README
WRITTEN BY: WHEATON L SCHROEDER
LATEST VERSION: 02/26/2020

FOLDER: 1.14.18.1_Alignments
PURPOSE: Stores reports of BLASTp alignments between E. dermatitidis tyrosinase gene copies and the E. dermatitidis genome in a
search for additional tyrosinases which may have not yet been annotated. None were found.

FOLDER:A_nidulans_model_files
PURPOSE: Store all files downloaded from the paper "Analysis of Apsergillus nidulans metabolism at the genome-scale" by
David, Ozcelik, Hoffmann and Nielsen.

FOLDER:A_nidulans_model_files
PURPOSE: Store all files downloaded from the paper "Analysis of Apsergillus nidulans metabolism at the genome-scale" by
David, Ozcelik, Hoffmann and Nielsen. Files include list of reactions, stoichiometries, metabolites, and enzymes used
in model construction.

FOLDER:A_niger_model_files
PURPOSE: Store all files downloaded from the paper Metabolic model integration of the bibliome, genome, metabolome, and
reactome of Aspergillus niger" by Andersen, Nielsen and Nielsen. Files include list of reactions, stoichiometries, 
metabolites, and enzymes used in model construction.

FOLDER:A_oryzae_model_files
PURPOSE: Store all files downloaded from the paper "Improved annotation through genome-scale metabolic modeling of 
Aspergillus oryzae" by Vongsangnak, Olsen, Hansen, Krogsgaard, and Nielsen. Files include list of reactions, 
stoichiometries, metabolites, and enzymes used in model construction.

FOLDER:A_terreus_model_files
PURPOSE: Store all files downloaded from the paper "Genome-scale reconstruction and in silico analysis of Aspergillus
terreus metabolism" by Liu, Gao, Xu and Liu.Files include list of reactions, stoichiometries, metabolites, and enzymes used
in model construction.

FOLDER: E_dermatitidis_tyrosinases
PURPOSE: Contains FASTA files for each tyrosinase gene copy in E. dermatitidis. File names correspond to asseccion numbers.

FOLDER: Supplemental_Files
PURPOSE: Contains the supplemental files included with the publication of the journal article related to this work.

FILE: BidirectionalBLAST.pl
PURPOSE: Perl code which is used to perform the bidirectional BLASTp analysis to attempt to identify enzymes provided by some
enzyme list file such as "EClist_1.txt" subject to the specifications of the "BlastSpect.txt" file. 

FILE: BlastSpect.txt
PURPOSE: Show formatting appropriate to the specifications file for the "BidirectionalBLAST.pl" code. This specifications file
generally specifies the allowable percent positive substitution and expect value cutoffs for accepting BLASTp sequence 
similarity in addition to providing the identity of the target organism and a list of organisms for which to use the amino
acid sequence of a given enzyme (from a list file such as "EClist_1.txt") to identify that enzyme in a target organism.

FILE: EClist_1.txt
PURPOSE: List of enzymes for the BidirectionalBLAST.pl code to search the target genome for. This shows the formatting of
such a list, but also highlights that for reasons of time, enzyme lists should be restricted to relatively small numbers and 
long lists should be split into several small lists, each of which has a parallel version of BidirectionalBLAST.pl applied to
it. 

FILE: Enzymes1of4.txt
PURPOSE: Full list of enzymes with compartmentalization that were unique to an Aspergillus model used in this work. 

FILE: Enzymes2of4.txt
PURPOSE: Full list of enzymes with compartmentalization that were common to exactly two Aspergillus model used in this work. 

FILE: Enzymes3of4.txt
PURPOSE: Full list of enzymes with compartmentalization that were common to exactly three Aspergillus model used in this work. 

FILE: NCBIProteinDetails.txt
PURPOSE: Comma seperated values table which has all the information about the E. dermatitidis genome downloaded from NCBI.

FILE: NCBI_get_ECs.pl
PURPOSE: perl code that takes the information downloaded from NCBI (file: "NCBIProteinDetails.txt") and uses the information in
that file to attempt to identify the associated EC number with each gene using a search in the BRENDA database.

FILE: Second_draft_E_Dermatitidis_Model.txt
PURPOSE: List of reactions assocaited with the second draft of the E. dermatitidis model. 

FILE: Third_draft_E_Dermatitidis_Model.txt
PURPOSE: List of reactions assocaited with the third draft of the E. dermatitidis model. 

FILE: Fourth_draft_E_Dermatitidis_Model.txt
PURPOSE: List of reactions assocaited with the fourth draft of the E. dermatitidis model. 

FILE: iEde2091.txt
PURPOSE: List of reactions assocaited with the iEde2091 model. 

FILE: UniProt_get_ECs.pl
PURPOSE: perl code that takes the information downloaded from UniProt (file: "Uniprot_E_dermatitidis.txt") and uses the
information in that file to attempt to identify the associated EC number with each gene using a search in the BRENDA database.

FILE: Uniprot_E_dermatitidis.csv
PURPOSE: Comma seperated values table which has all the information about the E. dermatitidis genome downloaded from UniProt.

FILE: common_functions.pl
PURPOSE: A library of Perl functions created by Wheaton L Schroeder utilized by many of the other Perl programs here to save
time, lines of code, etc. Generally required by other Perl programs here. 

FILE: ConvertDB1.py
PURPOSE: Python code that takes a list of stoichiometeries formatted as "1of4DB.txt" to create an array of files required to
use the database in GAMS code.

FILE: ConvertModel.py
PURPOSE: Python code that takes a list of stoichiometeries formatted as "iEde2091.txt" to create an array of files required to
use the database in GAMS code.

FILE: Curation_notes.txt
PURPOSE: A selection of curation notes made by Wheaton L Schroeder in the manual curation of the model form the first draft
model (not included here) to the created of the second draft model (saved as Second_draft_E_Dermatitidis_model.txt").

FILE: get_shadow_prices.gms
PURPOSE: GAMS code to run the iEde2091 model quickly through a number of different growth scenarios and report the shadow
price of certain metabolites in those secenarios. 

FILE: prep_for_optFill_ED1.pl
PURPOSE: Perl code which makes a input files necessary for running the final iteration of OptFill (enzyems unique to one
Aspergillus model). 

FILE: 1of4DB.txt
PURPOSE: contains the stoichiometery of all reactions in the database catalyzable by enzymes unique to one Aspergillus model
used here.

FILE: 2of4DB.txt
PURPOSE: contains the stoichiometery of all reactions in the database catalyzable by enzymes common to exactly two
Aspergillus models used here.

FILE: 3of4DB.txt
PURPOSE: contains the stoichiometery of all reactions in the database catalyzable by enzymes common to exactly three
Aspergillus models used here.

FILE: FVA.gms
PURPOSE: GAMS code which is used to perform Flux Variability Analysis (FVA) on the iEde2091 model.

FILE: FBA.gms
PURPOSE: GAMS code which is used to perform Flux Balance Analysis (FBA) on the iEde2091 model.