Computational Feature Performance and Domain Specific Architecture Evaluation of Software Applications Towards Metabolic Flux Analysis

Zeeshan, Saman; Majeed, Saman; Dandekar, Thomas

doi:10.2174/2213275911205030165

Cited by 4 publications

(2 citation statements)

References 46 publications

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“…For our comparison, we chose software applications from fields we are familiar with, yet tried to cover a broad range of different applications and compared Metabolic Flux Analysis (MFA) as well as software metabolic network analysis 81 , 82 , Mass Isotopomers Distribution Analysis (MIDA) including GC-MS data analysis 69 , 70 , and neurobiology applications for behavioral analysis of insects such as desert ants and fly 71 – 73 .…”

Section: Comparing Bioinformatics Toolsmentioning

confidence: 99%

Developing sustainable software solutions for bioinformatics by the “Butterfly” paradigm

Ahmed

Zeeshan

Dandekar³

2014

F1000Res

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Section: Comparing Bioinformatics Toolsmentioning

confidence: 99%

Developing sustainable software solutions for bioinformatics by the “Butterfly” paradigm

Ahmed

Zeeshan

Dandekar³

2014

F1000Res

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“…A number of theoretical techniques has been established to predict metabolic fluxes [1-4]. Implementing different mathematical parallel and sequential algorithms, several desktop and web based batch and interactive software applications [5] have been also developed towards quantitative metabolic flux analysis and modeling [6]. …”

Section: Introductionmentioning

confidence: 99%

Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling

et al. 2013

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BackgroundThe knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors into metabolic products can be taken as fingerprints of the metabolic events and dynamics through the metabolic networks. An open-source software is required that easily and rapidly calculates from mass spectra of labelled metabolites, derivatives and their fragments global isotope excess and isotopomer distribution.ResultsThe open-source software “Least Square Mass Isotopomer Analyzer” (LS-MIDA) is presented that processes experimental mass spectrometry (MS) data on the basis of metabolite information such as the number of atoms in the compound, mass to charge ratio (m/e or m/z) values of the compounds and fragments under study, and the experimental relative MS intensities reflecting the enrichments of isotopomers in 13C- or 15 N-labelled compounds, in comparison to the natural abundances in the unlabelled molecules. The software uses Brauman’s least square method of linear regression. As a result, global isotope enrichments of the metabolite or fragment under study and the molar abundances of each isotopomer are obtained and displayed.ConclusionsThe new software provides an open-source platform that easily and rapidly converts experimental MS patterns of labelled metabolites into isotopomer enrichments that are the basis for subsequent observation-driven analysis of pathways and fluxes, as well as for model-driven metabolic flux calculations.

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Developing sustainable software solutions for bioinformatics by the “Butterfly” paradigm

Ahmed

Zeeshan

Dandekar³

2014

F1000Res

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Software design and sustainable software engineering are essential for the long-term development of bioinformatics software. Typical challenges in an academic environment are short-term contracts, island solutions, pragmatic approaches and loose documentation. Upcoming new challenges are big data, complex data sets, software compatibility and rapid changes in data representation. Our approach to cope with these challenges consists of iterative intertwined cycles of development (“ Butterfly” paradigm) for key steps in scientific software engineering. User feedback is valued as well as software planning in a sustainable and interoperable way. Tool usage should be easy and intuitive. A middleware supports a user-friendly Graphical User Interface (GUI) as well as a database/tool development independently. We validated the approach of our own software development and compared the different design paradigms in various software solutions.

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Computational Feature Performance and Domain Specific Architecture Evaluation of Software Applications Towards Metabolic Flux Analysis

Cited by 4 publications

References 46 publications

Developing sustainable software solutions for bioinformatics by the “Butterfly” paradigm

Developing sustainable software solutions for bioinformatics by the “Butterfly” paradigm

Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling

Developing sustainable software solutions for bioinformatics by the “Butterfly” paradigm

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