Mercurial > repos > tduigou > doe_synbio_optdoe
changeset 3:645d10db2819 draft default tip
planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 537d7fefe58984b8f7ca66010153a2fdc35ddf4b
| author | tduigou |
|---|---|
| date | Wed, 14 Feb 2024 15:24:27 +0000 |
| parents | 8376287c2c02 |
| children | |
| files | optdoe.xml test-data/converter_proCFPS_parameters.tsv test-data/sampler/input/parameters.tsv test-data/sampler/output/sampling.test-1.tsv test-data/sampler/output/sampling.test-2.tsv test-data/sampler_sampling.test-1.tsv test-data/sampler_sampling.test-2.tsv |
| diffstat | 7 files changed, 227 insertions(+), 235 deletions(-) [+] |
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--- a/optdoe.xml Tue May 30 21:02:09 2023 +0000 +++ b/optdoe.xml Wed Feb 14 15:24:27 2024 +0000 @@ -187,23 +187,23 @@ Note: if advanced parameter "input_parts" is left empty, the following parts are used: - +---------+------------+--------------------------------------------------+ - | Name | Type | SynBioHub | - +=========+============+==================================================+ - | PlacUV5 | Promoter | https://synbiohub.org/public/igem/BBa_K1847014/1 | - +---------+------------+--------------------------------------------------+ - | Ptrc | Promoter | https://synbiohub.org/public/igem/BBa_J56012/1 | - +---------+------------+--------------------------------------------------+ - | BBR1 | Origin | https://synbiohub.org/public/igem/BBa_I50041/1 | - +---------+------------+--------------------------------------------------+ - | p15A | Origin | https://synbiohub.org/public/igem/BBa_I50032/1 | - +---------+------------+--------------------------------------------------+ - | ColE1 | Origin | https://synbiohub.org/public/igem/BBa_J64101/1 | - +---------+------------+--------------------------------------------------+ - | res1 | Resistance | https://synbiohub.org/public/igem/BBa_I13800/1 | - +---------+------------+--------------------------------------------------+ - | Ter | Terminator | https://synbiohub.org/public/igem/BBa_B1006/1 | - +---------+------------+--------------------------------------------------+ + +---------+------------+--------------+ + | Name | Type | SynBioHub | + +=========+============+==============+ + | PlacUV5 | Promoter | BBa_K1847014 | + +---------+------------+--------------+ + | Ptrc | Promoter | BBa_J56012 | + +---------+------------+--------------+ + | BBR1 | Origin | BBa_I50041 | + +---------+------------+--------------+ + | p15A | Origin | BBa_I50032 | + +---------+------------+--------------+ + | ColE1 | Origin | BBa_J64101 | + +---------+------------+--------------+ + | res1 | Resistance | BBa_I13800 | + +---------+------------+--------------+ + | Ter | Terminator | BBa_B1006 | + +---------+------------+--------------+ The source of this file can be found here as a model: https://raw.githubusercontent.com/pablocarb/doebase/master/doebase/data/ref_parts.csv
--- a/test-data/converter_proCFPS_parameters.tsv Tue May 30 21:02:09 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -Parameter maxValue stockConcentration deadVolume Ratios -Mg-glutamate 4 168 0 0.0 0.1 0.3 0.5 1.0 -k-glutamate 80 3360 0 -CoA 0.26 210 0 -3-PGA 30 1400 0 -NTP 1.5 630 0 -NAD 0.33 138.6 0 -Folinic acid 0.068 28.56 0 -Spermidine 1 420 0 -tRNA 0.2 84 0 -Amino acids 1.5 6 0 -CAMP 0.75 200 0 -Extract 30 300 2000 1 -HEPES 50 2100 0 1 -PEG 2 200 4000 1 -Promoter 10 300 0 1 -RBS 10 200 0 1 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampler/input/parameters.tsv Wed Feb 14 15:24:27 2024 +0000 @@ -0,0 +1,9 @@ +Component maxValue Ratios +Component_1 125 0.0 0.1 0.3 0.5 1.0 +Component_2 125 1 +Component_3 125 +Component_4 125 +Component_5 125 +Component_6 125 +Component_7 125 +Component_8 125
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampler/output/sampling.test-1.tsv Wed Feb 14 15:24:27 2024 +0000 @@ -0,0 +1,100 @@ +Component_1 Component_2 Component_3 Component_4 Component_5 Component_6 Component_7 Component_8 +0.0 125.0 125.0 0.0 31.25 93.75 62.5 93.75 +37.5 125.0 31.25 93.75 125.0 62.5 125.0 125.0 +37.5 125.0 0.0 93.75 31.25 31.25 31.25 0.0 +37.5 125.0 31.25 62.5 125.0 125.0 93.75 93.75 +12.5 125.0 31.25 31.25 93.75 125.0 31.25 31.25 +125.0 125.0 31.25 93.75 125.0 0.0 125.0 93.75 +0.0 125.0 93.75 0.0 93.75 125.0 31.25 125.0 +125.0 125.0 125.0 31.25 0.0 0.0 125.0 31.25 +37.5 125.0 125.0 125.0 125.0 93.75 62.5 0.0 +125.0 125.0 62.5 62.5 62.5 62.5 0.0 0.0 +62.5 125.0 93.75 0.0 93.75 62.5 62.5 62.5 +37.5 125.0 93.75 62.5 93.75 0.0 93.75 0.0 +125.0 125.0 62.5 62.5 93.75 93.75 93.75 125.0 +37.5 125.0 0.0 93.75 125.0 125.0 62.5 0.0 +0.0 125.0 31.25 0.0 0.0 0.0 93.75 0.0 +37.5 125.0 62.5 31.25 0.0 93.75 93.75 62.5 +12.5 125.0 31.25 62.5 125.0 125.0 125.0 62.5 +12.5 125.0 62.5 62.5 31.25 125.0 125.0 125.0 +125.0 125.0 0.0 125.0 31.25 62.5 93.75 31.25 +12.5 125.0 31.25 0.0 62.5 93.75 125.0 93.75 +62.5 125.0 0.0 125.0 0.0 31.25 125.0 31.25 +12.5 125.0 0.0 93.75 62.5 93.75 0.0 93.75 +0.0 125.0 62.5 125.0 62.5 125.0 0.0 125.0 +62.5 125.0 31.25 125.0 62.5 31.25 0.0 93.75 +37.5 125.0 0.0 62.5 0.0 62.5 62.5 31.25 +62.5 125.0 0.0 0.0 93.75 31.25 62.5 0.0 +12.5 125.0 0.0 93.75 0.0 62.5 31.25 31.25 +0.0 125.0 62.5 0.0 31.25 62.5 31.25 31.25 +125.0 125.0 0.0 125.0 125.0 31.25 62.5 62.5 +0.0 125.0 31.25 31.25 125.0 31.25 125.0 31.25 +12.5 125.0 31.25 0.0 125.0 0.0 62.5 93.75 +125.0 125.0 62.5 31.25 62.5 93.75 0.0 62.5 +37.5 125.0 125.0 62.5 0.0 0.0 125.0 0.0 +125.0 125.0 93.75 31.25 93.75 125.0 0.0 0.0 +0.0 125.0 62.5 31.25 0.0 62.5 93.75 62.5 +37.5 125.0 125.0 93.75 93.75 62.5 62.5 93.75 +12.5 125.0 31.25 62.5 0.0 0.0 0.0 93.75 +125.0 125.0 31.25 125.0 93.75 0.0 31.25 0.0 +62.5 125.0 93.75 0.0 62.5 125.0 31.25 125.0 +12.5 125.0 0.0 62.5 31.25 31.25 31.25 93.75 +62.5 125.0 93.75 31.25 125.0 125.0 62.5 125.0 +0.0 125.0 62.5 93.75 125.0 93.75 62.5 31.25 +37.5 125.0 93.75 93.75 62.5 31.25 0.0 0.0 +37.5 125.0 93.75 125.0 0.0 0.0 93.75 0.0 +0.0 125.0 62.5 0.0 31.25 93.75 93.75 0.0 +125.0 125.0 125.0 31.25 31.25 125.0 31.25 93.75 +62.5 125.0 125.0 93.75 31.25 31.25 0.0 125.0 +0.0 125.0 62.5 125.0 93.75 93.75 0.0 31.25 +37.5 125.0 31.25 31.25 0.0 62.5 62.5 0.0 +12.5 125.0 0.0 0.0 31.25 93.75 62.5 125.0 +62.5 125.0 0.0 125.0 125.0 93.75 93.75 0.0 +0.0 125.0 93.75 93.75 31.25 125.0 0.0 62.5 +125.0 125.0 0.0 0.0 93.75 31.25 31.25 62.5 +37.5 125.0 125.0 31.25 93.75 0.0 93.75 93.75 +62.5 125.0 31.25 0.0 93.75 31.25 125.0 0.0 +0.0 125.0 62.5 62.5 62.5 31.25 31.25 93.75 +37.5 125.0 125.0 62.5 62.5 0.0 93.75 62.5 +62.5 125.0 62.5 125.0 62.5 125.0 31.25 62.5 +125.0 125.0 0.0 31.25 125.0 93.75 93.75 31.25 +37.5 125.0 62.5 125.0 62.5 62.5 31.25 62.5 +12.5 125.0 0.0 31.25 0.0 62.5 62.5 125.0 +12.5 125.0 93.75 93.75 31.25 125.0 125.0 125.0 +12.5 125.0 93.75 93.75 31.25 31.25 31.25 93.75 +62.5 125.0 0.0 31.25 31.25 31.25 125.0 62.5 +37.5 125.0 31.25 93.75 125.0 62.5 0.0 62.5 +0.0 125.0 125.0 125.0 0.0 62.5 125.0 125.0 +62.5 125.0 31.25 125.0 0.0 31.25 93.75 31.25 +125.0 125.0 93.75 125.0 125.0 125.0 31.25 62.5 +12.5 125.0 62.5 31.25 62.5 93.75 125.0 31.25 +12.5 125.0 0.0 125.0 93.75 0.0 31.25 31.25 +12.5 125.0 93.75 125.0 125.0 62.5 93.75 31.25 +0.0 125.0 93.75 93.75 62.5 31.25 0.0 125.0 +62.5 125.0 125.0 0.0 93.75 0.0 125.0 93.75 +0.0 125.0 0.0 0.0 31.25 62.5 0.0 62.5 +62.5 125.0 62.5 31.25 31.25 62.5 31.25 125.0 +62.5 125.0 125.0 93.75 31.25 0.0 0.0 93.75 +125.0 125.0 62.5 0.0 125.0 125.0 93.75 62.5 +125.0 125.0 31.25 125.0 0.0 31.25 93.75 62.5 +0.0 125.0 125.0 62.5 93.75 0.0 0.0 31.25 +125.0 125.0 125.0 31.25 62.5 0.0 0.0 62.5 +0.0 125.0 0.0 31.25 93.75 31.25 62.5 31.25 +125.0 125.0 93.75 93.75 93.75 93.75 62.5 125.0 +0.0 125.0 125.0 31.25 62.5 0.0 62.5 125.0 +12.5 125.0 93.75 62.5 0.0 125.0 93.75 93.75 +12.5 125.0 125.0 0.0 125.0 62.5 0.0 62.5 +37.5 125.0 31.25 93.75 0.0 125.0 0.0 125.0 +0.0 125.0 93.75 0.0 62.5 125.0 31.25 125.0 +62.5 125.0 125.0 93.75 125.0 31.25 125.0 0.0 +125.0 125.0 93.75 62.5 62.5 0.0 125.0 125.0 +62.5 125.0 93.75 62.5 31.25 93.75 31.25 125.0 +37.5 125.0 31.25 0.0 93.75 93.75 125.0 93.75 +0.0 125.0 0.0 125.0 31.25 93.75 125.0 31.25 +62.5 125.0 125.0 31.25 62.5 62.5 62.5 0.0 +62.5 125.0 62.5 93.75 93.75 31.25 93.75 0.0 +62.5 125.0 93.75 62.5 31.25 0.0 125.0 93.75 +12.5 125.0 31.25 0.0 0.0 0.0 93.75 93.75 +12.5 125.0 125.0 62.5 125.0 93.75 62.5 31.25 +125.0 125.0 125.0 125.0 0.0 93.75 31.25 31.25 +125.0 125.0 62.5 62.5 0.0 125.0 0.0 0.0
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