PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis

The recent proliferation of high-resolution mass spectrometers has generated a wealth of new data analysis methods. However, flexible integration of these methods into configurations best suited to the research question is hampered by heterogeneous file formats and monolithic software development. The mzXML, mzData, and mzML file formats have enabled uniform access to unprocessed raw data. In this paper we present our efforts to produce an equally simple and powerful format, PeakML, to uniformly exchange processed intermediary and result data. To demonstrate the versatility of PeakML, we have developed an open source Java toolkit for processing, filtering, and annotating mass spectra in a customizable pipeline (mzMatch), as well as a user-friendly data visualization environment (PeakML Viewer). The PeakML format in particular enables the flexible exchange of processed data between software created by different groups or companies, as we illustrate by providing a PeakML-based integration of the widely used XCMS package with mzMatch data processing tools. As an added advantage, downstream analysis can benefit from direct access to the full mass trace information underlying summarized mass spectrometry results, providing the user with the means to rapidly verify results. The PeakML/mzMatch software is freely available at http://mzmatch.sourceforge.net, with documentation, tutorials, and a community forum.     

Photonic crystal fibre based all-optical modulation format conversions between NRZ and RZ with hybrid clock recovery from a PRZ signal

Several all-optical modulation format-converting schemes are described for non-return-to-zero (NRZ) and return-to-zero (RZ) modulation formats that make use of spectral filtering of either self-phase modulation (SPM) or cross-phase modulation (XPM) broadened signal spectrum in a highly-nonlinear dispersion-flattened photonic-crystal fibre. Format conversions have been performed between the most widely used modulation formats - NRZ and RZ. In addition, a hybrid clock recovery scheme is proposed to obtain the data rate of the NRZ signal for NRZ-to-RZ format conversion. All format-converting schemes are based on the extraction of the spectral components in a nonlinear phase modulation broadened signal spectrum. In NRZ-to-RZ format conversion, a periodic pulse train, at a repetition rate similar to the NRZ data rate, is used as a control that induces a nonlinear phase shift to the NRZ probe signal and broadens its spectrum. The spectral components, contributed by different time instances of the control pulse, can be extracted as the converted RZ signal output. In RZ-to-NRZ format conversion, the RZ signal serves as a control that induces a nonlinear phase shift to a continuous wave probe light, where a logic-inverted NRZ signal can be extracted by filtering out the chirped components. Format conversions between NRZ and RZ signals at 9.95328 GB/s (OC-192) are demonstrated. As the proposed optical signal-processing schemes make use of the fibre nonlinearity (SPM/XPM), it is possible to extend it to a high-speed operation <160 Gb/s. Therefore the proposed format-converting schemes can serve as a format converter between the optical time-division multiplexed networks and the wavelength division multiplexed networks     

The Effect of Social Presence on Affective and Cognitive Learning in an International Engineering Course Taught via Distance Learning

Background Distance learning course formats can alter modes of information exchange and interpersonal interaction relative to traditional course formats. Purpose (Hypothesis ) To determine the effect of a distance course format on the knowledge acquisition (cognitive learning) and satisfaction (affective learning) of students, we investigated student learning responses and social presence during a graduate‐level engineering course taught via traditional (i.e., professor present in the classroom) and synchronous distance‐learning formats. Design /Method Direct quantification of participation, academic performance assessment based on homework and exam scores, and survey‐based assessments of student perceptions of the course were collected. Based on these data, cognitive and affective learning responses to different technological and interaction‐based aspects of the course were determined for each course format. Results We show that while affective learning decreased for students in the distance format course relative to the traditional format, cognitive learning was comparable. Our results suggest that loss of satellite connection and audio losses had a stronger negative effect on student perceptions than video disturbances, and that participation was the most important factor influencing affective learning. Conclusions While our findings do not suggest that cognitive learning is strongly affected by social presence, implementing strategies to enhance social presence may improve the overall learning experience and make distance learning more enjoyable for students.     

Specification of an extensible and portable file format for electronic structure and crystallographic data

In order to allow different software applications, in constant evolution, to interact and exchange data, flexible file formats are needed. A file format specification for different types of content has been elaborated to allow communication of data for the software developed within the European Network of Excellence “NANOQUANTA”, focusing on first-principles calculations of materials and nanosystems. It might be used by other software as well, and is described here in detail. The format relies on the NetCDF binary input/output library, already used in many different scientific communities, that provides flexibility as well as portability across languages and platforms. Thanks to NetCDF, the content can be accessed by keywords, ensuring the file format is extensible and backward compatible.     

Modelling the checkpoint response to telomere uncapping in budding yeast

One of the DNA damage-response mechanisms in budding yeast is temporary cell-cycle arrest while DNA repair takes place. The DNA damage response requires the coordinated interaction between DNA repair and checkpoint pathways. Telomeres of budding yeast are capped by the Cdc13 complex. In the temperature-sensitive cdc13-1 strain, telomeres are unprotected over a specific temperature range leading to activation of the DNA damage response and subsequently cell-cycle arrest. Inactivation of cdc13-1 results in the generation of long regions of single-stranded DNA (ssDNA) and is affected by the activity of various checkpoint proteins and nucleases.This paper describes a mathematical model of how uncapped telomeres in budding yeast initiate the checkpoint pathway leading to cell-cycle arrest. The model was encoded in the Systems Biology Markup Language (SBML) and simulated using the stochastic simulation system Biology of Ageing e-Science Integration and Simulation (BASIS). Each simulation follows the time course of one mother cell keeping track of the number of cell divisions, the level of activity of each of the checkpoint proteins, the activity of nucleases and the amount of ssDNA generated. The model can be used to carry out a variety of in silico experiments in which different genes are knocked out and the results of simulation are compared to experimental data. Possible extensions to the model are also discussed.     

Inferring catalysis in biological systems

In systems biology, one is often interested in the communication patterns between several species, such as genes, enzymes or proteins. These patterns become more recognisable when temporal experiments are performed. This temporal communication can be structured by reaction networks such as gene regulatory networks or signalling pathways. Mathematical modelling of data arising from such networks can reveal important details, thus helping to understand the studied system. In many cases, however, corresponding models still deviate from the observed data. This may be due to unknown but present catalytic reactions. From a modelling perspective, the question of whether a certain reaction is catalysed leads to a large increase of model candidates. For large networks the calibration of all possible models becomes computationally infeasible. We propose a method which determines a substantially reduced set of appropriate model candidates and identifies the catalyst of each reaction at the same time. This is incorporated in a multiple‐step procedure which first extends the network by additional latent variables and subsequently identifies catalyst candidates using similarity analysis methods. Results from synthetic data examples suggest a good performance even for non‐informative data with few observations. Applied on CD95 apoptotic pathway our method provides new insights into apoptosis regulation.Inspec keywords: catalysis, catalysts, biochemistry, genetics, enzymes, biology computing, calibration, molecular clustersOther keywords: inferring catalysis, biological systems, systems biology, communication patterns, genes, enzymes, proteins, time‐resolved experiments, time‐resolved communication, reaction networks, gene regulatory networks, biochemical networks, signalling pathways, mathematical data modelling, catalytic reactions, calibration, catalyst, multiple‐step procedure, latent variables, similarity analysis methods, noninformative data, differentiation apoptotic pathway, cluster     

Towards a generic product modelling framework

In response to the current rapidly changing manufacturing environment, product modelling technology has been widely applied to provide the essential information for product development (PD) processes. The traditional product modelling technologies are unable to support the information exchange and share in various stages of PD processes that could be taken place among departments in a company or even among companies in distributed manufacturing environment. This has caused many problems such as information loss, data format incompatibility and reduced efficiency and effectiveness of product data applications. This has consequently created bottlenecks for the integration of PD processes. In this paper, a generic product modelling framework (GPMF) is proposed to overcome the abovementioned problems in today's manufacturing environment. This framework uses the standard for the exchange product model data (STEP) as a foundation. It consists of four functional components: an EXPRESS data model namely EDM; a STEP–based modelling environment; a “five-phase” modelling method; and three EDM data exchange and sharing methods. Case studies show that the product models built based on the GPMF are capable of integrating information in product design, manufacturing and assembly. The GPMF is compatible, comprehensive, and flexible, and is able to support information exchange and sharing.     

New generation of amino coumarin methyl sulfonate-based fluorogenic substrates for amidase assays in droplet-based microfluidic applications

Droplet-based microfluidics is a powerful tool for biology and chemistry as it allows the production and the manipulation of picoliter-size droplets acting as individual reactors. In this format, high-sensitivity assays are typically based on fluorescence, so fluorophore exchange between droplets must be avoided. Fluorogenic substrates based on the coumarin leaving group are widely used to measure a variety of enzymatic activities, but their application in droplet-based microfluidic systems is severely impaired by the fast transport of the fluorescent product between compartments. Here we report the synthesis of new amidase fluorogenic substrates based on 7-aminocoumarin-4-methanesulfonic acid (ACMS), a highly water-soluble dye, and their suitability for droplet-based microfluidics applications. Both substrate and product had the required spectral characteristics and remained confined in droplets from hours to days. As a model experiment, a phenylacetylated ACMS was synthesized and used as a fluorogenic substrate of Escherichia coli penicillin G acylase. Kinetic parameters (k(cat) and K(M)) measured in bulk and in droplets on-chip were very similar, demonstrating the suitability of this synthesis strategy to produce a variety of ACMS-based substrates for assaying amidase activities both in microtiter plate and droplet-based microfluidic formats.     

基于MAPGIS下DWG格式数据转换研究

本论文重点阐述了两者的数据格式的差异与联系,转换的具体操作过程和在转换过程中遇到的问题及解决的方法。实现两者的数据转换不仅是为了实现它们之间的数据共享,更重要的是要掌握数据转换的基本方法,那就是比较两种数据各自的特点,通过对照从而实现转换。     

Modelling biological modularity with CellML

In recent years advances in the construction of mathematical models of biological systems have yielded an array of valuable constructs. The authors seek to provide a 'leading practice' method for implementing modularised kinetic mass-action models in order to obtain a number of advantages in model construction, validation and derived insights. The authors advocate the consideration of 'accounting cycles' or 'chains' to define 'functional' components and the separate consideration of 'messenger' components for mobile or diffusive molecular species. From a conceptual modularisation the authors illustrate, with an example drawn from signal transduction, a component-based formulation in the model exchange format cellular modelling markup language (CellML) 1.1 - demonstrating loose coupling between functionally-focused reusable components. Finally, the authors discuss the dilemmas associated with modelling protein-to-protein interactions, and the vision for using future CellML enhancements to resolve potential duplications when combining independently developed models.     

Fixed-length two-dimensional modulation coding for imaging page-oriented optical data storage systems

We present a comprehensive discussion of modulation coding for page-oriented optical data storage (PODS) systems that write and read data in a two-dimensional (2-D) bit image format. We give several 2-D mathematical models for these systems, including two-photon optical data storage systems. Using these models, we describe the nature of intersymbol interference (ISI) in imaging PODS systems and find that its characteristics are different from ISI in conventional serial magnetic and optical data storage systems. To overcome the ISI in these imaging PODS systems, we present what is, to our knowledge, a novel 2-D modulation coding scheme. We also present many examples of fixed-length 2-D modulation codes with diverse properties. Finally, we analyze and compare the bit-error rate performance of these codes.     

UL-PML: constraint-enabled distributed product data model

The global economy has made manufacturing industry more distributed than ever before. Product design requires more involvement from various technical disciplines at different locations. In such a geographically and temporally distributed environment, efficient and effective collaboration on design is vital to maintain product quality and organizational competency. Current standard computer-aided design data formats do not support design collaboration effectively in terms of design information and knowledge capturing, exchange, and integration. Design constraints cannot be represented and transferred among different groups, and design information cannot be integrated efficiently within a distributed environment. A new design data model, the Universal Linkage model, is developed here to represent design-related information for network-based collaborative design. It incorporates geometric and non-geometric constraints with traditional geometric elements, thus allowing more design knowledge sharing in collaborative design. Segments of design information can be linked and integrated into a set of complete product data. Thus, lean information exchange can be realized. This model, which has good properties of openness and extensibility, is represented by Directed Hyper Graph and Product Markup Language.     

OpenGL环境下的模型数据库管理与复杂三维建模

OpenGL作为一个图形标准具有强大的三维图形处理功能,但建模功能较弱,而专业的三维建模软件却有着很强的建模功能.因此,将OpenGL与三维建模软件相结合,对三维建模软件所创建的模型采用Oracle数据库进行管理,再通过构建不同模型类别的转换模块,实现对最常用的三维模型格式转换的支持.读取模型数据,经转换后在OpenGL环境中重新构建三维模型,由此,解决了OpenGL中的复杂三维建模问题.     

Merging clinical pathway programs as part of overall health system mergers: a ten-step guide. Spectrum Health

BACKGROUND: Mergers, acquisitions, and reorganizations can be stressful and accompanied by ambivalence, confusion, and uncertainty. Providing clear and simple steps for merging clinical pathways may help organizations move through the transition process more smoothly. The ten steps according to which Spectrum Health merged its pathway program-conduct an inventory of previous efforts, plan for the ideal program, bring staff together early in the merger process, decide on a common format, standardize the development and revision process, standardize a reporting tool, create a clinical pathway manual, implement an educational plan, present the program to key customers, and appoint an advisory group-need not be done sequentially. The ten-step pathway merger program uses pathways as a means to improve the quality of the care provided, with a focus on multidisciplinary clinical pathway teamwork. Before the merger, the two hospital systems' pathway programs used different approaches to operations and pathway format. When the announcement to merge came in September 1997, steps to merge the clinical pathway programs began. DISCUSSION: More than two years into the merger, Spectrum Health continues to struggle with the evolution of the health system. Clinical pathways represent just one of the significant and extensive issues related to organizational mergers; organizational values, finances, vision, mission, customer relations, strategic priorities, and people issues are a few of the others. Focusing on merging programs such as clinical pathway programs can help put one large piece of the merger puzzle in place and reduce some of the ambiguity associated with all mergers. Executive support is critical to the success of the clinical pathway program.     

基于可视化呈现的数字化健康信息认知研究

目的 研究数字化健康信息的呈现状态和呈现方式对年轻用户健康信息认知理解的影响。方法 采用两因子组内设计的人因学实验,测试了18名年轻受试者在两种信息呈现状态（静态呈现,动态呈现）及三种信息呈现方式（条形图,仪表图,文本型）下的认知绩效、主观感知及眼动行为,并采用重复测量方差分析法分析实验数据。结果 信息呈现状态显著影响用户认知理解绩效,动态呈现方式能有效降低用户信息搜索时间。呈现方式显著影响感知易用性和满意度等主观评价指标,两种图形类方式主观感知评价显著高于文本型。信息呈现状态和呈现方式对眼动行为存在显著主效应及交互作用,条形图和文本型在动、静态呈现时的首次注视时间无显著差异,但动态仪表图的首次注视时间晚于静态仪表图。图形类呈现方式的总注视时长较之于文本型也较短,其信息认知效率较高。结论 呈现状态中,动态呈现能够提高用户提取重要信息的效率;而呈现方式中,图形类呈现方式有更好的用户主观认知评价。研究结果有助于揭示呈现状态和呈现方式对数字化健康信息认知的影响机制,为优化数字化健康信息的编码设计提供了指导。     

飞机空中交会显示格式对情境意识与认知绩效的影响

为考察飞机空中交会信息显示格式对情境意识和认知绩效的影响。实验采用模拟飞行相撞判断任务,以情境意识和相撞判断准确率为指标,对整合式显示与分离式显示这两种显示格式的视觉工效进行比较。结果表明:(1)整合式显示条件下情境意识与相撞判断的准确率均高于分离式显示;(2)信息显示格式以情境意识为中介对认知绩效产生显著影响。结论:整合式显示格式的相对优势可归因于该显示格式对情境意识的促进作用。     

版式设计在书籍装帧中的应用探析

目的探究版式设计在书籍装帧中的应用。方法结合版式设计的重要性,总结出版式设计在书籍装帧中的3个应用方向。结论设计师应挣脱传统思想的束缚,不断丰富和创新版式设计的表现形式,对不同类型的书籍进行不同版式的装帧,这有利于将书籍的艺术性和功能性完美结合。     

JViz.Rna--a Java tool for RNA secondary structure visualization

Many tools have been developed for visualization of RNA secondary structures using a variety of techniques and output formats. However, each tool is typically limited to one or two of the visualization models discussed in this paper, supports only a single file format, and is tied to a specific platform. In order for structure prediction researchers to better understand the results of their algorithms and to enable life science researchers to interpret RNA structure easily, it is helpful to provide them with a flexible and powerful tool. jViz.Rna is a multiplatform visualization tool capable of displaying RNA secondary structures encoded in a variety of file formats. The same structure can be viewed using any of the models supported, including linked graph, circle graph, dot plot, and classical structure. Also, the output is dynamic and can easily be further manipulated by the user. In addition, any of the drawings produced can be saved in either the EPS or PNG file formats enabling easy usage in publications and presentations.