10.6084/m9.figshare.3969072.v1
Daniel A. Cuevas
Daniel
A. Cuevas
Daniel Garza
Daniel
Garza
Savannah E. Sanchez
Savannah
E. Sanchez
Jason Rostron
Jason
Rostron
Chris S. Henry
Chris
S. Henry
Veronika Vonstein
Veronika
Vonstein
Ross A. Overbeek
Ross
A. Overbeek
Anca Segall
Anca
Segall
Forest Rohwer
Forest
Rohwer
Elizabeth Dinsdale
Elizabeth
Dinsdale
Robert A. Edwards
Robert
A. Edwards
Phenotypic profiling data for elucidating genomic gaps
f1000research.com
2016
phenotypic profiles
genomic gaps
Bacterial growth
Bioinformatics
Genetics
2016-10-17 15:52:46
Dataset
https://f1000.figshare.com/articles/dataset/Phenotypic_profiling_data_for_elucidating_genomic_gaps/3969072
<p>Dataset 1. Raw OD600 growth curves (raw_od_curves.csv).</p><p>MAPs optical density measurements from the plate reader for 96 wells. Numbered headers indicate the time (hrs) and the column contents indicate the OD600 measurement.</p><p>Dataset 2. Parameters for logistic curves (curve_logistic_parameters.csv).</p><p>Lag, maximum growth rate, and carrying capacity parameters for the 96 wells. Sum-squared error and growth level are included.</p><p>Dataset 3. C.sedlakii KBase phenotypes (c.sedlakii_phenotypes.csv).</p><p>Phenotype csv file required for KBase phenotype simulations. This file specifies media data object name, the KBase workspace, and growth. The gene knockout and additional compound columns were not used and set to none.</p><p>Dataset 4. (C. sedlakii_nogapfill.sbml)</p><p>The initial metabolic model of Citrobacter sedlakii built solely from the functional annotations.</p><p>Dataset 5. (C.sedlakii_ArgonneLB_gapfill.sbml)</p><p>The initial metabolic model of Citrobacter sedlakii with reactions identified by the gap-fill algorithm on the LB media
condition.</p><p>Dataset 6. (C.sedlakii_MAP_gapfill.sbml)</p><p>The LB-gap-filled model with reactions identified by
the gap-fill algorithm on the MAPs media conditions.</p>