Data collected and models code developed during the ATB project.  

For further information contact Joe Vallino listed on the ATB Home page

Microcosm Data

Below are the data collected on-line associated with O2, CO2 and CH4 gas concentrations and electrodes (pH and DO, but the latter became unreliable due to probe drift).  Concentration of nutrients in the bioreactors were also periodically sampled and analyzed as given below.

ATBexp1.dat: Contains gas concentrations in the reactor head space.  See ATBexp.hdr header file for a description of each data column.  The .dat file can be read by Tecplot.

ATBexp1.csv: Comma separated values file for dissolved oxygen (mg/L), pH and ORP (mV) for each microcosm. File contains experimental notes, such as instrument calibrations, etc.

ATBexp1.OnOff: Date, time and experimental time when methane to MCs #1 and #4 was turned on (0) and turned off (1).

ATBexp1_dCH4.dat: Concentration of dissolved methane form experimental probe (see here). The experimental probe only worked for a short time, but data was recorded anyway.

MonitorGases_4.03.f90 Fortran code compiled with Intel Visual Fortran used to monitor bioreactors.
julday.for: Used to calculated experimental elapsed time in days.

NO3alldata.csv: Nitrate+nitrite concentration in all four MCs plus in the feed medium (microMolar)

CHN.dat: Particulate organic C and N in all four MCs and feed (microMolar)

DOC-DON-TDN.dat: Dissolved organic C and N, and total dissolved organic N (microMolar)

NH4.dat: Ammonium concentration (microMolar)

PO4.csv: Inorganic phosphate concentration (microMolar).  Note, on 19-May-2011 (t = 272.60 d), 10 mM phosphate buffer was added to feed medium, so collection of phosphate samples stopped.

Sequence Data

DNA sequences of V4-V6 16S tags is publicly available on VAMPS under the project JAH_ENT_Bv6v4. Raw reads for V6 are available in the NCBI Short Read Archive under Accession Number PRJNA322031.


Below is the Fortran code and output associate with the modeling work described in the Vallino et. al (2014) paper listed under the Publications tab.  All source code was compiled with Intel Visual Fortran (without MKL), so there may be some complier associated function calls that may not compile without errors with other compilers, such as gfortran (this has not been tested though).

Methanotroph_BOBYQA_2_V4.1.f90: Main program for simulating both control and cycled microcosms described on this web site and in Vallino et al. (2014)..

Module_Thermo_V2.F90: Associated modules.

bobyqa_ArraysSpecified.f: Slightly modified version of Powell's BOBYQA for finding local optima without derivatives (also see here and here).

bim_NoWrite.f: Slightly modified version of BiM used to solve the set of governing ordinary differential equations.

subbim.f: Supporting routines used by BiM.

Below are the input files and all model output for simulations of both the control and cycled microcosms using different integration intervals in the receding horizon optimal control problem.  These runs correspond to the data presented in Table 18.2 in the above reference manuscript.  The zip archives also contain Tecplot files for visualizing output. Input and solutions for Δt = 0.1 and Δt* = 0.1 d Input and solutions for Δt = 0.1 and Δt* = 1 d Input and solutions for Δt = 1 and Δt* = 1 d Input and solutions for Δt = 1 and Δt* = 5 d Input and solutions for Δt = 10 and Δt* = 20 d Input and solutions for Δt = 20 and Δt* = 40 d Input and solutions for Δt = 20 and Δt* = 50 d