mechanism_id	part_id	param_name	param_val	comments
	e coli	Ribo	150	uM assuming ~100000 Ribosomes / e. coli with a volume 1 um^3
	e coli	RNAP	15	uM assuming ~10000 RNAP molecules / e. coli with a volume 1 um^3
	e coli	RNAase	45	uM assuming ~30000 RNAP molecules / e. coli with a volume 1 um^4
	e coli	cellular_processes	5	somewhat arbitary concentration for ~3000 genes in e. coli assuming weak loading on all of them
	e coli extract	protein_Ribo	24	1/5 th the Ribosome concentration of E. Coli
	e coli extract	protein_RNAP	3	1/5 th the rnap concentration of E. Coli
	e coli extract	protein_RNAase	6	1/5 th the rnaase concentration of E. Coli
	e coli extract 2	protein_Ribo	12	
	e coli extract 2	protein_RNAP	6	
	e coli extract 2	protein_RNAase	3	
		ktx	0.05	transcripts / second per polymerase assuming 50nt/s and transcript length of 1000
		ktl	0.05	proteins / second per ribosome assuming 15aa/s and protein length of 300
		cooperativity	2	Seems like a good default
		kb	100	assuming 10ms to diffuse across 1um (characteristic cell size)
		ku	10	"""90% binding"""
		kdil	0.001	assuming half life of ~20 minutes for everything (e coli doubling time)
rna_degredation_mm		kdeg	0.001	assuming a half life of ~10 minutes for mRNA
rna_degredation		kdil	0.001	assuming a half life of ~10 minutes for mRNA
simple_transcription		ktx	0.1	Assuming ~10% of e coli rnap working at ktx above
simple_translation		ktl	0.25	Assuming ~5% of e coli ribosomes working at ktx above
gene_expression		kexpress	0.28125	The product of the above two rates
negativehill_transcription		k	0.01875	Estimates from Repressilator paper and the above numbers
negativehill_transcription		K	20	Estimates from Repressilator paper and the above numbers
negativehill_transcription		n	2	Estimates from Repressilator paper and the above numbers
negativehill_transcription		kleak	0.000001	Estimates from Repressilator paper and the above numbers
	J23103	ku	588.2352941	Anderson promoter (17x) strengths are proportional but gain factor is arbitrary
	J23116	ku	25.25252525	Anderson promoter (396x) strengths are proportional but gain factor is arbitrary
	J23107	ku	11.01321586	Anderson promoter (908x) strengths are proportional but gain factor is arbitrary
	J23106	ku	8.438818565	Anderson promoter (1185x) strengths are proportional but gain factor is arbitrary
	J23102	ku	4.589261129	Anderson promoter (2179x) strengths are proportional but gain factor is arbitrary
	J23100	ku	3.926187672	Anderson promoter (2547x) strengths are proportional but gain factor is arbitrary
simple_transcription	J23103	ktx	0.0031875	Above rescaled by ktx for simple transcription
simple_transcription	J23116	ktx	0.07425	Above rescaled by ktx for simple transcription
simple_transcription	J23107	ktx	0.17025	Above rescaled by ktx for simple transcription
simple_transcription	J23106	ktx	0.2221875	Above rescaled by ktx for simple transcription
simple_transcription	J23102	ktx	0.4085625	Above rescaled by ktx for simple transcription
simple_transcription	J23100	ktx	0.4775625	Above rescaled by ktx for simple transcription
	BCD2	ku	0.5	Strong BCD param value made up
	BCD8	ku	10	Weak BCD param value made up
	BCD12	ku	5	medium BCD param value made up
simple_translation	BCD2	ktl	0.6	Above rescaled by ktl for simple translation
simple_translation	BCD8	ktl	0.075	Above rescaled by ktl for simple translation
simple_translation	BCD12	ktl	0.06	Above rescaled by ktl for simple translation
	strong	ku	0.5	Strong BCD param value made up
	medium	ku	10	Weak BCD param value made up
	weak	ku	5	medium BCD param value made up
simple_translation	strong	ktl	0.6	Above rescaled by ktl for simple translation
simple_translation	medium	ktl	0.075	Above rescaled by ktl for simple translation
simple_translation	weak	ktl	0.06	Above rescaled by ktl for simple translation
	weak	ktx	588.2352941	Anderson promoter (17x) strengths are proportional but gain factor is arbitrary
	medium	ktx	8.438818565	Anderson promoter (1185x) strengths are proportional but gain factor is arbitrary
	strong	ktx	3.926187672	Anderson promoter (2547x) strengths are proportional but gain factor is arbitrary
simple_transcription	weak	ktx	0.0031875	Above rescaled by ktx for simple transcription
simple_transcription	medium	ktx	0.2221875	Above rescaled by ktx for simple transcription
simple_transcription	strong	ktx	0.4775625	Above rescaled by ktx for simple transcription
	combinatorial_promoter_leak	ktx	0.0005	1% of ktx default
	combinatorial_promoter_leak	kexpress	0.0028125	1% of kexpress default
	regulated_promoter_leak	ktx	0.0005	1% of ktx default
	regulated_promoter_leak	kexpress	0.0028125	1% of kexpress default