A growing number of software tools have been developed for metabolomics data processing and analysis. Many new tools are contributed by metabolomics practitioners who have limited prior experience with software development, and the tools are subsequently implemented by users with expertise that ranges from basic point-and-click data analysis to advanced coding. This Perspective is intended to introduce metabolomics software users and developers to important considerations that determine the overall impact of a publicly available tool within the scientific community. The recommendations reflect the collective experience of an NIH-sponsored Metabolomics Consortium working group that was formed with the goal of researching guidelines and best practices for metabolomics tool development. The recommendations are aimed at metabolomics researchers with little formal background in programming and are organized into three stages: (i) preparation, (ii) tool development, and (iii) distribution and maintenance.

Organoids derived from the digested tissue are multicellular three-dimensional (3D) constructs that better recapitulate in vivo conditions than cell monolayers. Although they cannot completely model in vivo complexity, they retain some functionality of the original organ. In cancer models, organoids are commonly used to study tumor cell invasion. This protocol aims to develop and characterize organoids from the normal and irradiated mouse mammary gland tissue to evaluate the radiation response in normal tissues. These organoids can be applied to future in vitro cancer studies to evaluate tumor cell interactions with irradiated organoids. Mammary glands were resected, irradiated to 20 Gy and digested in a collagenase VIII solution. Epithelial organoids were separated via centrifugal differentiation, and 3D organoids were developed in 96-well low-adhesion microplates. Organoids expressed the characteristic epithelial marker cytokeratin 14. Macrophage interaction with the organoids was observed in co-culture experiments. This model may be useful for studying tumor-stromal interactions, infiltration of immune cells, and macrophage polarization within an irradiated microenvironment.

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High resolution mass spectrometry (HRMS) leveraged with transient isotope labeling experiments has untapped potential to provide novel insights on context-specific metabolism, yet manual analyses are error-prone and laborious. Comprehensive mining and quantifying tools are needed. We describe Stable Isotope-assisted Metabolomics for Pathway Elucidation (SIMPEL), a tool to simplify analysis and interpretation of isotope enriched HRMS datasets. The efficacy of SIMPEL is demonstrated through examples of central carbon and lipid metabolism.

Advances in computational technology and high-throughput modeling software have given rise to the tailored design of products that require accurate mathematical relationships for their assessment. Industrial emulsion-based products, ubiquitous to everyday life, are complex systems driven by interfacial phenomena that require quick property-prediction tools for their commercialization. In this work, by means of a multiscale approach, mathematical relationships to model oil-in-water emulsions and that can be applied to any commercial emulsion-based product are proposed. The energy consumption during the emulsification process ( E v , which transitions from monotonic increase to exponential growth at 80%  w / w ), a parameter responsible for finished product performance, was linked to final product properties at three different levels: (i) molecular, through the dynamics of the interdroplet interactions given their distribution and structure at a microscopic level; (ii) microscopic, through average droplet size yielding an inversely proportional exponential relationship ( D 4,3   ∝   E v − 4 ); and (iii) macroscopic, through the plateau value of the elastic modulus and the flow behavior index leading to inversely proportional quadratic relationships ( G ′ ∝   E v − 2 and η ∝   E v − 2 , respectively). These relationships are valid at dispersed phase concentrations beyond the 60%  w / w threshold where the packing of the droplets changes the emulsion’s microscopic structure giving rise to Van der Waals forces-driven phenomena. Finding this threshold allowed expanding the concentration ranges of previously reported models. The main expectation is that these results will aid researchers and process/product designers to optimize their work in different industrial applications.