gene_14586]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: AUTOMATED-NAME-MATCH
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−
* Gene: [[Tiso_gene_11012]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_13325]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_2448]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_8461]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_8601]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_17751]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
** Source: [[orthology-esiliculosus]]
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−
* Gene: [[Tiso_gene_3287]]
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−
** Source: [[orthology-esiliculosus]]
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−
* Gene: [[Tiso_gene_1960]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_538]]
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−
** Source: [[orthology-esiliculosus]]
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−
* Gene: [[Tiso_gene_537]]
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−
** Source: [[orthology-esiliculosus]]
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−
* Gene: [[Tiso_gene_3653]]
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−
** Source: [[orthology-esiliculosus]]
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−
* Gene: [[Tiso_gene_9243]]
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−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
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−
* Gene: [[Tiso_gene_2929]]
+
−
** Source: [[annotation-in-silico_annotation]]
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−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_8584]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_15320]]
+
−
** Source: [[orthology-esiliculosus]]
+
−
* Gene: [[Tiso_gene_6180]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_2451]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_2604]]
+
−
** Source: [[orthology-esiliculosus]]
+
−
* Gene: [[Tiso_gene_4194]]
+
−
** Source: [[orthology-esiliculosus]]
+
−
* Gene: [[Tiso_gene_10282]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
** Source: [[annotation-experimental_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_9234]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_7745]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_12899]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
** Source: [[annotation-experimental_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
** Source: [[orthology-athaliana]]
+
−
** Source: [[orthology-esiliculosus]]
+
−
* Gene: [[Tiso_gene_16478]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_4437]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_4436]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_2897]]
+
−
** Source: [[orthology-esiliculosus]]
+
−
* Gene: [[Tiso_gene_1444]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
** Source: [[annotation-experimental_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_15465]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_8164]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_2450]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_4026]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_19098]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_14816]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_572]]
+
−
** Source: [[orthology-esiliculosus]]
+
−
* Gene: [[Tiso_gene_14226]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_7123]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
** Source: [[annotation-experimental_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_8763]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_20236]]
+
−
** Source: [[orthology-esiliculosus]]
+
−
* Gene: [[Tiso_gene_6181]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_2176]]
+
−
** Source: [[orthology-esiliculosus]]
+
−
* Gene: [[Tiso_gene_15043]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_9004]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
** Source: [[annotation-experimental_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_4330]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_9114]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_13268]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_9959]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
* Gene: [[Tiso_gene_13681]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Assignment: EC-NUMBER
+
−
== Pathways  ==
+
−
== Reconstruction information  ==
+
−
* Category: [[orthology]]
+
−
** Source: [[orthology-athaliana]]
+
−
*** Tool: [[pantograph]]
+
−
** Source: [[orthology-esiliculosus]]
+
−
*** Tool: [[pantograph]]
+
−
* Category: [[annotation]]
+
−
** Source: [[annotation-in-silico_annotation]]
+
−
*** Tool: [[pathwaytools]]
+
−
** Source: [[annotation-experimental_annotation]]
+
−
*** Tool: [[pathwaytools]]
+
−
== External links  ==
+
−
* RHEA:
+
−
** [http://www.ebi.ac.uk/rhea/reaction.xhtml?id=19669 19669]
+
−
* LIGAND-RXN:
+
−
** [http://www.genome.jp/dbget-bin/www_bget?R00335 R00335]
+
−
{{#set: direction=LEFT-TO-RIGHT}}
+
−
{{#set: common name=at1g33290}}
+
−
{{#set: common name=uridine_kinase}}
+
−
{{#set: common name=ORF}}
+
−
{{#set: common name=atp-dependent_metalloprotease}}
+
−
{{#set: common name=member_of_the_hsp104_clp_superfamily}}
+
−
{{#set: common name=katanin_p60_atpase-containing_subunit_a-like_2}}
+
−
{{#set: common name=helicase_mov-10-_-like}}
+
−
{{#set: common name=replication_factor_c_subunit_5}}
+
−
{{#set: common name=e3_ubiquitin-protein_ligase_rnf213-like}}
+
−
{{#set: common name=replication_factor_c_subunit_2}}
+
−
{{#set: common name=atpase_family_aaa_domain-containing_protein_2b-_partial}}
+
−
{{#set: common name=adenylate_guanylate}}
+
−
{{#set: common name=replication_factor_c_subunit_3}}
+
−
{{#set: common name=adenylate_kinase_domain-containing_protein_1}}
+
−
{{#set: common name=replication_control_protein_1_like}}
+
−
{{#set: common name=aaa_family_cdc48_subfamily}}
+
−
{{#set: common name=fidgetin-like_protein1}}
+
−
{{#set: common name=dna-binding_protein_smubp-2}}
+
−
{{#set: common name=atp-dependent_zinc_metalloprotease}}
+
−
{{#set: common name=gtpase}}
+
−
{{#set: common name=cytosolic_fe-s_cluster_assembly_factor_nubp1_homolog}}
+
−
{{#set: common name=uncharacterized_transmembrane_protein_ddb_g0290641}}
+
−
{{#set: common name=isoform_m_of_dna_helicase_mcm9}}
+
−
{{#set: common name=replication_factor_c_subunit_1}}
+
−
{{#set: common name=26s_proteaseregulatorysubunit6bhomolog}}
+
−
{{#set: common name=atpase_family_associated_with_various_cellular_activities}}
+
−
{{#set: common name=nfx1-type_zinc_finger-containing_protein_1}}
+
−
{{#set: common name=gtpase_der}}
+
−
{{#set: common name=origin_recognition_complex_subunit_4}}
+
−
{{#set: common name=hsp104}}
+
−
{{#set: common name=atpase_afg2_protein}}
+
−
{{#set: common name=trna-splicing_endonuclease_positive_effector}}
+
−
{{#set: common name=sh2_domain_containing_protein}}
+
−
{{#set: common name=atp-dependent_proteaseatpasesubunit}}
+
−
{{#set: common name=atpase_aaa}}
+
−
{{#set: ec number=EC-3.6.5.1}}
+
−
{{#set: ec number=EC-3.6.5.2}}
+
−
{{#set: ec number=EC-3.6.5.3}}
+
−
{{#set: ec number=EC-3.6.5.4}}
+
−
{{#set: ec number=EC-3.6.5.5}}
+
−
{{#set: ec number=EC-3.6.5.6}}
+
−
{{#set: ec number=EC-3.6.1.15}}
+
−
{{#set: gene associated=Tiso_gene_19350|Tiso_gene_826|Tiso_gene_13653|Tiso_gene_1984|Tiso_gene_1959|Tiso_gene_8859|Tiso_gene_15500|Tiso_gene_9423|Tiso_gene_4155|Tiso_gene_20327|Tiso_gene_546|Tiso_gene_8950|Tiso_gene_12149|Tiso_gene_4596|Tiso_gene_4092|Tiso_gene_195|Tiso_gene_2452|Tiso_gene_20353|Tiso_gene_250|Tiso_gene_873|Tiso_gene_16252|Tiso_gene_12148|Tiso_gene_674|Tiso_gene_10221|Tiso_gene_2449|Tiso_gene_4726|Tiso_gene_5166|Tiso_gene_2068|Tiso_gene_199|Tiso_gene_8949|Tiso_gene_1611|Tiso_gene_1541|Tiso_gene_2447|Tiso_gene_14239|Tiso_gene_11098|Tiso_gene_14474|Tiso_gene_6614|Tiso_gene_5525|Tiso_gene_14227|Tiso_gene_14646|Tiso_gene_17449|Tiso_gene_9659|Tiso_gene_1610|Tiso_gene_8860|Tiso_gene_38|Tiso_gene_13738|Tiso_gene_13264|Tiso_gene_1291|Tiso_gene_2889|Tiso_gene_623|Tiso_gene_829|Tiso_gene_7387|Tiso_gene_4192|Tiso_gene_2631|Tiso_gene_2924|Tiso_gene_17616|Tiso_gene_5529|Tiso_gene_9926|Tiso_gene_7734|Tiso_gene_14586|Tiso_gene_11012|Tiso_gene_13325|Tiso_gene_2448|Tiso_gene_8461|Tiso_gene_8601|Tiso_gene_17751|Tiso_gene_3287|Tiso_gene_1960|Tiso_gene_538|Tiso_gene_537|Tiso_gene_3653|Tiso_gene_9243|Tiso_gene_2929|Tiso_gene_8584|Tiso_gene_15320|Tiso_gene_6180|Tiso_gene_2451|Tiso_gene_2604|Tiso_gene_4194|Tiso_gene_10282|Tiso_gene_9234|Tiso_gene_7745|Tiso_gene_12899|Tiso_gene_16478|Tiso_gene_4437|Tiso_gene_4436|Tiso_gene_2897|Tiso_gene_1444|Tiso_gene_15465|Tiso_gene_8164|Tiso_gene_2450|Tiso_gene_4026|Tiso_gene_19098|Tiso_gene_14816|Tiso_gene_572|Tiso_gene_14226|Tiso_gene_7123|Tiso_gene_8763|Tiso_gene_20236|Tiso_gene_6181|Tiso_gene_2176|Tiso_gene_15043|Tiso_gene_9004|Tiso_gene_4330|Tiso_gene_9114|Tiso_gene_13268|Tiso_gene_9959|Tiso_gene_13681}}
+
−
{{#set: in pathway=}}
+
−
{{#set: reconstruction category=orthology|annotation}}
+
−
{{#set: reconstruction source=annotation-in-silico_annotation|orthology-athaliana|annotation-experimental_annotation|orthology-esiliculosus}}
+
−
{{#set: reconstruction tool=pantograph|pathwaytools}}
+

Latest revision as of 20:26, 21 March 2018

Workflow command history

Command sequence

  • Check input:

Check the validity, consistency and presence of input files

  • Orthology based reconstruction:

Run the orthology based reconstruction.

  • Annotation based reconstruction:

Extract network data from Pathway Tools annotation output.

  • 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.

  • Get compartments:

Display all the compartments of the metabolic network.

  • Change compartment:

Modify a compartment in the metabolic network.

  • Change compartment:

Modify a compartment in the metabolic network.

  • Change compartment:

Modify a compartment in the metabolic network.

  • Change compartment:

Modify a compartment in the metabolic network.

  • Change compartment:

Modify a compartment in the metabolic network.

  • Change compartment:

Modify a compartment in the metabolic network.

  • Get compartments:

Display all the compartments of the metabolic network.

  • 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 export_biomass_rxn.csv.

  • Manual curation:

Apply the curation described in the form file reactions_PWY-6475_tiso_add.csv.

  • Set FBA:

Set the biomass reaction to run flux balance analysis on the network.

  • Test FBA:

Run flux balance analysis on the network.

  • Create Wiki pages:

Create Wiki pages to display the metabolic network.

Downloads

You can download the command log file here

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