Dataset Information

Nielsen1998_Glycolysis

ABSTRACT: This model was automatically converted from model BIOMD0000000042 by using libSBML . According to the BioModels Database terms of use , this generated model is not related with model BIOMD0000000042 any more.

SUBMITTER: Nicolas Le Novère

PROVIDER: BIOMD0000000042 | BioModels | 2024-09-02

REPOSITORIES: BioModels

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	BIOMD0000000042?filename=BIOMD0000000042-biopax2.owl	Owl
	BIOMD0000000042?filename=BIOMD0000000042-biopax3.owl	Owl
	BIOMD0000000042?filename=BIOMD0000000042-matlab.m	Other
	BIOMD0000000042?filename=BIOMD0000000042-octave.m	Other
	BIOMD0000000042?filename=BIOMD0000000042.cps	Other

Items per page:

1 - 5 of 18

Publications

Sustained oscillations in glycolysis: an experimental and theoretical study of chaotic and complex periodic behavior and of quenching of simple oscillations.

Nielsen K K Sørensen P G PG Hynne F F Busse H G HG

Biophysical chemistry 19980501 1-2

We report sustained oscillations in glycolysis conducted in an open system (a continuous-flow, stirred tank reactor; CSTR) with inflow of yeast extract as well as glucose. Depending on the operating conditions, we observe simple or complex periodic oscillations or chaos. We report the response of the system to instantaneous additions of small amounts of several substrates as functions of the amount added and the phase of the addition. We simulate oscillations and perturbations by a kinetic model ...[more]

PMID: 17029704

Publication: 1/3

Similar Datasets

Project description:Datasets contain protein identification and raw data from MALDI protein identifications. Identified proteins resulted from a comparison of GLC1 and GLC1 SCLC cell lines using 2D DIGE. MALDI-TOF-MS analyses were performed on an UltraFlexTM II (Bruker Daltonics) instrument according to the instructions of the manufacturer. The instrument was equipped with a scoutTM MTP MALDI target. The spectra were acquired in the positive ion mode according to the settings given by the manufacturer. For external calibration, a peptide standard (m/z 757.399, 1296.684, 1619.822, 2093.086 and 3147.471) was used. The MALDI-PMF spectra were processed using the FlexAnalysis™ 2.4 software (Bruker Daltonics) and converted in the .xml format. For peak detection, the spectra were subjected to an internal recalibration using 13 different monoisotopic masses from autolysis products of trypsin and fragments of keratins ranging from m/z 842.509 – 2825.406. Following parameters were applied: snap peak detection algorithm, signal to noise threshold of 6, maximal number of peaks 100, quality factor threshold 50 and baseline subtraction TopHat. The generated mass lists were subsequently sent to ProteinScapeTM 1.3 (Bruker Daltonics, Bremen, Germany), triggering database searches using ProFound (Version 2002.03.01, Proteometrics LLC) and MASCOT (Version 2.3.02, Matrix Science, London, UK). The following search parameters were selected: fixed cysteine modification with propionamide, variable modification due to methionine oxidation, one maximal missed cleavage sites in case of incomplete trypsin hydrolysis and no details about 2-DE derived protein mass and pI. Using the Score booster function of ProteinScapeTM the mass lists were recalibrated and background masses removed using a list containing 44 masses occurring in a minimum of 10% of generated peak lists. The database searches were run with a mass tolerance of 40 ppm using UniProt’s human complete proteome set (downloaded on 26.10.2012) containing 68.109 protein entries. The used database is a composite database consisting of the UniProtKB entries and a duplicate of the same database, in which the amino acid sequence of each protein entry was randomly shuffled. Proteins reaching Profound score > 1.5 or Mascot score > 64 were considered as identified. Using these criteria one decoy database entry was found by the search engines indicating high confidence of protein identifications. If several database entries of homologues proteins matched these criteria only the entry with the highest score was reported.