PNNL-CompBio/CONCERTO

Issues

• Obtain data from Pavlo where metabolomics and transcriptomics was measured in the same conditions

  #113 opened 8 months ago by djinnome
  1

• Concerto Discussion

  #112 opened 9 months ago by djinnome
  0

• Concerto Results

  #111 opened 9 months ago by djinnome
  0

• Concerto Methods

  #110 opened 9 months ago by djinnome
  0

• Concerto Introduction

  #109 opened 9 months ago by djinnome
  0

• Concerto Abstract

  #108 opened 9 months ago by djinnome
  0

• Bayesian MCA Discussion

  #105 opened 9 months ago by djinnome
  0

• Bayesian MCA Results

  #104 opened 9 months ago by djinnome
  0

• Bayesian MCA Methods

  #103 opened 9 months ago by djinnome
  0

• Test whether Azo grows on Glycolate with and without ammonium

  #107 opened 9 months ago by djinnome
  0

• Set up overleaf for milestone 6a. Concerto publication

  #106 opened 9 months ago by djinnome
  0

• Select dual carbon source for Azo-Rhodo consortia

  #100 opened a year ago by djinnome
  5

• Create FluxViz method

  #101 opened 10 months ago by ShantMahserejian
  0

• Bayesian MCA Abstract

  #102 opened 9 months ago by djinnome
  0

• Write code that converts FBA model to biocyc

  #54 opened a year ago by djinnome
  0

• Plan for designing Azo to depend on Rhodo for carbon

  #73 opened a year ago by djinnome
  1

• visualization-friendly version of Carbon dioxide flux

  #99 opened a year ago by djinnome
  6

• simulate rhodo on those rhodo+ azoto- carbon sources to see if anything it excretes can be ingested by azoto

  #70 opened a year ago by vladpetyuk
  1

• predict all secreted metabolites under 20 Rhodo+ Azo- biolog conditions and intersect with Azo+ biolog conditions

  #96 opened a year ago by djinnome
  3

• Updating the Cyano confusion matrix with the new model

  #94 opened a year ago by djinnome
  4

• simulate ternary consortium model to confirm no growth under tested media conditions

  #98 opened a year ago by djinnome
  0

• Generate Memote pull request for github actions compatibility

  #97 opened a year ago by djinnome
  1

• explore if there is a way to run dynamic FBA for microbial consortia

  #85 opened a year ago by vladpetyuk
  1

• get individual species growth data from rhodo/syn co-culture

  #56 opened a year ago by vladpetyuk
  1

• compare, evaluate disagreement of the simulations with the growth experimental data

  #59 opened a year ago by vladpetyuk
  3

• run simulation of the rhodo/syn co-culture under proper media conditions in MICOM

  #58 opened a year ago by vladpetyuk
  2

• Convert Pavlo's cyano-rhodo data to binary consortia unit tests

  #84 opened a year ago by djinnome
  1

• Swap colors between Azoto and Cyano

  #88 opened a year ago by djinnome
  2

• Visualization of Exchange Metabolites for Binary Models

  #66 opened a year ago by ShantMahserejian
  2

• ternary consortium does not have a dinitrogen flux

  #87 opened a year ago by djinnome
  9

• Add exchange reactions for each Biolog nutrient to each model.

  #75 opened a year ago by djinnome
  1

• Get binary rhodo-cyano working with CO2 as sole carbon (ammonia is fine as a nitrogen source)

  #92 opened a year ago by djinnome
  1

• Get binary azo-cyano working with CO2 and N2 as sole carbon and nitrogen sources

  #91 opened a year ago by djinnome
  1

• compile list of secreted metabolites for rhodo/syn co-culture

  #57 opened a year ago by vladpetyuk
  1

• Get binary azo-rhodo working with a carbon source that only rhodo grows on

  #93 opened a year ago by djinnome
  6

• Talk to Bill and Ethan about getting access to modified rhodo model

  #55 opened a year ago by djinnome
  1

• Visualization for Exchange Metabolites in Ternary Model

  #67 opened a year ago by ShantMahserejian
  1

• create ternary consortia GEM model

  #62 opened a year ago by vladpetyuk
  1

• Try loading cyano, rhodo, and azoto in Kbase prior to Monday meeting with Chris Henry

  #86 opened a year ago by djinnome
  3

• start the axenic samples

  #72 opened a year ago by vladpetyuk
  0

• Review additional community modeling frameworks

  #82 opened a year ago by djinnome
  0

• Get working BioCyc model

  #79 opened a year ago by djinnome
  0

• Fix MiCOM leaks

  #76 opened a year ago by djinnome
  0

• get information about genetic modifications of the azobacter strain so we can incorporate them into the model

  #74 opened a year ago by vladpetyuk
  0

• Write rxn files to sbml

  #71 opened a year ago by vladpetyuk
  0

• manuscript for describing good practices for microbial community modeling

  #68 opened a year ago by vladpetyuk
  0

• designed media for sustained growth of ternary consortium

  #65 opened a year ago by vladpetyuk
  0

• develop and document the protocol for refinement of the ternary consortia

  #64 opened a year ago by vladpetyuk
  0

• document the protocol for refining consortia

  #61 opened a year ago by vladpetyuk
  0

• (OPTIONAL) Design an objective goodness-of-fit function for evaluating how well simulation fits the experimental data

  #60 opened a year ago by vladpetyuk
  0