Nielsen Group resources
We run the Queenlsand Node of Metabolomics Australia. The facility is available to the public.
Genome Databases
We have developed Biocyc databases and genome scale models for most of the organisms we work with.
Mouse GEM - SBML for mouse genome scale model
Quek L-E, Nielsen LK (2008) On the reconstruction of the Mus musculus genome-scale metabolic network model. Genome Informatics 21:89-100.
AraFlux - A Matlab Toolbox for performing flux analysis using AraGEM genome scale model
de Oliveira Dal'molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK (2010) AraGEM - a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis thaliana. Plant Physiol. 152: 579–589. PMID: 20044452.
AraGEM COBRA - AraGEM SBML file for use with COBRA Toolbox in Matlab
de Oliveira Dal'molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK (2010) AraGEM - a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis thaliana. Plant Physiol. 152: 579–589. PMID: 20044452.
Mammalian MFA - Matlab files for mammalian cell culture MFA using reduced Mouse GEM
Quek L-E, Dietmair S; Kr?mer JO, Nielsen LK (2010) Metabolic flux analysis in mammalian cell culture. Metabolic Engineering 12: 161-171. PMID: 19833223.
C4GEM - SBML models for maize, sorghum and sugarcane
de Oliveira Dal'molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK (2010) C4GEM - Genome-Scale Metabolic Model to study C4 plant metabolism. Plant Physiol. 154:1871-85. PMID: 20974891.
C4 Flux Toolbox - Matlab Flux Toolbox with maize example
de Oliveira Dal'molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK (2010) C4GEM - Genome-Scale Metabolic Model to study C4 plant metabolism. Plant Physiol. 154:1871-85. PMID: 20974891.
iCA1273 version 1.01 - E. coli W genome scale model
Archer CT, Kim JF, Jeong H, Park JH, Vickers CE, Lee SY, Nielsen LK (2011) The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli. BMC Genomics 12:9. PMID: 21208457.
AlgaGEM - AlgaGEM SBML file for use with COBRA Toolbox in Matlab
Dal’Molin CGO, Quek LE, Palfreyman RW, Nielsen LK (2011) AlgaGEM - A genome-scale metabolic reconstruction of Algae based on Chlamydomonas reinhardtii genome. BMC Genomics 12(Supp 4): S5.http://www.biomedcentral.com/1471-2164/12/S4/S5.
Software
We make our software packages available.
Examples of Dirichlet Kernels (Bioinformatics submission)
The attached examples are for a submission in Bioinformatics only. Download: Dirichlet Kernel.zip
Fast-SNP
Saa PA, Nielsen LK (2016) Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models. Bioinformatics 32: 3807–3814.
Download: Fast_SNP_v10_10_16.zip
ll-ACHRB
Saa PA, Nielsen LK (2016) ll-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks. Bioinformatics 32: 2330–2337.
ll-ACHRB software ver 1.1 (introduces faster warm up using efficient loopless optimization): ll_ACHRB ver 1.1.zip
B-DMFA
Martínez VS, Buchsteiner M, Gray P, Nielsen LK, Quek LE (2015) Dynamic Metabolic Flux Analysis using B-splines to study the effects of temperature shift on CHO cell metabolism. Met Eng Comm 2: 46-57.
B-DMFA is available either as quadratic spline or generic order.
MultiGEM - multi-tissue GEM framework
Dal'molin CGDO, Quek LE, Saa PA, Nielsen LK (2015) A multi-tissue genome-scale metabolic modelling framework for the analysis of whole plant systems. Front. Plant Sci. 6:4. Online.
Download software from this site.
Supplementary Data for OpenFlux
Quek L-E, Wittmann C, Nielsen LK, Kroemer JO (2009) OpenFLUX: Efficient Modelling Software for 13C-Based Metabolic Flux Analysis. Microbial Cell Factories 8:25. PMID: 19409084.
Quek LE, Nielsen LK (2014) Steady-State 13C Fluxomics Using OpenFLUX. In: Krömer JO, Nielsen LK, Blank LM (eds) Metabolic Flux Analysis: Methods and Protocols. Series: Methods in Molecular Biology, vol. 1191. Chapter 13: 65-78. PMID: 25178793.
Registration (please register for use of OpenFlux)
C. glutamicum model (Excel file)
PathLogic
Fearnley LG, Nielsen LK (2012) PATHLOGIC-S: A scalable Boolean framework for modelling cellular signalling. PLoS ONE 7(8): e41977. PMID: 22879903.
Available from Sourceforge.
NExT
Martínez VS, Quek LE, Nielsen LK ( 2014) Network thermodynamic curation of human and yeast genome-scale metabolic models. Biophys J 107:493-503. PMID: 25028891.
Martinez VS, Nielsen LK (2014) NExT: Integration of Thermodynamic Constraints and Metabolomics Data into a Metabolic Network. In: Krömer JO, Nielsen LK, Blank LM (eds) Metabolic Flux Analysis: Methods and Protocols. Series: Methods in Molecular Biology, vol. 1191. Chapter 4: 209-224. PMID: 25178784.
Download software from this site.