The increasing availability of metabolomics data necessitates novel methods for deeper data analysis and interpretation. We present a flux balance analysis method that allows for the computation of dynamic intracellular metabolic changes at the cellular scale through integration of time-course absolute quantitative metabolomics. This approach, termed "unsteady-state flux balance analysis" (uFBA...

evaporation from the soil surface has an important role in the water balance model in nature, so that the major part of rain fall and irrigation water in arid and semi-arid regions is lost via evaporation from the soil surface. in such areas, there are some regions with high water table and because of evaporation from the soil surface, salts accumulation also occur in the soil surface. so evapo...

Microbial strains can be manipulated to improve product yield and improve growth characteristics. Optimization algorithms are developed to identify the effects of gene knockout on the results. However, this process is often faced the problem of being trapped in local minima and slow convergence due to repetitive iterations of algorithm. In this paper, we proposed Bees Hill Flux Balance Analysis...

The initiation of a marine ice-sheet instability (MISI) is generally discussed from the ocean side of the ice sheet. It has been shown that the reduction in ice-shelf buttressing and softening of the coastal ice can destabilize a marine ice sheet if the bedrock is sloping upward towards the ocean. Using a conceptional flow-line geometry, we investigate the possibility of whether a MISI can be t...

The snow surface temperature is an important quantity in the snow energy balance, since it modulates the exchange of energy between the surface and the atmosphere as well as the conduction of energy into the snowpack. It is therefore important to correctly model snow surface temperatures in energy balance snowmelt models. This paper focuses on the relationship between snow surface temperature a...

A central focus in studies of microbial communities is the elucidation of the relationships between genotype, phenotype, and dynamic community structure. Here, we present a new computational method called community flux balance analysis (cFBA) to study the metabolic behavior of microbial communities. cFBA integrates the comprehensive metabolic capacities of individual microorganisms in terms of...

Flux balance analysis (FBA) is an increasingly useful approach for modeling the behavior of metabolic systems. However, standard FBA modeling of genetic knockouts cannot predict drug combination synergies observed between serial metabolic targets, even though such synergies give rise to some of the most widely used antibiotic treatments. Here we extend FBA modeling to simulate responses to chem...

Systems level modelling and simulations of biological processes are proving to be invaluable in obtaining a quantitative and dynamic perspective of various aspects of cellular function. In particular, constraint-based analyses of metabolic networks have gained considerable popularity for simulating cellular metabolism, of which flux balance analysis (FBA), is most widely used. Unlike mechanisti...

Motivation Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. Results DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia....

Motivation Intratumour heterogeneity poses many challenges to the treatment of cancer. Unfortunately, the transcriptional and metabolic information retrieved by currently available computational and experimental techniques portrays the average behaviour of intermixed and heterogeneous cell subpopulations within a given tumour. Emerging single-cell genomic analyses are nonetheless unable to char...