Tools and resources for metabolomics research community: A 2017–2018 update

The scale at which MS‐ and NMR‐based platforms generate metabolomics datasets for both research, core, and clinical facilities to address challenges in the various sciences—ranging from biomedical to agricultural—is underappreciated. Thus, metabolomics efforts spanning microbe, environment, plant, animal, and human systems have led to continual and concomitant growth of in silico resources for analysis and interpretation of these datasets. These software tools, resources, and databases drive the field forward to help keep pace with the amount of data being generated and the sophisticated and diverse analytical platforms that are being used to generate these metabolomics datasets. To address challenges in data preprocessing, metabolite annotation, statistical interrogation, visualization, interpretation, and integration, the metabolomics and informatics research community comes up with hundreds of tools every year. The purpose of the present review is to provide a brief and useful summary of more than 95 metabolomics tools, software, and databases that were either developed or significantly improved during 2017–2018. We hope to see this review help readers, developers, and researchers to obtain informed access to these thorough lists of resources for further improvisation, implementation, and application in due course of time.     

GrInvIn in a nutshell

GrInvIn (Graph Invariant Investigator) is a software framework for teaching graph theory and for research in graph theory and graph theoretic chemistry. It enables users to construct graphs, compute invariants (e.g. topological indices in chemistry) and investigate relations between these concepts. The design of GrInvIn emphasizes easy usage and makes use of software engineering techniques that enable the user to easily extend the system (e.g. by adding new topological indices to investigate).     

日本岛津产ICP1000型等离子体发射光谱仪的改造方法(软件部分)

提出了日本岛津1000型ICP改造后的软件设计方法,详细介绍了核心控制程序软件、服务程序框图和终端操作界面,阐明了标定放大系数、制作校准曲线的原理和方法。为该种大型精密光学仪器的改造做了有益的尝试。     

SPINEVOLUTION: a powerful tool for the simulation of solid and liquid state NMR experiments

Exact numerical simulations of NMR experiments are often required for the development of new techniques and for the extraction of structural and dynamic information from the spectra. Simulations of solid-state magic angle spinning (MAS) experiments can be particularly demanding both computationally and in terms of the programming required to carry them out, even if special simulation software is used. We recently developed a number of approaches that dramatically improve the efficiency and allow a high degree of automation of these computations. In the present paper, we describe SPINEVOLUTION, a highly optimized computer program that implements the new methodology. The algorithms used in the program will be described separately. Although particularly efficient for the simulation of experiments with complex pulse sequences and multi-spin systems in solids, SPINEVOLUTION is a versatile and easy to use tool for the simulation and optimization of virtually any NMR experiment. The performance of SPINEVOLUTION was compared with that of another recently developed NMR simulation package, SIMPSON. Benchmarked on a series of examples, SPINEVOLUTION was consistently found to be orders of magnitude faster. At the time of publication, the program is available gratis for non-commercial use.     

A composite (stacked) picture generation technique for spectral profile representation of dye laser

In this paper, a new technique for data representation format from video recording of spectral profile of tunable dye laser has been formulated. Only a part of the acquired images acquired sequentially in programmed time interval, was used to make the composite picture to measure variation of the parameters. A CCD camera based imaging system was used to confine the spectral pattern. No additional hardware other than image capturing device was used. The technique developed reduces the storage space required in the computer and also enhances the measurement speed significantly. The software algorithm developed has been used effectively to measure various parameters of tunable dye lasers and other optical sources.     

Prediction of the sound reduction index: a modal approach

Different methods for the calculation of the sound reduction index using modal analysis are described. The calculations use two steps: a vibratory study to determine the transverse displacement of the plate and a study of radiation. Orthotropic plates are studied in particular and the resulting calculation algorithm has been programmed. Initial hypotheses are indicated, as well as results obtained for various plates or partitions. Modal analysis calculation results are then compared to results of the Cremer-Sewell approach.     

波长色散X射线荧光仪器进展

本文叙述了自１９９０年以来波长色散Ｘ射线荧光光谱仪及分析技术的最新进展，介绍分为波长色散Ｘ射线荧光分析仪的整机特点，设计思想的发展，新技术应用，计算机及软件发展和定性定量分析等部分。     

Efficient and accurate determination of the overall rotational diffusion tensor of a molecule from (15)N relaxation data using computer program ROTDIF

We present a computer program ROTDIF for efficient determination of a complete rotational diffusion tensor of a molecule from NMR relaxation data. The derivation of the rotational diffusion tensor in the case of a fully anisotropic model is based on a six-dimensional search, which could be very time consuming, particularly if a grid search in the Euler angle space is involved. Here, we use an efficient Levenberg-Marquardt algorithm combined with Monte Carlo generation of initial guesses. The result is a dramatic, up to 50-fold improvement in the computational efficiency over the previous approaches. This method is demonstrated on a computer-generated and real protein systems. We also address the issue of sensitivity of the diffusion tensor determination from (15)N relaxation measurements to experimental errors in the relaxation rates and discuss possible artifacts from applying higher-symmetry tensor model and how to recognize them.