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18,621 results for “development;”
The process of HDAC11 Assay Development: Buffer optimization again
<p>The pH range used earlier was expanded for further optimization to check if the activity could improve.</p> <p> </p> <p><strong>Note: </strong>1. In the assay buffer, BSA conc. is 0.5 mg/ml (instead of 0.5%).</p> <p> 2. In the 7.5 ul developer solution, 40 uM of TSA (Trichostatin A) is also included.</p>
Microclimate and the development rate of mosquito vectors
<b>Description: </b><p>This data sets includes microclimate data, mosquito development rate and mosquito wing size measurements collected from primary forest, logged forest and oil palm plantations. Microclimate data was recorded using Ibutton data loggers which measured soil temeprature at given sample sites. All mosquito eggs collected were reared under field conditions. Each mosquito sample was monitored daily in order to record the proportion emerging at each developemnt stage (larva, pupa and adult) along with the numebr of transition days between each development stage. Adult wing length (of each adult mosquito collected) was used as a simple proxy to measure adult vectorial capacity. </p><p><b>Project: </b>This dataset was collected as part of the following SAFE research project: <a href="https://www.safeproject.net/projects/project_view/21"><b>The impact of altered forest microclimate on the development rate of mosquito vectors</b></a></p><p><b>XML metadata: </b>GEMINI compliant metadata for this dataset is available <a href="https://www.safeproject.net/datasets/xml_metadata?id=110">here</a></p><p><b>Files: </b>This consists of 1 file: template_PsomosMosquitoes.xlsx</p><p><b>template_PsomosMosquitoes.xlsx</b></p><p>This file contains dataset metadata and 3 data tables:</p><ol><li><p><b>Soil temperature</b> (described in worksheet Soiltemp)</p><p>Description: Datalogger records of soil temperature time series as sample sites</p><p>Number of fields: 4</p><p>Number of data rows: 875</p><p>Fields: </p><ul><li><b>Site</b>: SAFE Project sample site (Field type: Location)</li><li><b>Day</b>: Day of measurement; each site had records collected over seven days (Field type: Numeric)</li><li><b>Time</b>: Time of measurement (Field type: Time)</li><li><b>Soil Temperature</b>: Soil temperature (Field type: Numeric)</li></ul></li><li><p><b>Mosquito size</b> (described in worksheet Mosquito_wing_length)</p><p>Description: Wing measurements on individual mosquitoes</p><p>Number of fields: 3</p><p>Number of data rows: 119</p><p>Fields: </p><ul><li><b>Site</b>: SAFE Project sample site (Field type: Location)</li><li><b>SampleNumber</b>: Each replicate within a site represents a different mosquito that was measured (Field type: Replicate)</li><li><b>WingSize</b>: Adult mosquito wing length (Field type: Numeric Trait)</li></ul></li><li><p><b>Mosquito life history stages</b> (described in worksheet Development_data)</p><p>Description: Abundance and time frame for mosquito development</p><p>Number of fields: 8</p><p>Number of data rows: 26</p><p>Fields: </p><ul><li><b>Site</b>: SAFE Project sample site (Field type: Location)</li><li><b>Eggs</b>: Number eggs (Field type: Abundance)</li><li><b>Larvae</b>: Number larvae (Field type: Abundance)</li><li><b>Pupae</b>: Number pupae (Field type: Abundance)</li><li><b>Adults</b>: Number adults (Field type: Abundance)</li><li><b>egg-larvae</b>: Number of days to develop from egg to larvae (Field type: Numeric Trait)</li><li><b>larvae-pupae</b>: Number of days to develop from larvae to pupae (Field type: Numeric Trait)</li><li><b>pupae-adult</b>: Number of days to develop from pupae to adult (Field type: Numeric Trait)</li></ul></li></ol><p><b>Date range: </b>2015-05-01 to 2015-07-13</p><p><b>Latitudinal extent: </b>4.6532 to 4.7520</p><p><b>Longitudinal extent: </b>116.9635 to 117.5932</p><p><b>Taxonomic coverage: </b><br> All taxon names are validated against the GBIF backbone taxonomy. If a dataset uses a synonym, the accepted usage is shown followed by the dataset usage in brackets. Taxa that cannot be validated, including new species and other unknown taxa, morphospecies, functional groups and taxonomic levels not used in the GBIF backbone are shown in square brackets.</p><div>Animalia<br> - Arthropoda<br> -  - Insecta<br> -  -  - Diptera<br> -  -  -  - Culicidae<br></div><p></p>
The process of HDAC11 Assay Development: Effect of DMSO
<p>For the purpose of compound library screenings, the compounds would be made available in DMSO and thus, when they would be incubated with the protein, the protein solution will now contain DMSO as well. It is important to determine the concentration of DMSO that could be tolerated by the protein such that the protein stays active. Hence, the effect of varying concentration of DMSO was analyzed on HDAC11 activity.</p>
The process of HDAC11 Assay Development: Effect of Detergent
<p>The presence of detergent can prevent the sticking of the fluorophore to the sides of the wells of the plate and thus improve the signals. Hence, the effect of detergent was observed on the overall signals and the activity of HDAC11.</p>
The process of HDAC11 Assay Development: Check for linearity and Km-repeat
<p>The linearity for HDAC11 activity for Boc-Lys-(TFA)-AMC substrate was monitored using the newly optimized buffer conditions. This was followed upon by Km calculation.</p>
The process of HDAC11 Assay Development: time-course study follow-up-effect of additives
<p>Since the activity of HDAC11 has been observed to be quite low as per the previous data, a preliminary test was performed to check any drastic increase in the activity in the presence of an additive. </p> <p>version2 (v2) has updated reaction recipe.</p>
The process of HDAC11 Assay Development: time-course study follow-up
<p>The time of incubation and conc. of the developer to be used are important parameters during HDAC11 assay optimization and thus, have been considered here.</p> <p>Version2 (v2) has updated reaction recipe.</p>
The process of HDAC11 Assay Development: time-course study follow-up
<p>A follow-up to check the increased fluorescence signals at 0 min of the HDAC11 reaction with its substrate was performed. </p> <p>Version2 (v2) is updated with the reaction recipe.</p>
The process of HDAC11 Assay Development: time-course study
<p>Using Boc-Lys-(TFA)-AMC substrate, a preliminary time-course study was initiated to determine the appropriate HDAC11 concentration and the time to be used for the reaction (which are essential parameters to perform Km calculations later).</p> <p>The updated version2 (v2) has the corrected reaction recipe.</p>
The process of HDAC11 Assay Development: a kit-free method
<p>In order to develop an assay for HDAC11, a kit-free method is being attempted wherein Boc-Lys-(TFA)-AMC, a previously reported substrate was used to check the activity of HDAC11 in a preliminary experiment.</p> <p>In version2 (v2), the reaction recipe components are corrected (a missing component in previous version).</p>
Comparing developer-provided to user-provided tests for fault localization and automated program repair: Artifacts
<p>Artifacts for the paper <em>Comparing developer-provided to user-provided tests for fault localization and automated program repair.</em></p> <p>Note that the artifacts are maintained in the following repositories:</p> <ul> <li>https://github.com/rjust/defects4j</li> <li>https://bitbucket.org/rjust/tests-tested-data</li> <li>https://bitbucket.org/rjust/fault-localization-data</li> </ul>
The process of HDAC11 Assay Development: Z'-factor
<p>As a last step, to check if the assay qualifies for the screening purposes, Z’-factor was calculated here.</p>
Dataset from 'Billino, J., van Belle, G., Rossion, B., & Schwarzer, G. (2018). The nature of individual face recognition in preschool children: Insights from a gaze-contingent paradigm. Cognitive Development, 47, 168-180. DOI: 10.1016/j.cogdev.2018.06.007
<p>The folder contains a data file and a description file providing column labels.</p> <p>For further questions, please contact:<br> jutta.billino[at]psychol.uni-giessen.de</p>
CICE6 simulations: Quality Control for Community Based Sea Ice Model Development
<p>CICE6 simulations: Quality Control for Community Based Sea Ice Model Development<br> -----------------------------------------------------------------------------------</p> <p>Data from the CICE6 simulations by Elizabeth C. Hunke at Los Alamos National Laboratory described in the manuscript:</p> <p>Roberts, Hunke, Allard, Bailey, Craig, Lemieux and Turner (2018): Quality Control for Community Based Sea Ice Model Development.</p> <p>It was produced using the CICE sea ice model version 6.0.0.alpha with the baseline namelist:</p> <p>&setup_nml<br> days_per_year = 365<br> use_leap_years = .false.<br> year_init = 1990<br> istep0 = 0<br> dt = 3600.0<br> npt = 43800<br> ndtd = 1<br> runtype = 'continue'<br> ice_ic = '/usr/projects/climate/eclare/DATA/Consortium/CICE_data/ic/gx1/iced_gx1_v5.nc'<br> restart = .true.<br> restart_ext = .false.<br> use_restart_time = .true.<br> restart_format = 'nc'<br> lcdf64 = .false.<br> restart_dir = './restart/'<br> restart_file = 'iced'<br> pointer_file = './ice.restart_file'<br> dumpfreq = 'm'<br> dumpfreq_n = 1<br> dump_last = .false.<br> bfbflag = .false.<br> diagfreq = 24<br> diag_type = 'stdout'<br> diag_file = 'ice_diag.d'<br> print_global = .true.<br> print_points = .true.<br> latpnt(1) = 90.<br> lonpnt(1) = 0.<br> latpnt(2) = -65.<br> lonpnt(2) = -45.<br> dbug = .false.<br> histfreq = 'm','d','x','x','x'<br> histfreq_n = 1 , 1 , 1 , 1 , 1<br> hist_avg = .true.<br> history_dir = './history/'<br> history_file = 'iceh'<br> write_ic = .true.<br> incond_dir = './history/'<br> incond_file = 'iceh_ic'<br> /</p> <p>&grid_nml<br> grid_format = 'bin'<br> grid_type = 'displaced_pole'<br> grid_file = '/usr/projects/climate/eclare/DATA/Consortium/CICE_data/grid/gx1/grid_gx1.bin'<br> kmt_file = '/usr/projects/climate/eclare/DATA/Consortium/CICE_data/grid/gx1/kmt_gx1.bin'<br> gridcpl_file = 'unknown_gridcpl_file'<br> kcatbound = 0<br> /</p> <p>&domain_nml<br> nprocs = 32<br> processor_shape = 'slenderX2'<br> distribution_type = 'cartesian'<br> distribution_wght = 'latitude'<br> ew_boundary_type = 'cyclic'<br> ns_boundary_type = 'open'<br> maskhalo_dyn = .false.<br> maskhalo_remap = .false.<br> maskhalo_bound = .false.<br> /</p> <p>&tracer_nml<br> tr_iage = .true.<br> restart_age = .false.<br> tr_FY = .true.<br> restart_FY = .false.<br> tr_lvl = .true.<br> restart_lvl = .false.<br> tr_pond_cesm = .false.<br> restart_pond_cesm = .false.<br> tr_pond_topo = .false.<br> restart_pond_topo = .false.<br> tr_pond_lvl = .true.<br> restart_pond_lvl = .false.<br> tr_aero = .false.<br> restart_aero = .false.<br> /</p> <p>&thermo_nml<br> kitd = 1<br> ktherm = 2<br> conduct = 'bubbly'<br> a_rapid_mode = 0.5e-3<br> Rac_rapid_mode = 10.0<br> aspect_rapid_mode = 1.0<br> dSdt_slow_mode = -5.0e-8<br> phi_c_slow_mode = 0.05<br> phi_i_mushy = 0.85<br> /</p> <p>&dynamics_nml<br> kdyn = 1<br> ndte = 120<br> revised_evp = .false.<br> advection = 'remap'<br> kstrength = 1<br> krdg_partic = 1<br> krdg_redist = 1<br> mu_rdg = 3<br> Cf = 17.<br> Ktens = 0.<br> e_ratio = 2.<br> basalstress = .false.<br> /</p> <p>&shortwave_nml<br> shortwave = 'dEdd'<br> albedo_type = 'default'<br> albicev = 0.78<br> albicei = 0.36<br> albsnowv = 0.98<br> albsnowi = 0.70 <br> ahmax = 0.3<br> R_ice = 0.<br> R_pnd = 0.<br> R_snw = 1.5<br> dT_mlt = 1.5<br> rsnw_mlt = 1500.<br> kalg = 0.6<br> /</p> <p>&ponds_nml<br> hp1 = 0.01<br> hs0 = 0.<br> hs1 = 0.03<br> dpscale = 1.e-3<br> frzpnd = 'hlid'<br> rfracmin = 0.15<br> rfracmax = 1.<br> pndaspect = 0.8<br> /</p> <p>&zbgc_nml<br> tr_brine = .false.<br> restart_hbrine = .false.<br> tr_zaero = .false.<br> modal_aero = .false.<br> skl_bgc = .false.<br> z_tracers = .false.<br> dEdd_algae = .false.<br> solve_zbgc = .false.<br> bgc_flux_type = 'Jin2006'<br> restore_bgc = .false.<br> restart_bgc = .false.<br> scale_bgc = .false.<br> solve_zsal = .false.<br> restart_zsal = .false.<br> bgc_data_dir = '/uknown_bgc_data_dir'<br> sil_data_type = 'default'<br> nit_data_type = 'default'<br> fe_data_type = 'default'<br> tr_bgc_Nit = .true.<br> tr_bgc_C = .true.<br> tr_bgc_chl = .false.<br> tr_bgc_Am = .true.<br> tr_bgc_Sil = .true.<br> tr_bgc_DMS = .false.<br> tr_bgc_PON = .true.<br> tr_bgc_hum = .true.<br> tr_bgc_DON = .false.<br> tr_bgc_Fe = .true. <br> grid_o = 0.006<br> grid_o_t = 0.006<br> l_sk = 0.024<br> grid_oS = 0.0<br> l_skS = 0.028<br> phi_snow = -0.3<br> initbio_frac = 0.8<br> frazil_scav = 0.8 <br> ratio_Si2N_diatoms = 1.8 <br> ratio_Si2N_sp = 0.0<br> ratio_Si2N_phaeo = 0.0<br> ratio_S2N_diatoms = 0.03 <br> ratio_S2N_sp = 0.03 <br> ratio_S2N_phaeo = 0.03<br> ratio_Fe2C_diatoms = 0.0033<br> ratio_Fe2C_sp = 0.0033<br> ratio_Fe2C_phaeo = 0.1<br> ratio_Fe2N_diatoms = 0.023 <br> ratio_Fe2N_sp = 0.023<br> ratio_Fe2N_phaeo = 0.7<br> ratio_Fe2DON = 0.023<br> ratio_Fe2DOC_s = 0.1<br> ratio_Fe2DOC_l = 0.033<br> fr_resp = 0.05<br> tau_min = 5200.0<br> tau_max = 173000.0<br> algal_vel = 0.0000000111<br> R_dFe2dust = 0.035<br> dustFe_sol = 0.005<br> chlabs_diatoms = 0.03<br> chlabs_sp = 0.01<br> chlabs_phaeo = 0.05<br> alpha2max_low_diatoms = 0.8<br> alpha2max_low_sp = 0.67<br> alpha2max_low_phaeo = 0.67<br> beta2max_diatoms = 0.018<br> beta2max_sp = 0.0025<br> beta2max_phaeo = 0.01<br> mu_max_diatoms = 1.44<br> mu_max_sp = 0.851<br> mu_max_phaeo = 0.851<br> grow_Tdep_diatoms = 0.06<br> grow_Tdep_sp = 0.06<br> grow_Tdep_phaeo = 0.06<br> fr_graze_diatoms = 0.0<br> fr_graze_sp = 0.1<br> fr_graze_phaeo = 0.1<br> mort_pre_diatoms = 0.007<br> mort_pre_sp = 0.007<br> mort_pre_phaeo = 0.007<br> mort_Tdep_diatoms = 0.03<br> mort_Tdep_sp = 0.03<br> mort_Tdep_phaeo = 0.03<br> k_exude_diatoms = 0.0<br> k_exude_sp = 0.0<br> k_exude_phaeo = 0.0<br> K_Nit_diatoms = 1.0<br> K_Nit_sp = 1.0<br> K_Nit_phaeo = 1.0<br> K_Am_diatoms = 0.3<br> K_Am_sp = 0.3<br> K_Am_phaeo = 0.3<br> K_Sil_diatoms = 4.0<br> K_Sil_sp = 0.0<br> K_Sil_phaeo = 0.0<br> K_Fe_diatoms = 1.0<br> K_Fe_sp = 0.2<br> K_Fe_phaeo = 0.1<br> f_don_protein = 0.6<br> kn_bac_protein = 0.03<br> f_don_Am_protein = 0.25<br> f_doc_s = 0.4<br> f_doc_l = 0.4<br> f_exude_s = 1.0<br> f_exude_l = 1.0<br> k_bac_s = 0.03<br> k_bac_l = 0.03<br> T_max = 0.0<br> fsal = 1.0<br> op_dep_min = 0.1<br> fr_graze_s = 0.5<br> fr_graze_e = 0.5<br> fr_mort2min = 0.5<br> fr_dFe = 0.3<br> k_nitrif = 0.0<br> t_iron_conv = 3065.0<br> max_loss = 0.9<br> max_dfe_doc1 = 0.2<br> fr_resp_s = 0.75<br> y_sk_DMS = 0.5<br> t_sk_conv = 3.0<br> t_sk_ox = 10.0<br> algaltype_diatoms = 0.0<br> algaltype_sp = 0.5<br> algaltype_phaeo = 0.5<br> nitratetype = -1.0<br> ammoniumtype = 1.0<br> silicatetype = -1.0<br> dmspptype = 0.5<br> dmspdtype = -1.0<br> humtype = 1.0<br> doctype_s = 0.5<br> doctype_l = 0.5<br> dontype_protein = 0.5<br> fedtype_1 = 0.5<br> feptype_1 = 0.5<br> zaerotype_bc1 = 1.0<br> zaerotype_bc2 = 1.0<br> zaerotype_dust1 = 1.0<br> zaerotype_dust2 = 1.0<br> zaerotype_dust3 = 1.0<br> zaerotype_dust4 = 1.0<br> ratio_C2N_diatoms = 7.0<br> ratio_C2N_sp = 7.0<br> ratio_C2N_phaeo = 7.0<br> ratio_chl2N_diatoms= 2.1<br> ratio_chl2N_sp = 1.1<br> ratio_chl2N_phaeo = 0.84<br> F_abs_chl_diatoms = 2.0<br> F_abs_chl_sp = 4.0<br> F_abs_chl_phaeo = 5.0<br> ratio_C2N_proteins = 7.0<br> /</p> <p>&forcing_nml<br> formdrag = .false.<br> atmbndy = 'default'<br> fyear_init = 1990<br> ycycle = 20<br> atm_data_format = 'bin'<br> atm_data_type = 'LYq'<br> atm_data_dir = '/usr/projects/climate/eclare/DATA/Consortium/CICE_data/forcing/gx1/COREII'<br> calc_strair = .true.<br> highfreq = .false.<br> natmiter = 5<br> calc_Tsfc = .true.<br> precip_units = 'mm_per_sec'<br> ustar_min = 0.0005<br> fbot_xfer_type = 'constant'<br> update_ocn_f = .false.<br> l_mpond_fresh = .false.<br> tfrz_option = 'mushy'<br> oceanmixed_ice = .true.<br> ocn_data_format = 'nc'<br> sss_data_type = 'ncar'<br> sst_data_type = 'ncar'<br> ocn_data_dir = '/usr/projects/climate/eclare/DATA/gx1v3/gx1v3/forcing/'<br> oceanmixed_file = 'oceanmixed_ice_depth.nc'<br> restore_sst = .false.<br> trestore = 90<br> restore_ice = .false.<br> /</p> <p>&icefields_nml<br> f_tmask = .true.<br> f_blkmask = .true.<br> f_tarea = .true.<br> f_uarea = .true.<br> f_dxt = .false.<br> f_dyt = .false.<br> f_dxu = .false.<br> f_dyu = .false.<br> f_HTN = .false.<br> f_HTE = .false.<br> f_ANGLE = .true.<br> f_ANGLET = .true.<br> f_NCAT = .true.<br> f_VGRDi = .false.<br> f_VGRDs = .false.<br> f_VGRDb = .false.<br> f_VGRDa = .true.<br> f_bounds = .false.<br> f_aice = 'm' <br> f_hi = 'm'<br> f_hs = 'm' <br> f_Tsfc = 'm' <br> f_sice = 'm' <br> f_uvel = 'm' <br> f_vvel = 'm' <br> f_uatm = 'm' <br> f_vatm = 'm' <br> f_fswdn = 'm' <br> f_flwdn = 'm'<br> f_snowfrac = 'x'<br> f_snow = 'x' <br> f_snow_ai = 'm' <br> f_rain = 'x' <br> f_rain_ai = 'm' <br> f_sst = 'm' <br> f_sss = 'm' <br> f_uocn = 'm' <br> f_vocn = 'm' <br> f_frzmlt = 'm'<br> f_fswfac = 'm'<br> f_fswint_ai = 'm'<br> f_fswabs = 'x' <br> f_fswabs_ai = 'm' <br> f_albsni = 'm' <br> f_alvdr = 'x'<br> f_alidr = 'x'<br> f_alvdf = 'x'<br> f_alidf = 'x'<br> f_alvdr_ai = 'x'<br> f_alidr_ai = 'x'<br> f_alvdf_ai = 'x'<br> f_alidf_ai = 'x'<br> f_albice = 'x'<br> f_albsno = 'x'<br> f_albpnd = 'x'<br> f_coszen = 'x'<br> f_flat = 'x' <br> f_flat_ai = 'm' <br> f_fsens = 'x' <br> f_fsens_ai = 'm' <br> f_fswup = 'x' <br> f_flwup = 'x' <br> f_flwup_ai = 'm' <br> f_evap = 'x' <br> f_evap_ai = 'm' <br> f_Tair = 'm' <br> f_Tref = 'x' <br> f_Qref = 'x'<br> f_congel = 'm' <br> f_frazil = 'm' <br> f_snoice = 'm' <br> f_dsnow = 'x' <br> f_melts = 'm'<br> f_meltt = 'm'<br> f_meltb = 'm'<br> f_meltl = 'm'<br> f_fresh = 'x'<br> f_fresh_ai = 'm'<br> f_fsalt = 'x'<br> f_fsalt_ai = 'm'<br> f_fbot = 'm'<br> f_fhocn = 'x' <br> f_fhocn_ai = 'm' <br> f_fswthru = 'x' <br> f_fswthru_ai = 'm' <br> f_fsurf_ai = 'x'<br> f_fcondtop_ai = 'x'<br> f_fmeltt_ai = 'x' <br> f_strairx = 'm' <br> f_strairy = 'm' <br> f_strtltx = 'x' <br> f_strtlty = 'x' <br> f_strcorx = 'x' <br> f_strcory = 'x' <br> f_strocnx = 'x' <br> f_strocny = 'x' <br> f_strintx = 'x' <br> f_strinty = 'x'<br> f_taubx = 'x'<br> f_tauby = 'x'<br> f_strength = 'm'<br> f_divu = 'm'<br> f_shear = 'm'<br> f_sig1 = 'm' <br> f_sig2 = 'm' <br> f_dvidtt = 'm' <br> f_dvidtd = 'm' <br> f_daidtt = 'm'<br> f_daidtd = 'm' <br> f_dagedtt = 'm'<br> f_dagedtd = 'm' <br> f_mlt_onset = 'm'<br> f_frz_onset = 'm'<br> f_hisnap = 'd'<br> f_aisnap = 'd'<br> f_trsig = 'm'<br> f_icepresent = 'm'<br> f_iage = 'm'<br> f_FY = 'x'<br> f_aicen = 'x'<br> f_vicen = 'x'<br> f_vsnon = 'x'<br> f_snowfracn = 'x'<br> f_keffn_top = 'x'<br> f_Tinz = 'x'<br> f_Sinz = 'x'<br> f_Tsnz = 'x'<br> f_fsurfn_ai = 'x'<br> f_fcondtopn_ai = 'x'<br> f_fmelttn_ai = 'x'<br> f_flatn_ai = 'x'<br> f_fsensn_ai = 'x'<br> /</p> <p>&icefields_mechred_nml<br> f_alvl = 'm'<br> f_vlvl = 'm'<br> f_ardg = 'm'<br> f_vrdg = 'm'<br> f_dardg1dt = 'x'<br> f_dardg2dt = 'x'<br> f_dvirdgdt = 'x'<br> f_opening = 'x'<br> f_ardgn = 'x'<br> f_vrdgn = 'x'<br> f_dardg1ndt = 'x'<br> f_dardg2ndt = 'x'<br> f_dvirdgndt = 'x'<br> f_krdgn = 'x'<br> f_aparticn = 'x'<br> f_aredistn = 'x'<br> f_vredistn = 'x'<br> f_araftn = 'x'<br> f_vraftn = 'x'<br> /</p> <p>&icefields_pond_nml<br> f_apondn = 'x'<br> f_apeffn = 'x'<br> f_hpondn = 'x'<br> f_apond = 'm'<br> f_hpond = 'm'<br> f_ipond = 'm'<br> f_apeff = 'm'<br> f_apond_ai = 'm'<br> f_hpond_ai = 'm'<br> f_ipond_ai = 'm'<br> f_apeff_ai = 'm'<br> /</p> <p>&icefields_bgc_nml<br> f_faero_atm = 'x'<br> f_faero_ocn = 'x'<br> f_aero = 'x' <br> f_fbio = 'm'<br> f_fbio_ai = 'm'<br> f_zaero = 'x'<br> f_bgc_S = 'm'<br> f_bgc_N = 'm'<br> f_bgc_C = 'x'<br> f_bgc_DOC = 'm'<br> f_bgc_DIC = 'x'<br> f_bgc_chl = 'x'<br> f_bgc_Nit = 'm'<br> f_bgc_Am = 'm'<br> f_bgc_Sil = 'm'<br> f_bgc_DMSPp = 'x'<br> f_bgc_DMSPd = 'x'<br> f_bgc_DMS = 'x'<br> f_bgc_DON = 'x' <br> f_bgc_Fe = 'm' <br> f_bgc_hum = 'm' <br> f_bgc_PON = 'm'<br> f_bgc_ml = 'm'<br> f_upNO = 'm'<br> f_upNH = 'm'<br> f_bTin = 'm'<br> f_bphi = 'm' <br> f_iDi = 'm'<br> f_iki = 'm'<br> f_fbri = 'm' <br> f_hbri = 'm'<br> f_zfswin = 'm'<br> f_bionet = 'm'<br> f_biosnow = 'm'<br> f_grownet = 'm'<br> f_PPnet = 'm'<br> f_algalpeak = 'm'<br> f_zbgc_frac = 'm'<br> /</p> <p>&icefields_drag_nml<br> f_drag = 'x'<br> f_Cdn_atm = 'x'<br> f_Cdn_ocn = 'x'<br> /</p>
RASM simulations: Quality Control for Community Based Sea Ice Model Development
<p>RASM simulations: Quality Control for Community Based Sea Ice Model Development<br> -----------------------------------------------------------------------------------</p> <p>Data from the Regional Arctic System Model (RASM) simulations by Andrew F. Roberts at Naval Postgraduate School, described in the manuscript:</p> <p>Roberts, Hunke, Allard, Bailey, Craig, Lemieux and Turner (2018): Quality Control for Community Based Sea Ice Model Development.</p> <p>It was produced using RASM with CICE sea ice model version 5.2 with the namelist:</p> <p>&setup_nml<br> bfbflag = .false. <br> diagfreq = 24 <br> hist_avg = .true. <br> histfreq = 'h','x','x','x','x'<br> histfreq_n = 1,0,0,0,0<br> ice_ic = '/work4/projects/apcraig_dir/RACM/inputdata/ccsm4_init/R1008Gcaaa01a_loop2/1979-09-01/R1008Gcaaa01a_loop2.cice.r.1979-09-01-00000.nc'<br> latpnt = 90.0,-65.0 <br> lcdf64 = .true. <br> lonpnt = 0.0,-45.0 <br> ndtd = 1 <br> pointer_file = './rpointer.ice'<br> print_global = .true. <br> print_points = .false. <br> restart_ext = .false. <br> restart_format = 'pio'<br> year_init = 1 <br> /<br> &grid_nml<br> grid_file = '/work4/projects/apcraig_dir/RACM/inputdata/ice/cice/ar9v3_20101118.grid'<br> grid_format = 'bin'<br> grid_type = 'regional'<br> gridcpl_file = '/work4/projects/apcraig_dir/RACM/inputdata/ice/cice/domain.ocn.ar9v4.100920.nc'<br> kcatbound = 0 <br> kmt_file = '/work4/projects/apcraig_dir/RACM/inputdata/ice/cice/ar9v3_20110106.kmt'<br> /<br> &tracer_nml<br> restart_aero = .false. <br> restart_age = .false. <br> restart_fy = .false. <br> restart_lvl = .false. <br> restart_pond_cesm = .false. <br> restart_pond_lvl = .false. <br> restart_pond_topo = .false. <br> tr_aero = .false.<br> tr_fy = .true. <br> tr_iage = .true. <br> tr_lvl = .true. <br> tr_pond_cesm = .false. <br> tr_pond_lvl = .true. <br> tr_pond_topo = .false. <br> /<br> &thermo_nml<br> a_rapid_mode = 0.5e-03 <br> aspect_rapid_mode = 1.0 <br> conduct = 'bubbly'<br> dsdt_slow_mode = -1.5e-07 <br> kitd = 1 <br> ktherm = 2 <br> phi_c_slow_mode = 0.05 <br> phi_i_mushy = 0.85 <br> rac_rapid_mode = 10 <br> /<br> &dynamics_nml<br> advection = 'remap'<br> cf = 21.3<br> kdyn = 2 (EAP) or kdyn = 2 (EVP)<br> krdg_partic = 1<br> krdg_redist = 1<br> kstrength = 1 <br> mu_rdg = 3.0<br> ndte = 600 <br> revised_evp = .false. <br> /<br> &shortwave_nml<br> ahmax = 0.3 <br> albedo_type = 'default'<br> albicei = 0.45<br> albicev = 0.75<br> albsnowi = 0.73<br> albsnowv = 0.98<br> dt_mlt = 1.00 <br> kalg = 0.0 <br> r_ice = 0.0 <br> r_pnd = 0.0 <br> r_snw = 0.50 <br> rsnw_mlt = 1000. <br> shortwave = 'dEdd'<br> /<br> &ponds_nml<br> dpscale = 1.0e-3 <br> frzpnd = 'hlid'<br> hp1 = 0.01 <br> hs0 = 0.03 <br> hs1 = 0.03 <br> pndaspect = 0.8 <br> rfracmax = 0.85 <br> rfracmin = 0.15 <br> /<br> &forcing_nml<br> fbot_xfer_type = 'constant'<br> formdrag = .false.<br> highfreq = .true.<br> l_mpond_fresh = .false.<br> natmiter = 25 <br> tfrz_option = 'mushy'<br> /<br> &domain_nml<br> distribution_type = 'roundrobin'<br> ew_boundary_type = 'cyclic'<br> maskhalo_bound = .true.<br> maskhalo_dyn = .true.<br> maskhalo_remap = .true.<br> ns_boundary_type = 'open'<br> processor_shape = 'null'<br> /<br> &zbgc_nml<br> bgc_data_dir = 'unknown_bgc_data_dir'<br> bgc_flux_type = 'Jin2006'<br> nit_data_type = 'unknown'<br> phi_snow = 0.5 <br> restart_bgc = .false. <br> restart_hbrine = .false. <br> restore_bgc = .false. <br> sil_data_type = 'unknown'<br> skl_bgc = .false. <br> tr_bgc_am_sk = .false. <br> tr_bgc_c_sk = .false. <br> tr_bgc_chl_sk = .false. <br> tr_bgc_dms_sk = .false. <br> tr_bgc_dmspd_sk = .false. <br> tr_bgc_dmspp_sk = .false. <br> tr_bgc_sil_sk = .false. <br> tr_brine = .false. <br> /<br> &icefields_bgc_nml<br> f_aero = 'mxxxx'<br> f_aeron = 'xxxxx'<br> f_bgc_am_ml = 'xxxxx'<br> f_bgc_am_sk = 'xxxxx'<br> f_bgc_c = 'xxxxx'<br> f_bgc_c_sk = 'xxxxx'<br> f_bgc_chl = 'xxxxx'<br> f_bgc_chl_sk = 'xxxxx'<br> f_bgc_dms = 'xxxxx'<br> f_bgc_dms_ml = 'xxxxx'<br> f_bgc_dms_sk = 'xxxxx'<br> f_bgc_dmsp_ml = 'xxxxx'<br> f_bgc_dmspd = 'xxxxx'<br> f_bgc_dmspd_sk = 'xxxxx'<br> f_bgc_dmspp = 'xxxxx'<br> f_bgc_dmspp_sk = 'xxxxx'<br> f_bgc_n = 'xxxxx'<br> f_bgc_n_sk = 'xxxxx'<br> f_bgc_nh = 'xxxxx'<br> f_bgc_nit_ml = 'xxxxx'<br> f_bgc_nit_sk = 'xxxxx'<br> f_bgc_no = 'xxxxx'<br> f_bgc_s = 'xxxxx'<br> f_bgc_sil = 'xxxxx'<br> f_bgc_sil_ml = 'xxxxx'<br> f_bgc_sil_sk = 'xxxxx'<br> f_bphi = 'xxxxx'<br> f_btin = 'xxxxx'<br> f_faero_atm = 'mxxxx'<br> f_faero_ocn = 'mxxxx'<br> f_fbri = 'xxxxx'<br> f_fn = 'xxxxx'<br> f_fn_ai = 'xxxxx'<br> f_fnh = 'xxxxx'<br> f_fnh_ai = 'xxxxx'<br> f_fno = 'xxxxx'<br> f_fno_ai = 'xxxxx'<br> f_fsil = 'xxxxx'<br> f_fsil_ai = 'xxxxx'<br> f_grownet = 'xxxxx'<br> f_hbri = 'xxxxx'<br> f_ppnet = 'xxxxx'<br> /<br> &icefields_drag_nml<br> f_cdn_atm = 'hxxxx'<br> f_cdn_ocn = 'hxxxx'<br> f_drag = 'hxxxx'<br> /<br> &icefields_mechred_nml<br> f_alvl = 'hxxxx'<br> f_aparticn = 'xxxxx'<br> f_araftn = 'xxxxx'<br> f_ardg = 'hxxxx'<br> f_ardgn = 'hxxxx'<br> f_aredistn = 'xxxxx'<br> f_dardg1dt = 'xxxxx'<br> f_dardg1ndt = 'xxxxx'<br> f_dardg2dt = 'xxxxx'<br> f_dardg2ndt = 'xxxxx'<br> f_dvirdgdt = 'xxxxx'<br> f_dvirdgndt = 'xxxxx'<br> f_krdgn = 'xxxxx'<br> f_opening = 'hxxxx'<br> f_vlvl = 'hxxxx'<br> f_vraftn = 'xxxxx'<br> f_vrdg = 'hxxxx'<br> f_vrdgn = 'hxxxx'<br> f_vredistn = 'xxxxx'<br> /<br> &icefields_pond_nml<br> f_apeff = 'hxxxx'<br> f_apeff_ai = 'hxxxx'<br> f_apeffn = 'hxxxx'<br> f_apond = 'hxxxx'<br> f_apond_ai = 'hxxxx'<br> f_apondn = 'hxxxx'<br> f_hpond = 'hxxxx'<br> f_hpond_ai = 'hxxxx'<br> f_hpondn = 'hxxxx'<br> f_ipond = 'hxxxx'<br> f_ipond_ai = 'hxxxx'<br> /<br> &icefields_nml<br> f_a11 = 'hxxxx'<br> f_a12 = 'hxxxx'<br> f_aice = 'hxxxx'<br> f_aicen = 'hxxxx'<br> f_aisnap = 'hxxxx'<br> f_albice = 'hxxxx'<br> f_albpnd = 'hxxxx'<br> f_albsni = 'hxxxx'<br> f_albsno = 'hxxxx'<br> f_alidf = 'hxxxx'<br> f_alidr = 'hxxxx'<br> f_alvdf = 'hxxxx'<br> f_alvdr = 'hxxxx'<br> f_angle = .true.<br> f_anglet = .true.<br> f_blkmask = .true.<br> f_bounds = .false.<br> f_congel = 'hxxxx'<br> f_coszen = 'hxxxx'<br> f_daidtd = 'hxxxx'<br> f_daidtt = 'hxxxx'<br> f_divu = 'hxxxx'<br> f_dsnow = 'hxxxx'<br> f_dvidtd = 'hxxxx'<br> f_dvidtt = 'hxxxx'<br> f_dxt = .false.<br> f_dxu = .false.<br> f_dyt = .false.<br> f_dyu = .false.<br> f_e11 = 'xxxxx'<br> f_e12 = 'xxxxx'<br> f_e22 = 'xxxxx'<br> f_evap = 'hxxxx'<br> f_evap_ai = 'hxxxx'<br> f_fcondtop_ai = 'hxxxx'<br> f_fcondtopn_ai = 'hxxxx'<br> f_fhocn = 'hxxxx'<br> f_fhocn_ai = 'hxxxx'<br> f_flat = 'hxxxx'<br> f_flat_ai = 'hxxxx'<br> f_flatn_ai = 'hxxxx'<br> f_flwdn = 'hxxxx'<br> f_flwup = 'hxxxx'<br> f_flwup_ai = 'hxxxx'<br> f_fmeltt_ai = 'hxxxx'<br> f_fmelttn_ai = 'hxxxx'<br> f_frazil = 'hxxxx'<br> f_fresh = 'hxxxx'<br> f_fresh_ai = 'hxxxx'<br> f_frz_onset = 'hxxxx'<br> f_frzmlt = 'hxxxx'<br> f_fsalt = 'hxxxx'<br> f_fsalt_ai = 'hxxxx'<br> f_fsens = 'hxxxx'<br> f_fsens_ai = 'hxxxx'<br> f_fsensn_ai = 'hxxxx'<br> f_fsurf_ai = 'hxxxx'<br> f_fsurfn_ai = 'hxxxx'<br> f_fswabs = 'hxxxx'<br> f_fswabs_ai = 'hxxxx'<br> f_fswdn = 'hxxxx'<br> f_fswfac = 'hxxxx'<br> f_fswint_ai = 'xxxxx'<br> f_fswthru = 'hxxxx'<br> f_fswthru_ai = 'hxxxx'<br> f_fy = 'hxxxx'<br> f_hi = 'hxxxx'<br> f_hisnap = 'xxxxx'<br> f_hs = 'hxxxx'<br> f_hte = .false.<br> f_htn = .false.<br> f_iage = 'hxxxx'<br> f_icepresent = 'hxxxx'<br> f_keffn_top = 'xxxxx'<br> f_meltb = 'hxxxx'<br> f_meltl = 'hxxxx'<br> f_melts = 'hxxxx'<br> f_meltt = 'hxxxx'<br> f_mlt_onset = 'hxxxx'<br> f_ncat = .true.<br> f_qref = 'hxxxx'<br> f_rain = 'hxxxx'<br> f_rain_ai = 'hxxxx'<br> f_s11 = 'hxxxx'<br> f_s12 = 'hxxxx'<br> f_s22 = 'hxxxx'<br> f_shear = 'hxxxx'<br> f_sice = 'hxxxx'<br> f_sig1 = 'hxxxx'<br> f_sig2 = 'hxxxx'<br> f_sinz = 'xxxxx'<br> f_snoice = 'hxxxx'<br> f_snow = 'hxxxx'<br> f_snow_ai = 'hxxxx'<br> f_sss = 'hxxxx'<br> f_sst = 'hxxxx'<br> f_strairx = 'hxxxx'<br> f_strairy = 'hxxxx'<br> f_strcorx = 'hxxxx'<br> f_strcory = 'hxxxx'<br> f_strength = 'hxxxx'<br> f_strintx = 'hxxxx'<br> f_strinty = 'hxxxx'<br> f_strocnx = 'hxxxx'<br> f_strocny = 'hxxxx'<br> f_strtltx = 'hxxxx'<br> f_strtlty = 'hxxxx'<br> f_tair = 'hxxxx'<br> f_tarea = .true.<br> f_tinz = 'xxxxx'<br> f_tmask = .true.<br> f_tref = 'hxxxx'<br> f_trsig = 'hxxxx'<br> f_tsfc = 'hxxxx'<br> f_tsnz = 'xxxxx'<br> f_uarea = .true.<br> f_uatm = 'hxxxx'<br> f_uocn = 'hxxxx'<br> f_uvel = 'hxxxx'<br> f_vatm = 'hxxxx'<br> f_vgrdb = .true.<br> f_vgrdi = .true.<br> f_vgrds = .true.<br> f_vicen = 'hxxxx'<br> f_vocn = 'hxxxx'<br> f_vsnon = 'hxxxx'<br> f_vvel = 'hxxxx'<br> f_yieldstress11 = 'hxxxx'<br> f_yieldstress12 = 'hxxxx'<br> f_yieldstress22 = 'hxxxx'<br> /<br> &ice_prescribed_nml<br> prescribed_ice = .false.<br> /</p>
Development of a specific PCR to detect thiocyanate-oxidizing Thioalkalivibrio strains in their environment
<p>Data repository for my thesis named 'Development of a specific PCR to detect thiocyanate-oxidizing <em>Thioalkalivibrio</em> strains in their environment' at the University of Amsterdam. The folder consists of 2 subfolders, namely the alignment, in both AA and NA forms, of the TcDH-sequences of the 10 Thioalkalivibrio strains, shown in <em>Figure 21</em> (1) and the alignment of the TcDH-sequences and names of the organisms used while making the phylogenetic tree of <em>Figure 2</em> (2).</p>
GOFS simulations: Quality Control for Community Based Sea Ice Model Development
<p>GOFS simulations: Quality Control for Community Based Sea Ice Model Development<br> -----------------------------------------------------------------------------------</p> <p>Data from the Global Ocean Forecast System (GOFS 3.1) from the Naval Research Laboratory, curated by Richard Allard, and described in the manuscript:</p> <p>Roberts, Hunke, Allard, Bailey, Craig, Lemieux and Turner (2018): Quality Control for Community Based Sea Ice Model Development.</p> <p>It was produced using GOFS with CICE sea ice model version 4.0 with the namelist:</p> <p>&setup_nml<br> days_per_year= 366<br> , year_init = 1901<br> , istep0 = 0<br> , dt = 225.0<br> , npt = -1 <br> , ndyn_dt = 1<br> , inserthr = 0<br> , runtype = 'continue'<br> , ice_ic = 'default'<br> , restart = .true.<br> , restart_dir = './'<br> , restart_file = 'cice.restart'<br> , pointer_file = './cice.restart_file'<br> , histfreq = 'h'<br> , histfreq_n = 12<br> , dumpfreq = '5'<br> , dumpfreq_n = 1<br> , diagfreq = 8<br> , diag_type = 'stdout'<br> , diag_file = 'ice.diag.d'<br> , print_global = .true.<br> , print_points = .true.<br> , latpnt(1) = 72.011<br> , lonpnt(1) = -149.987<br> , latpnt(2) = 90.<br> , lonpnt(2) = 0.<br> , dbug = .false.<br> , incond_dir = <br> , incond_file = './cice'<br> /<br> &grid_nml<br> grid_format = 'bin'<br> , grid_type = 'hycom'<br> , grid_file = 'regional.cice.r'<br> , kmt_file = 'kmt'<br> , kcatbound = 0 <br> /<br> &domain_nml<br> nprocs = 1800<br> , processor_shape = 'slenderX4'<br> , distribution_type = 'cartesian'<br> , distribution_wght = 'latitude'<br> , ew_boundary_type = 'cyclic'<br> , ns_boundary_type = 'tripole'<br> /<br> &tracer_nml<br> tr_iage = .false.<br> , restart_age = .false.<br> , tr_pond = .false.<br> , restart_pond = .false.<br> /<br> &ice_nml<br> kitd = 1<br> , kdyn = 1<br> , ndte = 120<br> , kstrength = 1<br> , krdg_partic = 1<br> , krdg_redist = 1<br> , advection = 'remap'<br> , heat_capacity = .true.<br> , shortwave = 'default'<br> , albedo_type = 'default'<br> , albicev = 0.78<br> , albicei = 0.36<br> , albsnowv = 0.98<br> , albsnowi = 0.70 <br> , R_ice = 0.0<br> , R_pnd = 0.0<br> , R_snw = 0.0<br> , atmbndy = 'default'<br> , fyear_init = 1911 <br> , ycycle = 1 <br> , atm_data_format = 'bin'<br> , atm_data_type= 'cfsr'<br> , atm_data_dir = './cice.'<br> , calc_strair = .true.<br> , calc_Tsfc = .true.<br> , precip_units = 'mm_per_month'<br> , Tfrzpt = 'linear_S'<br> , update_ocn_f = .false.<br> , oceanmixed_ice = .true.<br> , ocn_data_format = 'bin'<br> , sss_data_type= 'cfsr'<br> , sst_data_type= 'cfsr'<br> , ocn_data_dir = 'COUPLED'<br> , oceanmixed_file= 'pop_frc.gx1v3.051202.nc'<br> , restore_sst = .true.<br> , insert_ssmi = .true.<br> , insert_sih = .false.<br> , trestore = 1 <br> , atm_netrad = .false.<br> , albnetrad = 0.00<br> /<br> &icefields_nml<br> f_tmask = .false.<br> , f_tarea = .false.<br> , f_uarea = .false.<br> , f_dxt = .false.<br> , f_dyt = .false.<br> , f_dxu = .false.<br> , f_dyu = .false.<br> , f_HTN = .false.<br> , f_HTE = .false.<br> , f_ANGLE = .false.<br> , f_ANGLET = .false.<br> , f_bounds = .false.<br> , f_hi = .true.<br> , f_hs = .true. <br> , f_Tsfc = .true. <br> , f_aice = .true. <br> , f_uvel = .true. <br> , f_vvel = .true. <br> , f_fswdn = .true. <br> , f_flwdn = .true.<br> , f_snow = .true. <br> , f_snow_ai = .true. <br> , f_rain = .false. <br> , f_rain_ai = .true. <br> , f_sst = .true. <br> , f_sss = .true. <br> , f_uocn = .true. <br> , f_vocn = .true. <br> , f_frzmlt = .true.<br> , f_fswabs = .true. <br> , f_fswabs_ai = .true. <br> , f_albsni = .true. <br> , f_alvdr = .false.<br> , f_alidr = .false.<br> , f_flat = .false. <br> , f_flat_ai = .true. <br> , f_fsens = .false. <br> , f_fsens_ai = .true. <br> , f_flwup = .false. <br> , f_flwup_ai = .true. <br> , f_evap = .false. <br> , f_evap_ai = .true. <br> , f_Tair = .true. <br> , f_Tref = .false. <br> , f_Qref = .false.<br> , f_congel = .true. <br> , f_frazil = .true. <br> , f_snoice = .true. <br> , f_meltt = .true.<br> , f_meltb = .true.<br> , f_meltl = .true.<br> , f_fresh = .false.<br> , f_fresh_ai = .true.<br> , f_fsalt = .false.<br> , f_fsalt_ai = .true.<br> , f_fhocn = .false. <br> , f_fhocn_ai = .true. <br> , f_fswthru = .false. <br> , f_fswthru_ai= .true. <br> , f_fsurf_ai = .false.<br> , f_fcondtop_ai= .false.<br> , f_fmeltt_ai = .false. <br> , f_strairx = .true. <br> , f_strairy = .true. <br> , f_strtltx = .false. <br> , f_strtlty = .false. <br> , f_strcorx = .true. <br> , f_strcory = .true. <br> , f_strocnx = .true. <br> , f_strocny = .true. <br> , f_strintx = .false. <br> , f_strinty = .false.<br> , f_strength = .true.<br> , f_divu = .true.<br> , f_shear = .false.<br> , f_sig1 = .false. <br> , f_sig2 = .false. <br> , f_dvidtt = .false. <br> , f_dvidtd = .false. <br> , f_daidtt = .false.<br> , f_daidtd = .false. <br> , f_mlt_onset = .false.<br> , f_frz_onset = .false.<br> , f_dardg1dt = .false.<br> , f_dardg2dt = .false.<br> , f_dvirdgdt = .false.<br> , f_opening = .true.<br> , f_hisnap = .false.<br> , f_aisnap = .false.<br> , f_trsig = .false.<br> , f_icepresent= .false.<br> , f_iage = .false.<br> , f_aicen = .false.<br> , f_vicen = .false.<br> , f_fsurfn_ai = .false.<br> , f_fcondtopn_ai = .false.<br> , f_fmelttn_ai = .false.<br> , f_flatn_ai = .false.<br> /</p> <p> </p> <p> </p>
ECCC simulations: Quality Control for Community Based Sea Ice Model Development
<p>ECCC simulations: Quality Control for Community Based Sea Ice Model Development<br> -----------------------------------------------------------------------------------</p> <p>Data from the Environment and Climate Change Canada (ECCC) simulation by Jean-François Lemieux at Environment and Climate Change Canada, described in the manuscript:</p> <p>Roberts, Hunke, Allard, Bailey, Craig, Lemieux and Turner (2018): Quality Control for Community Based Sea Ice Model Development.</p> <p>It was produced using ECCC with CICE sea ice model version 4.0 with the namelist:</p> <p>&setup_nml<br> days_per_year = 365<br> , year_init = 2001100100<br> , istep0 = 0<br> , dt = 600<br> , npt = 2880<br> , ndyn_dt = 1<br> , runtype = 'continue'<br> , ice_ic = 'default'<br> , restart = .true.<br> , restart_dir = 'not_used_at_cmc'<br> , restart_file = 'not_used_at_cmc'<br> , pointer_file = './ice.restart_file'<br> , dumpfreq = 's'<br> , dumpfreq_n = 2880<br> , diagfreq = 144<br> , diag_type = 'file'<br> , diag_file = 'ice_stdout'<br> , print_global = .false.<br> , print_points = .false.<br> , latpnt(1) = 90.<br> , lonpnt(1) = 0.<br> , latpnt(2) = -65.<br> , lonpnt(2) = -45.<br> , dbug = .false.<br> , histfreq = 's' <br> , histfreq_n = 144<br> , hist_avg = .false.<br> , history_dir = './history/'<br> , history_file = 'iceh'<br> , history_format = 'nc'<br> , write_ic = .false.<br> , incond_dir = './history/'<br> , incond_file = 'iceh_ic'<br> /</p> <p>&grid_nml<br> grid_format = 'cmc'<br> , grid_type = 'cmc'<br> , grid_file = 'not_used_at_cmc'<br> , kmt_file = 'not_used_at_cmc'<br> , kcatbound = 2<br> /</p> <p>&domain_nml<br> nprocs = 72<br> , processor_shape = 'square-pop'<br> , distribution_type = 'cartesian'<br> , distribution_wght = 'block'<br> , ew_boundary_type = 'closed'<br> , ns_boundary_type = 'closed'<br> /</p> <p>&tracer_nml<br> tr_iage = .false.<br> , restart_age = .false.<br> , tr_pond = .false.<br> , restart_pond = .false.<br> /</p> <p>&ice_nml<br> kitd = 1<br> , kdyn = 1<br> , ndte = 900<br> , kstrength = 0<br> , Pstar = 27.5e3<br> , floediam = 300.0<br> , hfrazilmin = 0.05 <br> , iceruf = 0.0004<br> , krdg_partic = 1<br> , krdg_redist = 1<br> , advection = 'remap'<br> , heat_capacity = .true.<br> , shortwave = 'default'<br> , albedo_type = 'default'<br> , albicev = 0.85<br> , albicei = 0.40<br> , albsnowv = 0.98<br> , albsnowi = 0.70 <br> , R_ice = 0.<br> , R_pnd = 0.<br> , R_snw = 0.<br> , atmbndy = 'default'<br> , fyear_init = 1000<br> , ycycle = 1<br> , atm_data_format = 'not_used_at_cmc'<br> , atm_data_type = 'cmc'<br> , atm_data_dir = 'not_used_at_cmc'<br> , calc_strair = .true.<br> , calc_Tsfc = .true.<br> , precip_units = 'mks'<br> , Tfrzpt = 'nonlin'<br> , update_ocn_f = .true.<br> , oceanmixed_ice = .false.<br> , oceanmixed_frc = .false.<br> , ocn_data_format = 'not_used_at_cmc'<br> , sss_data_type = 'cmcint'<br> , sst_data_type = 'cmcint'<br> , ocn_data_dir = 'not_used_at_cmc'<br> , oceanmixed_file = 'not_used_at_cmc'<br> , restore_sst = .false.<br> , trestore = 0<br> , dirassm_ice = .false.<br> , restore_ice = .false.<br> , restore_nul = .false.<br> , l_thermo = .true.<br> , l_dynmcs = .true.<br> , z0io = 0.0165<br> , l_dragio_r = .false.<br> , l_basalstress = .true.<br> , k1 = 8.0<br> , k2 = 15.0<br> , u0 = 5e-5<br> , CC = 20.0<br> , Ktens = 0.05<br> , e_ratio = 1.4<br> /</p> <p>&namcmc_nml<br> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!<br> ! CMC grid parameters (cmc_ln_gemgrid = T ==> grtyp=Z, else grtyp=X)<br> ! The buffer zone is not output <br> ! cmc_ln_bdyopn=T ==> open boundaries including buffer zone<br> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!<br> cmc_ln_gemgrid = .false.<br> , cmc_ln_nemogrid = .true.<br> , cmc_nbuff_zone = 0<br> , cmc_ln_bdyopn = .false.<br> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!<br> ! CMC atmospheric forcing parameters<br> cmc_dt_frcd = -9<br> , cmc_dt_prec = -9<br> , cmc_ln_intrp = .true.<br> , cmc_dateo = '20011001.000000' <br> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!<br> ! Input varables ! Long name (doc only) ! nomvar ! Constant (C) or Field (F) !<br> ! ...! Value (if C) ! Binary (B) or Integer (I) (if F) !<br> ! ...! ip1_1 ! ip1_2 ! scaling ! offset !<br> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!<br> ! Grid ...<br> cmc_ulat = 'u-Lat(deg)','ULAT','F',-999.0,'B',-1 ,-1 , 1., 0.<br> cmc_ulon = 'u-Lon(deg)','ULON','F',-999.0,'B',-1 ,-1 , 1., 0.<br> cmc_tlat = 't-Lat(deg)','TLAT','F',-999.0,'B',-1 ,-1 , 1., 0.<br> cmc_tlon = 't-Lon(deg)','TLON','F',-999.0,'B',-1 ,-1 , 1., 0.<br> cmc_kmt = 'Mask (0-1)','KMT', 'F',-999.0,'I',-1 ,-1 , 1., 0.<br> cmc_hte = 'HTE (m) ','HTE' ,'F',-999.0,'B',-1 ,-1 , 1., 0.<br> cmc_htn = 'HTN (m) ','HTN' ,'F',-999.0,'B',-1 ,-1 , 1., 0.<br> ! Ice-ocean state ...<br> cmc_ln_gslcat = .false.<br> cmc_ln_wmocat = .false.<br> cmc_ln_avgcat = .true.<br> cmc_ln_itdspr = .true.<br> cmc_gl = 'GL de CMC ','GL' ,'F',-999.0,'B',-1 ,-1 , 1., 0.<br> cmc_i8 = 'I8 de CMC ','I8' ,'F',-999.0,'B',-1 ,-1 , 1., 0.<br> cmc_uice0 = 'U ice Vel.','null','C', 0.0,' ',-999999999,-999999999, -999., -999.<br> cmc_vice0 = 'V ice Vel.','null','C', 0.0,' ',-999999999,-999999999, -999., -999.<br> ! Ocean forcing ...<br> cmc_ln_frcsss = .false.<br> cmc_ln_frcsst = .false.<br> cmc_ln_frcuvo = .false.<br> ! Atm forcing ... (for ice I. C. internal temp override by restart)<br> cmc_tair = 'Air temp ','TT', 'C', 273.15,' ',999999999,999999999, 999., 999.<br> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!<br> ! Mixed layer parameters<br> cmc_frzeps = 0.0005<br> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!<br> ! Output parameters (cmc_ofmt='F' or 'H', Forecast or Hindcast style)<br> cmc_ofmt = 'H'<br> cmc_npako = -32<br> cmc_ln_stdrsti = .true.<br> cmc_ln_stdrsto = .true.<br> cmc_npakri = -64<br> cmc_npakro = -64<br> cmc_etiket = 'CREG_HCST'<br> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!<br> /</p> <p>&icefields_nml<br> f_tmask = .false.<br> , f_tarea = .false.<br> , f_uarea = .false.<br> , f_dxt = .false.<br> , f_dyt = .false.<br> , f_dxu = .false.<br> , f_dyu = .false.<br> , f_HTN = .false.<br> , f_HTE = .false.<br> , f_ANGLE = .false.<br> , f_ANGLET = .false.<br> , f_bounds = .false.<br> , f_hi = .true.<br> , f_hs = .false. <br> , f_Tsfc = .false. <br> , f_aice = .true. <br> , f_uvel = .false. <br> , f_vvel = .false. <br> , f_fswdn = .false. <br> , f_flwdn = .false.<br> , f_snow = .false. <br> , f_snow_ai = .false. <br> , f_rain = .false. <br> , f_rain_ai = .false. <br> , f_sst = .false. <br> , f_sss = .false. <br> , f_uocn = .false. <br> , f_vocn = .false. <br> , f_frzmlt = .false.<br> , f_fswfac = .false.<br> , f_fswabs = .false. <br> , f_fswabs_ai = .false. <br> , f_albsni = .false. <br> , f_alvdr = .false.<br> , f_alidr = .false.<br> , f_albice = .false.<br> , f_albsno = .false.<br> , f_albpnd = .false.<br> , f_coszen = .false.<br> , f_flat = .false. <br> , f_flat_ai = .false. <br> , f_fsens = .false. <br> , f_fsens_ai = .false. <br> , f_flwup = .false. <br> , f_flwup_ai = .false. <br> , f_evap = .false. <br> , f_evap_ai = .false. <br> , f_Tair = .false. <br> , f_Tref = .false. <br> , f_Qref = .false.<br> , f_congel = .false. <br> , f_frazil = .false. <br> , f_snoice = .false. <br> , f_meltt = .false.<br> , f_meltb = .false.<br> , f_meltl = .false.<br> , f_fresh = .false.<br> , f_fresh_ai = .false.<br> , f_fsalt = .false.<br> , f_fsalt_ai = .false.<br> , f_fhocn = .false. <br> , f_fhocn_ai = .false. <br> , f_fswthru = .false. <br> , f_fswthru_ai = .false. <br> , f_fsurf_ai = .false.<br> , f_fcondtop_ai = .false.<br> , f_fmeltt_ai = .false. <br> , f_strairx = .false. <br> , f_strairy = .false. <br> , f_strtltx = .false. <br> , f_strtlty = .false. <br> , f_strcorx = .false. <br> , f_strcory = .false. <br> , f_strocnx = .false. <br> , f_strocny = .false. <br> , f_strintx = .false. <br> , f_strinty = .false.<br> , f_strength = .false.<br> , f_divu = .false.<br> , f_shear = .false.<br> , f_sig1 = .false. <br> , f_sig2 = .false. <br> , f_sigI = .false. <br> , f_dvidtt = .false. <br> , f_dvidtd = .false. <br> , f_daidtt = .false.<br> , f_daidtd = .false. <br> , f_mlt_onset = .false.<br> , f_frz_onset = .false.<br> , f_dardg1dt = .false.<br> , f_dardg2dt = .false.<br> , f_dvirdgdt = .false.<br> , f_opening = .false.<br> , f_hisnap = .false.<br> , f_aisnap = .false.<br> , f_trsig = .false.<br> , f_icepresent = .false.<br> , f_iage = .false.<br> , f_aicen = .false.<br> , f_vicen = .false.<br> , f_fsurfn_ai = .false.<br> , f_fcondtopn_ai = .false.<br> , f_fmelttn_ai = .false.<br> , f_flatn_ai = .false.<br> , f_apondn = .false.<br> , f_tau_bu = .false.<br> , f_tau_bv = .false.<br> /</p> <p> </p>
2SPT Test Time Series: Quality Control for Community Based Sea Ice Model Development
<p>2SPT Test Time Series: Quality Control for Community Based Sea Ice Model Development</p> <p>------------------------------------------------------------------------------------</p> <p>This dataset comes from Regional Arctic System Model (RASM) simulations by Andrew F. Roberts at Naval Postgraduate School, described and used in Figure 3 in the manuscript:</p> <p>Roberts, Hunke, Allard, Bailey, Craig, Lemieux and Turner (2018): Quality Control for Community Based Sea Ice Model Development.</p> <p>Files for the series in Figure 3 as they appear in that paper to demonstrate the Two-Stage Paired Thickness Test:</p> <p>Figure 3a:</p> <p>R1009RBRcevp01a.cice.h.hi.1996_2000.North_Pole.nc</p> <p>R1009RBRcevp01a_2.cice.h.hi.1996_2000.North_Pole.nc</p> <p> </p> <p>Figure 3b:</p> <p>R1009RBRcevp01a.cice.h.hi.1996_2000.North_Pole.nc</p> <p>R1009RBRceap01a.cice.h.hi.1996_2000.North_Pole.nc</p> <p> </p> <p>Figure 3c:</p> <p>R1009RBRcevp01a.cice.h.hi.1996_2000.North_Bathurst_Island.nc</p> <p>R1009RBRceap01a.cice.h.hi.1996_2000.North_Bathurst_Island.nc</p> <p> </p> <p>Where the name "evp" or "eap" in the file name corresponds to the EVP and EAP simulations as described in the manuscript. These are selected timeseries from 1996 to 2000 from the RASM simasimulations described in section 2 of the above manuscript. CICE namelist settings are identical to the description for the dataset:</p> <p>Roberts, A. (2018). RASM simulations: Quality Control for Community Based Sea Ice Model Development [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1308236</p> <p> </p>
Towards a Theory of Software Development Expertise — Supplementary Material
<p>Software development includes diverse tasks such as implementing new features, analyzing requirements, and fixing bugs. Being an expert in those tasks requires a certain set of skills, knowledge, and experience. Several studies investigated individual aspects of software development expertise, but what is missing is a comprehensive theory. We present a first conceptual theory of software development expertise that is grounded in data from a mixed-methods survey with 335 software developers and in literature on expertise and expert performance. Our theory currently focuses on programming, but already provides valuable insights for researchers, developers, and employers. The theory describes important properties of software development expertise and which factors foster or hinder its formation, including how developers' performance may decline over time. Moreover, our quantitative results show that developers' expertise self-assessments are context-dependent and that experience is not necessarily related to expertise.</p>
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