ypd: In Sillico YPD Medium
In sybil: Efficient Constrained Based Modelling

Description Usage Arguments Details Value Author(s) References See Also

Apply in sillico medium to bakers yeast metabolic network model iND750 by Duarte et al. 2004.

1	ypd(model, def_bnd = SYBIL_SETTINGS("MAXIMUM"), ver = "harrison2007")

`model`	An object of class `modelorg`.
`def_bnd`	A single numeric value. Absolute value for uppper and lower bounds for reaction bounds. Default: `SYBIL_SETTINGS("MAXIMUM")`.
`ver`	A single character string giving the version of the YPD medium. Can be set to `harrison2007` or `bilu2006` (see Details below). Default: `harrison2007`.

The function ypd identifies exchange reactions via the function findExchReact. The lower bounds of all exchange fluxes is set to zero (not allowing any flux into the network) and the upper bounds are set to the value of def_bnd (default: output is unbounded). The lower bound input of the input fluxes is set like in the table below.

Two different versions of YPD medium are available: Harrison et al. 2007 and Bilu et al. 2006.

Harrison et al 2007:

`EX_ala_L(e)`	-0.5
`EX_arg_L(e)`	-0.5
`EX_asn_L(e)`	-0.5
`EX_asp_L(e)`	-0.5
`EX_chol(e)`	-0.5
`EX_cys_L(e)`	-0.5
`EX_dcyt(e)`	-0.5
`EX_ergst(e)`	-0.5
`EX_glc(e)`	-20
`EX_glu_L(e)`	-0.5
`EX_gly(e)`	-0.5
`EX_gua(e)`	-0.5
`EX_h(e)`	`def_bnd * -1`
`EX_hdca(e)`	-0.5
`EX_his_L(e)`	-0.5
`EX_leu_L(e)`	-0.5
`EX_lys_L(e)`	-0.5
`EX_met_L(e)`	-0.5
`EX_nh4(e)`	`def_bnd * -1`
`EX_o2(e)`	-2
`EX_ocdca(e)`	-0.5
`EX_pi(e)`	`def_bnd * -1`
`EX_pro_L(e)`	-0.5
`EX_ser_L(e)`	-0.5
`EX_so4(e)`	`def_bnd * -1`
`EX_thr_L(e)`	-0.5
`EX_thymd(e)`	-0.5
`EX_trp_L(e)`	-0.5
`EX_ttdca(e)`	-0.5
`EX_tyr_L(e)`	-0.5
`EX_ura(e)`	-0.5

Bilu et al 2006:

`EX_nh4(e)`	`def_bnd * -1`
`EX_pi(e)`	`def_bnd * -1`
`EX_so4(e)`	`def_bnd * -1`
`EX_glc(e)`	-20
`EX_o2(e)`	-2
`EX_ala_L(e)`	-0.5
`EX_arg_L(e)`	-0.5
`EX_asn_L(e)`	-0.5
`EX_asp_L(e)`	-0.5
`EX_cys_L(e)`	-0.5
`EX_his_L(e)`	-0.5
`EX_leu_L(e)`	-0.5
`EX_lys_L(e)`	-0.5
`EX_met_L(e)`	-0.5
`EX_pro_L(e)`	-0.5
`EX_ser_L(e)`	-0.5
`EX_thr_L(e)`	-0.5
`EX_trp_L(e)`	-0.5
`EX_tyr_L(e)`	-0.5
`EX_dcyt(e)`	-0.5
`EX_gly(e)`	-0.5
`EX_gua(e)`	-0.5
`EX_thymd(e)`	-0.5
`EX_h2o(e)`	`def_bnd * -1`
`EX_na1(e)`	`def_bnd * -1`
`EX_k(e)`	`def_bnd * -1`
`EX_co2(e)`	`def_bnd * -1`
`EX_ade(e)`	-0.5
`EX_gln_L(e)`	-0.5
`EX_ile_L(e)`	-0.5
`EX_phe_L(e)`	-0.5
`EX_val_L(e)`	-0.5

An instance of class modelorg with input fluxes set corresponding to the desired YPD medium.

Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>

Maintainer: Mayo Roettger <mayo.roettger@hhu.de>

Harrison, R., Papp, B., Pal, C., Oliver, S. G. and Delnert, D. (2007) Plasticity of genetic interactions in metabolic networks of yeast. PNAS 104, 2307–2312.

Bilu, Y., Shlomi, T., Barkai, N. and Ruppin, E. (2006) Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states. PLoS Comput Biol 2, 932–938.

modelorg, findExchReact and SYBIL_SETTINGS

sybil documentation built on May 31, 2021, 5:08 p.m.