Nature Methods
This journal is a forum for the publication of novel methods and significant improvements to tried-and-tested basic research techniques in the life sciences.
Using photons as neurotransmitters in C. elegans
The connectivity between individual neurons is fundamental to neuronal networks and brain function. Here, we replace the flavor of chemical neurotransmission with the color of photons emitted from presynaptic luciferases and light-gated ion channels in the postsynapse.
Data architecture for collaborative neuroscience
How to process, store and (publicly) share the large datasets acquired in many laboratories distributed across the globe? These questions were faced by the International Brain Laboratory; solutions found are likely to be of interest to all our global and open Neuroscience community.
EnzymeML: seamless data flow and modelling of enzymatic data
The design of biocatalytic reaction systems is highly complex due to the dependency of the estimated kinetic parameters on the enzyme, the reaction conditions, and the modelling method. Consequently, reproducibility of enzymatic experiments and re-usability of enzymatic data are challenging.
We developed the XML–based markup language EnzymeML to enable storage and exchange of enzymatic data such as reaction conditions, time course of substrate and product, kinetic parameters, and kinetic model, thus making enzymatic data findable, accessible, interoperable, and reusable (FAIR). The feasibility and usefulness of the EnzymeML toolbox is demonstrated in six scenarios, where data and metadata of different enzymatic reactions are collected and analysed.
EnzymeML serves as a seamless communication channel between experimental platforms, electronic lab notebooks, tools for modelling of enzyme kinetics, publication platforms, and enzymatic reaction databases. EnzymeML is open, transparent, and invites the community to contribute. All documents and codes are freely available at https://enzymeml.org/.
Improving Structural Variation Detection Accuracy in Repetitive Regions Using Hybrid Algorithms and SFS Signatures
SVDSS combines ideas from traditional mapping-based and assembly-based SV detection algorithms with the novel mapping-free Substring-free Sample-specific Strings (SFS) framework to achieve a 15% recall improvement over state-of-the-art methods in detecting SVs in repetitive regions of the genome.
Ultraflat graphene membrane shapes uniform thin ice for cryo-EM analysis
Ultraflat graphene membrane is developed here as the supporting film for cryo-EM specimen preparation, which improves the image quality of vitrified samples and enables the high-resolution reconstruction of small macromolecules (<100KD).