Integrating open‐source software applications to build molecular dynamics systems

Three open‐source applications, NanoEngineer‐1, packmol, and mis2lmp are integrated using an open‐source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open‐source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol‐a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real‐world research requirements and integrated to create a new capability. © 2014 Wiley Periodicals, Inc.     

Software tools for green and sustainable chemistry

In this review, we consider green chemistry metrics, related software tools, and the opportunities and challenges for their use in research laboratories. We provide an overview of state-of-the-art software designed both to aid researchers in planning and conducting chemical experiments and to assess sustainability of individual reactions and synthetic routes. The increasing digitalisation of research means that there is great opportunity for more extensive use of computational tools by synthetic chemists and for closer integration of green chemistry principles into the routine work of chemical laboratories. We discuss the scope for using software tools in the laboratory and assisting synthetic chemists in the adoption of green and sustainable chemistry approaches that are suitable for their specific purposes.     

互联网B/S架构交互式软件在核心概念教学中的应用*——以国际IB课程中“电解质”内容为例

基于核心概念教学的思路,国际IB课程互联网B/S架构交互式软件能够使学生围绕“电解质”核心概念,通过自行操作软件获得多个从微观到宏观、定性与定量相结合、可视化的实验证据,有利于学生深度理解概念与概念之间的逻辑和发展关系,促进学科知识系统框架的形成。     

半实物仿真中试验总控软件的设计与实现

试验总控软件是应用于半实物仿真中对参试系统进行管理和控制的一种软件,它可以对半实物仿真中的参试系统进行配置,实现对整个试验仿真的管理和监控。解析各参试系统的数据交互协议是试验总控软件对参试系统进行监控和管理的关键功能。通常试验总控软件解析功能代码完全按照各参试系统数据交互协议开发,这样一旦数据交互协议发生更改,解析功能代码需要根据新协议重新开发导致软件重复开发,影响软件开发效率和通用性。为了解决这个问题,文中提出一种试验总控软件设计框架并采用动态解析数据帧技术将解析代码与数据交互协议隔离,不仅提高软件通用性,同时缩短半实物仿真开发周期,减少人力财力开支。     

Overview of software options for processing,analysis and interpretation of mass spectrometric proteomic data

Recently, the interests in proteomics have been intensively increased, and the proteomic methods have been widely applied to many problems in cell biology. If the age of 1990s is considered to be a decade of genomics, we can claim that the following years of the new century is a decade of proteomics. The rapid evolution of proteomics has continued through these years, with a series of innovations in separation techniques and the core technologies of two‐dimensional gel electrophoresis and MS. Both technologies are fueled by automation and high throughput computation for profiling of proteins from biological systems. As Patterson ever mentioned, ‘data analysis is the Achilles heel of proteomics and our ability to generate data now outstrips our ability to analyze it’. The development of automatic and high throughput technologies for rapid identification of proteins is essential for large‐scale proteome projects and automatic protein identification and characterization is essential for high throughput proteomics. This review provides a snap shot of the tools and applications that are available for mass spectrometric high throughput biocomputation. The review starts with a brief introduction of proteomics and MS. Computational tools that can be employed at various stages of analysis are presented, including that for data processing, identification, quantification, and the understanding of the biological functions of individual proteins and their dynamic interactions. The challenges of computation software development and its future trends in MS‐based proteomics have also been speculated. Copyright © 2014 John Wiley & Sons, Ltd.     

Distributed and multicore QuBiLS-MIDAS software v2.0: Computing chiral,fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra

Advances to the distributed, multi-core and fully cross-platform QuBiLS-MIDAS software v2.0 ( http://tomocomd.com/qubils-midas ) are reported in this article since the v1.0 release. The QuBiLS-MIDAS software is the only one that computes atom-pair and alignment-free geometrical MDs (3D-MDs) from several distance metrics other than the Euclidean distance, as well as alignment-free 3D-MDs that codify structural information regarding the relations among three and four atoms of a molecule. The most recent features added to the QuBiLS-MIDAS software v2.0 are related (a) to the calculation of atomic weightings from indices based on the vertex-degree invariant (e.g., Alikhanidi index); (b) to consider central chirality during the molecular encoding; (c) to use measures based on clustering methods and statistical functions to codify structural information among more than two atoms; (d) to the use of a novel method based on fuzzy membership functions to spherically truncate inter-atomic relations; and (e) to the use of weighted and fuzzy aggregation operators to compute global 3D-MDs according to the importance and/or interrelation of the atoms of a molecule during the molecular encoding. Moreover, a novel module to compute QuBiLS-MIDAS 3D-MDs from their headings was also developed. This module can be used either by the graphical user interface or by means of the software library. By using the library, both the predictive models built with the QuBiLS-MIDAS 3D-MDs and the QuBiLS-MIDAS 3D-MDs calculation can be embedded in other tools. A set of predefined QuBiLS-MIDAS 3D-MDs with high information content and low redundancy on a set comprised of 20,469 compounds is also provided to be employed in further cheminformatics tasks. This set of predefined 3D-MDs evidenced better performance than all the universe of Dragon (v5.5) and PaDEL 0D-to-3D MDs in variability studies, whereas a linear independence study proved that these QuBiLS-MIDAS 3D-MDs codify chemical information orthogonal to the Dragon 0D-to-3D MDs. This set of predefined 3D-MDs would be periodically updated as long as new results be achieved. In general, this report highlights our continued efforts to provide a better tool for a most suitable characterization of compounds, and in this way, to contribute to obtaining better outcomes in future applications.     

An efficient solution for resolving iTRAQ and TMT channel cross‐talk

Isobaric tagging reagents such as isobaric tag for relative and absolute quantitation (iTRAQ) and tandem mass tag (TMT) typically have isotopic impurities that cause significant cross‐talk between channels. Here, we present an efficient solution to compensate for channel cross‐talk using linear algebra and find that it is between 20× and 120× faster than previous methods. We also find that the effects of channel cross‐talk are as important to manage as the effects of ratio compression because of precursor impurities, and we have released an open‐source tool to perform both types of calculations.     

HPLC method transfer study for simultaneous determination of seven angiotensin II receptor blockers

In this study, a sensitive high‐performance liquid chromatography method was developed and validated for the simultaneous determination of seven angiotensin II receptor blockers, namely, hydrochlorothiazide, chlorthalidone, eprosartan mesylate, valsartan, losartan potassium, irbesartan, and candesartan cilexetil. Different chromatographic parameters were tested and fully optimized. Best chromatographic separation was accomplished on a reversed‐phase octadecylsilyl column (250 × 4.6 mm id; 5 μm) under gradient elution using methanol/sodium phosphate monobasic buffer (0.01 M, pH 6.5) as mobile phase. The detection of target analytes was obtained at 254 nm. The pH of the buffer has been selected according to Marvin^® sketch software. The proposed method was validated according to ICH guidelines and showed good precision (relative standard deviation < 1), good linearity (square of correlation coefficient ≥ 0.999), and high accuracy (between 98 and 102%) with detection limit and quantitation limit (40 and 160 ng/mL, respectively) for all the detected analytes.