Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem

We present the application of a Java remote method invocation (RMI) based open source architecture to distributed chemical computing. This architecture was previously employed for distributed data harvesting of chemical information from the Internet via the Google application programming interface (API; ChemXtreme). Due to its open source character and its flexibility, the underlying server/client framework can be quickly adopted to virtually every computational task that can be parallelized. Here, we present the server/client communication framework as well as an application to distributed computing of chemical properties on a large scale (currently the size of PubChem; about 18 million compounds), using both the Marvin toolkit as well as the open source JOELib package. As an application, for this set of compounds, the agreement of log P and TPSA between the packages was compared. Outliers were found to be mostly non-druglike compounds and differences could usually be explained by differences in the underlying algorithms. ChemStar is the first open source distributed chemical computing environment built on Java RMI, which is also easily adaptable to user demands due to its "plug-in architecture". The complete source codes as well as calculated properties along with links to PubChem resources are available on the Internet via a graphical user interface at http://moltable.ncl.res.in/chemstar/.     

Open computing grid for molecular science and engineering

Grid is an emerging infrastructure for distributed computing that provides secure and scalable mechanisms for discovering and accessing remote software and data resources. Applications built on this infrastructure have great potential for addressing and solving large scale chemical, pharmaceutical, and material science problems. The article describes the concept behind grid computing and will present the OpenMolGRID system that is an open computing grid for molecular science and engineering. This system provides grid enabled components, such as a data warehouse for chemical data, software for building QSPR/QSAR models, and molecular engineering tools for generating compounds with predefined chemical properties or biological activities. The article also provides an overview about the availability of chemical applications in the grid.     

GridMol: a grid application for molecular modeling and visualization

In this paper we present GridMol, an extensible tool for building a high performance computational chemistry platform in the grid environment. GridMol provides computational chemists one-stop service for molecular modeling, scientific computing and molecular information visualization. GridMol is not only a visualization and modeling tool but also simplifies control of remote Grid software that can access high performance computing resources. GridMol has been successfully integrated into China National Grid, the most powerful Chinese Grid Computing platform. In Section “Grid computing” of this paper, a computing example is given to show the availability and efficiency of GridMol. GridMol is coded using Java and Java3D for portability and cross-platform compatibility (Windows, Linux, MacOS X and UNIX). GridMol can run not only as a stand-alone application, but also as an applet through web browsers. In this paper, we will present the techniques for molecular visualization, molecular modeling and grid computing. GridMol is available free of charge under the GNU Public License (GPL) from our website: Contact:      

Web servers and services for electrostatics calculations with APBS and PDB2PQR

APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization of electrostatic potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/.     

Harvesting chemical information from the Internet using a distributed approach: ChemXtreme

The Internet is a comprehensive resource of chemical information which is at the same time largely unstructured. It provides a wealth of scientific information such as experimental data and requires a suitable automated data mining and analysis tool for its meaningful exploration. The Java based software presented here, ChemXtreme, is developed for harvesting chemical information from the Internet employing the Google API in combination with a distributed client/server text analysis architecture based on JavaRMI. It represents the first and until now the only toolkit for automated structured data retrieval from the Internet which is itself open source. ChemXtreme employs the "search the search engine" strategy, where the URLs returned from the search engine are analyzed further via textual pattern analysis. This process resembles the manual analysis of the hit list, where relevant data are captured and, by means of human intervention, are mined into a format suitable for further analysis. ChemXtreme on the other hand transforms chemical information automatically into a structured format suitable for storage in databases and further analysis and also provides links to the original information source. The query data retrieved from the search engine by the server is encoded, encrypted, and compressed and then sent to all the participating active clients in the network for parsing. Relevant information identified by the clients on the retrieved Web sites is sent back to the server, verified, and added to the database for data mining and further analysis. The distributed further analysis of URLs in a client/server architecture scales very favorably, thus producing only minimal overhead.     

NMR Spectroscopy: Learned and Delivered on the Internet

The NMR Collaborative Training Partnership is an NSF sponsored project that provides several nearby two-year and four-year institutions access to a 300-MHz FT-NMR. Using Web-based materials we teach students who do not have direct access to an instrument the basics of how an NMR spectrum is generated. We also have a Web server and remote software that allows students to generate real spectra from samples they have submitted to their instructor. In this way, students who do not have a local FT-NMR can gain experience with this important technique.     

Electron tunneling in proteins program

We developed a unique integrated software package (called Electron Tunneling in Proteins Program or ETP) which provides an environment with different capabilities such as tunneling current calculation, semi‐empirical quantum mechanical calculation, and molecular modeling simulation for calculation and analysis of electron transfer reactions in proteins. ETP program is developed as a cross‐platform client‐server program in which all the different calculations are conducted at the server side while only the client terminal displays the resulting calculation outputs in the different supported representations. ETP program is integrated with a set of well‐known computational software packages including Gaussian, BALLVIEW, Dowser, pKip, and APBS. In addition, ETP program supports various visualization methods for the tunneling calculation results that assist in a more comprehensive understanding of the tunneling process. © 2016 Wiley Periodicals, Inc.     

Internet推动的化学信息学重要进展*

Internet的普及为专业人员获取数据信息、利用计算工具提供了统一的平台,由此为化学信息学的发展带来了新的空间,推动了化学信息学以网络为基础,以化学相关的数据、信息及计算资源共享为目标的快速发展。本文将从不同侧面回顾近10年来化学信息学的重要进展, 包括：(1) 网络化学信息检索：索引对象从化学浅层网向化学深层网发展;检索工具从Web化学信息资源导航向化学专业搜索引擎(包括文本信息和化合物标识信息)、及化学深层网检索引擎 (化合物物性数据提取)发展;索引粒度从Web站点向页面、乃至页面中的特定内容发展,一般页面特定内容的数据提取(即非结构化数据提取)是未来发展的方向。(2)可共享的化学数据库：从可免费访问和使用的化学数据库向数据库内容通过集成多来源数据(包括数据库拥有者主动收集、多来源数据主动提交达到共享的方式,repository)实现数据库内容免费下载和共享,以及不同数据库之间的相关内容实现无缝连接的方向发展(如NIH建成的药物小分子共享数据库PubChem)。(3) 开源(open source)化学软件工具包：从化学结构基本处理模块如CDK、JOELib向集成开发环境如化学信息学与生物信息学集成环境Bioclipse发展。(4) 与化合物及其数据共享相关的推荐标准：包括用于共享数据交换的化学标记语言CML、IUPAC推荐的学术论文相关热力学实验数据提交标准ThermoML及化合物结构唯一描述码InChI。(5) 计算化学资源共享及基于网格的应用：从可执行程序的下载向在线计算、基于网格的应用发展。(6) eChemistry和虚拟研究环境：网络也成为化学相关日常的科学活动中不可缺少的平台。构建以网络为平台、支持开展科研活动的数字化基础设施和服务的eChemstry探索开始出现,根据需要自主集成多来源数据和计算资源,形成不同层次的支持协同工作的虚拟研究环境是未来数据和计算资源共享方式的发展方向。     

Database of C-glycosylporphyrins in Web fashion

The aim of this work was to organize chemical data in a client-server environment using Database Management System and Web fashion for the client interface. To solve this ancient problem (for us) merging text data, reaction schemes, tridimensional structures, and NMR, CD, and UV spectra images, we have based our implementation on a few fundamental points: no cost for the user, availability of data via the Internet, standard and freeware software, and a Web browser for the database inquiry. These functions are delivered in a platform-independent manner via the Internet and are used by computational experts and nonexperts alike. C-Glycosylporphyrins is the class of compounds chosen to test our applications. These results can be exportable for many other classes of chemical compounds.     

The need for scientific software engineering in the pharmaceutical industry

Scientific software engineering is a distinct discipline from both computational chemistry project support and research informatics. A scientific software engineer not only has a deep understanding of the science of drug discovery but also the desire, skills and time to apply good software engineering practices. A good team of scientific software engineers can create a software foundation that is maintainable, validated and robust. If done correctly, this foundation enable the organization to investigate new and novel computational ideas with a very high level of efficiency.     

Two-dimensional electrophoresis resources available from ExPASy

This paper describes the set of two-dimensional electrophoresis (2-DE) resources currently available from the ExPASy proteomics Web server. These resources include the SWISS-2DPAGE database, 2-DE software packages, 2-DE technical and educational services, as well as indexes and search engines for 2-DE related sites over the Internet.     

SENECA: A platform-independent, distributed, and parallel system for computer-assisted structure elucidation in organic chemistry.

The program package SENECA for Computer-Assisted Structure Elucidation (CASE) of organic molecules is described. SENECA is written completely in the programming language Java and divided into a server, a client, and a gatekeeper part. While the client allows for input of spectroscopic information, the server part performs the actual structure elucidation by stochastically walking through constitution space while optimizing the molecule toward agreement with given spectral properties. The convergence is guided by simulated annealing. The gatekeeper administers a list of server processes, which can be retrieved by the client. The package is completely platform-independent and its server part can be distributed over the Internet or an intranet using a heterogeneous network of almost any number and type of computers, thus allowing for parallel CASE computations on ordinary networks, present in almost any institution.     

Hydra: a self regenerating high performance computing grid for drug discovery

Computer aided drug design is progressing and playing an increasingly important role in drug discovery. Computational methods are being used to evaluate larger and larger numbers of real and virtual compounds. New methods based on molecular simulations that take protein and ligand flexibility into account also contribute to an ever increasing need for compute time. Computational grids are therefore becoming a critically important tool for modern drug discovery, but can be expensive to deploy and maintain. Here, we describe the low cost implementation of a 165 node, computational grid at Anadys Pharmaceuticals. The grid makes use of the excess computing capacity of desktop computers deployed throughout the company and of outdated desktop computers which populate a central computing grid. The performance of the grid grows automatically with the size of the company and with advances in computer technology. To ensure the uniformity of the nodes in the grid, all computers are running the Linux operating system. The desktop computers run Linux inside MS Windows using coLinux as virtualization software. HYDRA has been used to optimize computational models, for virtual screening and for lead optimization.     

Data Acquisition and Transfer System for In-situ Atomic Emission Spectroscopic Analysis

A new method of data acquisition,proceeding and data share is introduced and a data acquisition and transfer system targeting in-situ spectroscopic analysis in metallurgy is established. This system is designed for the critical control of steelmaking, which greatly requires rapid and suitable information feedback. The information includes analysis data, measurement data and controls. The analysis data are acquired from the serial port of the computer-aided spectrometers or other devices and are identified, converted and then stored to the standard database in a network server. The network is based on the Intranet structure and works on the Windows NT operation system. It supports remote access and Internet connection so that the analysis data can be shared,proceeded and developed by certified personnel throughout the network. A set of specially designed data transfer devices with display panel are used in the severe places to display real-time analysis data and other information, which are offered from the nearest workstation on the network. These devices are dust-proofed and anti-magnetic. Each device offers up to 30 terminals with the limited distance of 3000 meters at 2400 baud-rates under the industrial condition. The application program for the data proceeding is integrated to the system. It includes system security, data acquisition, data transfer, data process and display. It also includes auxiliary functions such as operation help, system's resources monitoring and other customer-defined parameters. The software's functions directly related to the system are detailed discussed. Associated with another management and control software programmed for this system,the critical control of steelmaking can be approached.     

Workflow based framework for life science informatics

Workflow technology is a generic mechanism to integrate diverse types of available resources (databases, servers, software applications and different services) which facilitate knowledge exchange within traditionally divergent fields such as molecular biology, clinical research, computational science, physics, chemistry and statistics. Researchers can easily incorporate and access diverse, distributed tools and data to develop their own research protocols for scientific analysis. Application of workflow technology has been reported in areas like drug discovery, genomics, large-scale gene expression analysis, proteomics, and system biology. In this article, we have discussed the existing workflow systems and the trends in applications of workflow based systems.     

A computer-aided drug discovery system for chemistry teaching

The Schools Malaria Project (http://emalaria.soton.ac.uk/) brings together school students with university researchers in the hunt for a new antimalaria drug. The design challenge being offered to students is to use a distributed drug search and selection system to design potential antimalaria drugs. The system is accessed via a Web interface. This e-science project displays the results of the trials in an accessible manner, giving students an opportunity for discussion and debate both with peers and with the university contacts. The project has been implemented by using distributed computing techniques, spreading computer load over a network of machines that cross institutional boundaries, forming a grid. This provides access to greater computing power and allows a much more complex and detailed formulation of the drug design problem to be tackled for research, teaching, and learning.     

SpecPad: device‐independent NMR data visualization and processing based on the novel DART programming language and Html5 Web technology

SpecPad is a new device‐independent software program for the visualization and processing of one‐dimensional and two‐dimensional nuclear magnetic resonance (NMR) time domain (FID) and frequency domain (spectrum) data. It is the result of a project to investigate whether the novel programming language DART, in combination with Html5 Web technology, forms a suitable base to write an NMR data evaluation software which runs on modern computing devices such as Android, iOS, and Windows tablets as well as on Windows, Linux, and Mac OS X desktop PCs and notebooks. Another topic of interest is whether this technique also effectively supports the required sophisticated graphical and computational algorithms. SpecPad is device‐independent because DART's compiled executable code is JavaScript and can, therefore, be run by the browsers of PCs and tablets. Because of Html5 browser cache technology, SpecPad may be operated off‐line. Network access is only required during data import or export, e.g. via a Cloud service, or for software updates. A professional and easy to use graphical user interface consistent across all hardware platforms supports touch screen features on mobile devices for zooming and panning and for NMR‐related interactive operations such as phasing, integration, peak picking, or atom assignment. Copyright © 2017 John Wiley & Sons, Ltd.     

Code interoperability and standard data formats in quantum chemistry and quantum dynamics: The Q5/D5Cost data model

Code interoperability and the search for domain‐specific standard data formats represent critical issues in many areas of computational science. The advent of novel computing infrastructures such as computational grids and clouds make these issues even more urgent. The design and implementation of a common data format for quantum chemistry (QC) and quantum dynamics (QD) computer programs is discussed with reference to the research performed in the course of two Collaboration in Science and Technology Actions. The specific data models adopted, Q5Cost and D5Cost, are shown to work for a number of interoperating codes, regardless of the type and amount of information (small or large datasets) to be exchanged. The codes are either interfaced directly, or transfer data by means of wrappers; both types of data exchange are supported by the Q5/D5Cost library. Further, the exchange of data between QC and QD codes is addressed. As a proof of concept, the H + H₂ reaction is discussed. The proposed scheme is shown to provide an excellent basis for cooperative code development, even across domain boundaries. Moreover, the scheme presented is found to be useful also as a production tool in the grid distributed computing environment. © 2013 Wiley Periodicals, Inc.     

Accelerating molecular modeling applications with graphics processors

Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such simulations are limited in size and timescale by the available computing resources. State-of-the-art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, a tremendous computational resource that can now be utilized for general purpose computing as a result of recent advances in GPU hardware and software architecture. In this article, an overview of recent advances in programmable GPUs is presented, with an emphasis on their application to molecular mechanics simulations and the programming techniques required to obtain optimal performance in these cases. We demonstrate the use of GPUs for the calculation of long-range electrostatics and nonbonded forces for molecular dynamics simulations, where GPU-based calculations are typically 10-100 times faster than heavily optimized CPU-based implementations. The application of GPU acceleration to biomolecular simulation is also demonstrated through the use of GPU-accelerated Coulomb-based ion placement and calculation of time-averaged potentials from molecular dynamics trajectories. A novel approximation to Coulomb potential calculation, the multilevel summation method, is introduced and compared with direct Coulomb summation. In light of the performance obtained for this set of calculations, future applications of graphics processors to molecular dynamics simulations are discussed.     

Development and application of an internet electron microscopy system for the outreach program in Japan.

The development of a remotely operated scanning electron microscopy (SEM) system and its use by high school students and the public as an outreach program are reported. The SEM and the server are located in the National Institute for Materials Science, Tsukuba, Japan, with client computers installed at a science museum and high schools. Using a secure virtual private network system and scheduling/management groupware, observation of SEM images and energy dispersive X-ray analysis are widely and frequently performed throughout Japan.