Dataset Information

SAXS4COLL: an integrated software tool for analysing fibrous collagen-based tissues.

ABSTRACT: This article provides an overview of a new integrated software tool for reduction and analysis of small-angle X-ray scattering (SAXS) data from fibrous collagen tissues, with some wider applicability to other cylindrically symmetric scattering systems. SAXS4COLL combines interactive features for data pre-processing, bespoke background subtraction, semi-automated peak detection and calibration. Both equatorial and meridional SAXS peak parameters can be measured, and the former can be deconstructed into cylinder and lattice contributions. Finally, the software combines functionality for determination of collagen spatial order parameters with a rudimentary orientation plot capability.

SUBMITTER: Abass A

PROVIDER: S-EPMC5541358 | biostudies-other | 2017 Aug

REPOSITORIES: biostudies-other

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<i>SAXS4COLL</i>: an integrated software tool for analysing fibrous collagen-based tissues.

Abass Ahmed A Bell James S JS Spang Martin T MT Hayes Sally S Meek Keith M KM Boote Craig C

Journal of applied crystallography 20170707 Pt 4

This article provides an overview of a new integrated software tool for reduction and analysis of small-angle X-ray scattering (SAXS) data from fibrous collagen tissues, with some wider applicability to other cylindrically symmetric scattering systems. <i>SAXS4COLL</i> combines interactive features for data pre-processing, bespoke background subtraction, semi-automated peak detection and calibration. Both equatorial and meridional SAXS peak parameters can be measured, and the former can be decon ...[more]

PMID: 28808439

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Project description:BackgroundComputational mathematical models of biological and biomedical systems have been successfully applied to advance our understanding of various regulatory processes, metabolic fluxes, effects of drug therapies, and disease evolution and transmission. Unfortunately, despite community efforts leading to the development of SBML and the BioModels database, many published models have not been fully exploited, largely due to a lack of proper documentation or the dependence on proprietary software. To facilitate the reuse and further development of systems biology and systems medicine models, an open-source toolbox that makes the overall process of model construction more consistent, understandable, transparent, and reproducible is desired.Results and discussionWe provide an update on the development of modelbase, a free, expandable Python package for constructing and analysing ordinary differential equation-based mathematical models of dynamic systems. It provides intuitive and unified methods to construct and solve these systems. Significantly expanded visualisation methods allow for convenient analysis of the structural and dynamic properties of models. After specifying reaction stoichiometries and rate equations modelbase can automatically assemble the associated system of differential equations. A newly provided library of common kinetic rate laws reduces the repetitiveness of the computer programming code. modelbase is also fully compatible with SBML. Previous versions provided functions for the automatic construction of networks for isotope labelling studies. Now, using user-provided label maps, modelbase v1.2.3 streamlines the expansion of classic models to their isotope-specific versions. Finally, the library of previously published models implemented in modelbase is growing continuously. Ranging from photosynthesis to tumour cell growth to viral infection evolution, all these models are now available in a transparent, reusable and unified format through modelbase.ConclusionWith this new Python software package, which is written in currently one of the most popular programming languages, the user can develop new models and actively profit from the work of others. modelbase enables reproducing and replicating models in a consistent, tractable and expandable manner. Moreover, the expansion of models to their isotopic label-specific versions enables simulating label propagation, thus providing quantitative information regarding network topology and metabolic fluxes.

Dataset Information

SAXS4COLL: an integrated software tool for analysing fibrous collagen-based tissues.

Publications

<i>SAXS4COLL</i>: an integrated software tool for analysing fibrous collagen-based tissues.

Similar Datasets

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