Package WholeCellKB :: Package public :: Module models
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Module models

source code


Whole-cell data model

Author: Jonathan Karr, jkarr@stanford.edu
Affiliation: Covert Lab, Department of Bioengineering, Stanford University
Last updated: 2012-07-17

Classes [hide private]
  UserProfile
  Evidence
  EntryData
  EvidencedEntryData
  EntryBooleanData
  EntryCharData
  EntryFloatData
  EntryPositiveFloatData
  EntryTextData
  BindingSite
  BiomassComposition
  Codon
  CoenzymeParticipant
  CrossReference
  DisulfideBond
  DNAFootprint
  EnzymeParticipant
  Homolog
  Kinetics
  MediaComposition
  MetaboliteMapCoordinate
  ModificationReaction
  ProstheticGroupParticipant
  ProteinComplexBiosythesisParticipant
  ReactionMapCoordinate
  ReactionStoichiometryParticipant
  SignalSequence
  SimulationProperty
  Synonym
  Entry
  SpeciesComponent
  Molecule
  Protein
  Chromosome
  ChromosomeFeature
  Compartment
  Gene
  Metabolite
  Note
  Parameter
  Pathway
  Process
  ProteinComplex
  ProteinMonomer
  Reaction
  Reference
  Species
  State
  Stimulus
  TranscriptionUnit
  TranscriptionalRegulation
  Type
  ModelProperty
Functions [hide private]
 
validate_dna_sequence(seq) source code
 
validate_kinetics(reaction, direction) source code
 
parse_regulatory_rule(equation, all_obj_data, species_wid) source code
 
calculate_nucleic_acid_pi(seq) source code
 
format_list_html(val, comma_separated=False, numbered=False, separator=None, force_list=False, vertical_spacing=False, default_items=5) source code
 
format_with_evidence(obj=None, txt=None, list_item=False) source code
 
format_evidence(evidence) source code
 
sub_rate_law(species_wid) source code
Variables [hide private]
  CHOICES_DIRECTION = 'f', 'Forward', ('r', 'Reverse'),
  CHOICES_REFERENCE_TYPE = 'article', 'Article', ('book', 'Book'...
  CHOICES_STRANDEDNESS = 'dsDNA', 'dsDNA', ('ssDNA', 'ssDNA'), (...
  CHOICES_VMAX_UNITS = '1/min', '1/min', ('U/mg', 'U/mg'),
  CHOICES_HOMOLOG_SPECIES = 'B. subtilis', 'B. subtilis', ('E. c...
  HOMOLOG_SPECIES_URLS = {"B. subtilis": "http://www.genome.jp/d...
  CHOICES_CROSS_REFERENCE_SOURCES = 'ATCC', 'ATCC', ('BiGG', 'Bi...
  CROSS_REFERENCE_SOURCE_URLS = {"ATCC": "http://www.atcc.org/AT...
  CHOICES_GENETIC_CODE = '1', 'Standard', ('2', 'Vertebrate'), (...
  CHOICES_REACTION_DIRECTION = 'f', 'Forward', ('b', 'Backward')...
  CHOICES_SIGNAL_SEQUENCE_LOCATION = 'N', 'N-terminus', ('C', 'C...
  CHOICES_SIGNAL_SEQUENCE_TYPE = 'lipoprotein', 'Lipoprotein', (...
END: CHOICES
Variables Details [hide private]

CHOICES_REFERENCE_TYPE

Value:
'article', 'Article', ('book', 'Book'), ('thesis', 'Thesis'), ('misc',\
 'Miscellaneous'),

CHOICES_STRANDEDNESS

Value:
'dsDNA', 'dsDNA', ('ssDNA', 'ssDNA'), ('xsDNA', 'xsDNA'),

CHOICES_HOMOLOG_SPECIES

Value:
'B. subtilis', 'B. subtilis', ('E. coli', 'E. coli'), ('M. hyopneumoni\
ae', 'M. hyopneumoniae'), ('M. mobile', 'M. mobile'), ('M. pneumoniae'\
, 'M. pneumoniae'), ('S. coelicolor', 'S. coelicolor'), ('S. oneidensi\
s', 'S. oneidensis'),

HOMOLOG_SPECIES_URLS

Value:
{"B. subtilis": "http://www.genome.jp/dbget-bin/www_bget?bsu:%s", "E. \
coli": "http://www.genome.jp/dbget-bin/www_bget?eco:%s", "M. hyopneumo\
niae": "http://www.genome.jp/dbget-bin/www_bget?mhj:%s", "M. mobile": \
"http://www.genome.jp/dbget-bin/www_bget?mmo:%s", "M. pneumoniae": "ht\
tp://www.genome.jp/dbget-bin/www_bget?mpn:%s", "S. coelicolor": "http:\
//www.genome.jp/dbget-bin/www_bget?sco:%s", "S. oneidensis": "http://w\
ww.genome.jp/dbget-bin/www_bget?son:%s",}

CHOICES_CROSS_REFERENCE_SOURCES

Value:
'ATCC', 'ATCC', ('BiGG', 'BiGG'), ('BioCyc', 'BioCyc'), ('BioProject',\
 'BioProject'), ('CAS', 'CAS'), ('ChEBI', 'ChEBI'), ('CMR', 'CMR'), ('\
EC', 'EC'), ('GenBank', 'GenBank'), ('ISBN', 'ISBN'), ('KEGG', 'KEGG')\
, ('KNApSAcK', 'KNApSAcK'), ('LipidBank', 'LipidBank'), ('LIPIDMAPS', \
'LIPIDMAPS'), ('PDB', 'PDB'), ('PDBCCD', 'PDBCCD'), ('PubChem', 'PubCh\
em'), ('PubMed', 'PubMed'), ('RefSeq', 'RefSeq'), ('SABIO-RK', 'SABIO-\
RK'), ('SwissProt', 'SwissProt'), ('Taxonomy', 'Taxonomy'), ('ThreeDME\
T', 'ThreeDMET'), ('URL', 'URL'),

CROSS_REFERENCE_SOURCE_URLS

Value:
{"ATCC": "http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails\
/tabid/452/Default.aspx?Template=bacteria&ATCCNum=%s", "BiGG": "http:/\
/bigg.ucsd.edu/bigg/postMet.pl?organism=3307911&organism=1461534&organ\
ism=222668&organism=3277493&organism=2795088&organism=2423527&organism\
=1823466&compartment_list=any&pathway_list=any&name_text=%s", "BioCyc"\
: "http://biocyc.org/MGEN243273/NEW-IMAGE?type=GENE&object=%s", "BioPr\
oject": "http://www.ncbi.nlm.nih.gov/bioproject/%s", "CAS": "http://ww\
w.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&term=%s", "ChEBI": "http\
...

CHOICES_GENETIC_CODE

Value:
'1', 'Standard', ('2', 'Vertebrate'), ('3', 'Yeast'), ('4', 'Mold, pro\
tozoa, coelenterate mitochondria, mycoplasma, and spiroplasma'), ('5',\
 'Invertebrate mitochondria'), ('6', 'Ciliate, dasycladacean and hexam\
ita'), ('9', 'Echinoderm and flatworm mitochondria'), ('10', 'Euplotid\
'), ('11', 'Bacteria, archaea and plant plastids'), ('12', 'Alternativ\
e yeast'), ('13', 'Ascidian mitochondria'), ('14', 'Alternative flatwo\
rm mitochondria'), ('15', 'Blepharisma'), ('16', 'Chlorophycean mitoch\
ondria'), ('21', 'Trematode mitochondria'), ('22', 'Scenedesmus obliqu\
...

CHOICES_REACTION_DIRECTION

Value:
'f', 'Forward', ('b', 'Backward'), ('r', 'Reversible'),

CHOICES_SIGNAL_SEQUENCE_LOCATION

Value:
'N', 'N-terminus', ('C', 'C-terminus'),

CHOICES_SIGNAL_SEQUENCE_TYPE

END: CHOICES 

Value:
'lipoprotein', 'Lipoprotein', ('secretory', 'Secretory'),