Database and tools for metabolic network analysis

Metabolic network analysis has attracted much attention in the area of systems biology. It has a profound role in understanding the key features of organism metabolic networks and has been successfully applied in several fields of systems biology, including in silico gene knockouts, production yield improvement using engineered microbial strains, drug target identification, and phenotype prediction. A variety of metabolic network databases and tools have been developed in order to assist research in these fields. Databases that comprise biochemical data are normally integrated with the use of metabolic network analysis tools in order to give a more comprehensive result. This paper reviews and compares eight databases as well as twenty one recent tools. The aim of this review is to study the different types of tools in terms of the features and usability, as well as the databases in terms of the scope and data provided. These tools can be categorised into three main types: standalone tools; toolbox-based tools; and web-based tools. Furthermore, comparisons of the databases as well as the tools are also provided to help software developers and users gain a clearer insight and a better understanding of metabolic network analysis. Additionally, this review also helps to provide useful information that can be used as guidance in choosing tools and databases for a particular research interest.     

重庆玉米洞遗址发现的骨角牙制品初步研究

在狩猎采集经济的旧石器时代,古人类依赖动物而生存。作为动物资源的副产品,骨角牙制品是古人类对肉食资源深度开发利用的表现。玉米洞遗址是重庆巫山县新发现的一处文化面貌特殊的旧石器时代洞穴遗址,其骨角牙制品颇具特色。本文主要对该遗址的骨角牙制品进行初步的类型学研究,将观察的材料分为骨器(n=104)、骨片(n=2)、骨断块(n=5)、牙器(n=6)和角器(n=3)进行详细记述;同时试图从操作链角度分析该遗址骨角牙制品的制作技术和反映的人类行为,显示出古人类简单粗放、灵活高效的技术特征和生存策略;最后对该遗址出土骨角牙器的时代及古人类行为现代性问题进行了探讨,认为玉米洞的骨角牙器的时代介于中更新世-早全新世,简单加工骨角牙制品与精致加工骨角器之间存在连续或断续的发展演变关系,以骨角器的发现作为衡量中国古人类"行为现代性"的标准需要重新考量。     

Assessing sustainability at farm-level: Lessons learned from a comparison of tools in practice

In the past decades a wide variety of tools have been developed to assess the sustainability performance of farms. Although multiple studies have compared tools on a theoretical basis, little attention has been paid to the comparing tools in practice. This research compared indicator-based sustainability assessment tools to gain insight in practical requirements, procedures and complexity involved in applying sustainability assessment tools. In addition, the relevance of the tools, as perceived by farmers, was evaluated. An overview of 48 indicator-based sustainability assessment tools was developed to, subsequently, select tools that address the environmental, social and economic dimension of sustainability, are issued in a scientific publication and suitable for assessing the sustainability performance of livestock and arable farms in Denmark. Only four tools (RISE, SAFA, PG and IDEA) complied with the selection criteria and were used to assess the sustainability performance of five Danish farms. The tools vary widely in their scoring and aggregation method, time requirement and data input. The farmers perceived RISE as the most relevant tool to gain insight in the sustainability performance of their farm. The findings emphasize the importance of context specificity, user-friendliness, complexity of the tool, language use, and a match between value judgements of tool developers and farmers. Even though RISE was considered as the most relevant tool, the farmers expressed a hesitation to apply the outcomes of the four tools in their decision making and management. Furthermore, they identified limitations in their options to improve their sustainability performance. Additional efforts are needed to support farmers in using the outcomes in their decision making. The outcomes of sustainability assessment tools should therefore be considered as a starting point for discussion, reflection and learning.     

Diversification and cumulative evolution in New Caledonian crow tool manufacture

Many animals use tools but only humans are generally considered to have the cognitive sophistication required for cumulative technological evolution. Three important characteristics of cumulative technological evolution are: (i) the diversification of tool design; (ii) cumulative change; and (iii) high-fidelity social transmission. We present evidence that crows have diversified and cumulatively changed the design of their pandanus tools. In 2000 we carried out an intensive survey in New Caledonia to establish the geographical variation in the manufacture of these tools. We documented the shapes of 5550 tools from 21 sites throughout the range of pandanus tool manufacture. We found three distinct pandanus tool designs: wide tools, narrow tools and stepped tools. The lack of ecological correlates of the three tool designs and their different, continuous and overlapping geographical distributions make it unlikely that they evolved independently. The similarities in the manufacture method of each design further suggest that pandanus tools have gone through a process of cumulative change from a common historical origin. We propose a plausible scenario for this rudimentary cumulative evolution.     

Data extraction from proteomics raw data: an evaluation of nine tandem MS tools using a large Orbitrap data set

In shot-gun proteomics raw tandem MS data are processed with extraction tools to produce condensed peak lists that can be uploaded to database search engines. Many extraction tools are available but to our knowledge, a systematic comparison of such tools has not yet been carried out. Using raw data containing more than 400,000 tandem MS spectra acquired using an Orbitrap Velos we compared 9 tandem MS extraction tools, freely available as well as commercial. We compared the tools with respect to number of extracted MS/MS events, fragment ion information, number of matches, precursor mass accuracies and agreement in-between tools. Processing a primary data set with 9 different tandem MS extraction tools resulted in a low overlap of identified peptides. The tools differ by assigned charge states of precursors, precursor and fragment ion masses, and we show that peptides identified very confidently using one extraction tool might not be matched when using another tool. We also found a bias towards peptides of lower charge state when extracting fragment ion data from higher resolution raw data without deconvolution. Collecting and comparing the extracted data from the same raw data allow adjusting parameters and expectations and selecting the right tool for extraction of tandem MS data.     

Knowledge-engineering software. A demonstration of a high-end tool

Many investigators wanting to apply knowledge-based systems (KBSs) as consultants for cancer diagnosis have turned to tools running on personal computers. While some of these tools serve well for small tasks, they lack the power available with such high-end KBS tools as KEE (Knowledge Engineering Environment) and ART (Automated Reasoning Tool). These tools were originally developed on Lisp machines and have the full functionality of the Lisp language as well as many additional features. They provide a rich and highly productive environment for the software developer. This paper illustrates the capability of one of these high-end tools. First, a table showing the classification of benign soft tissue tumors was converted into a KEE knowledge base. The tools available in KEE were then used to identify the tumor type for a hypothetical patient.     

Number and type of guideline implementation tools varies by guideline,clinical condition,country of origin,and type of developer organization: content analysis of guidelines

Background

Guideline implementation tools (GI tools) can improve clinician behavior and patient outcomes. Analyses of guidelines published before 2010 found that many did not offer GI tools. Since 2010 standards, frameworks and instructions for GI tools have emerged. This study analyzed the number and types of GI tools offered by guidelines published in 2010 or later.

Methods

Content analysis and a published GI tool framework were used to categorize GI tools by condition, country, and type of organization. English-language guidelines on arthritis, asthma, colorectal cancer, depression, diabetes, heart failure, and stroke management were identified in the National Guideline Clearinghouse. Screening and data extraction were in triplicate. Findings were reported with summary statistics.

Results

Eighty-five (67.5%) of 126 eligible guidelines published between 2010 and 2017 offered one or more of a total of 464 GI tools. The mean number of GI tools per guideline was 5.5 (median 4.0, range 1 to 28) and increased over time. The majority of GI tools were for clinicians (239, 51.5%), few were for patients (113, 24.4%), and fewer still were to support implementation (66, 14.3%) or evaluation (46, 9.9%). Most clinician GI tools were guideline summaries (116, 48.5%), and most patient GI tools were condition-specific information (92, 81.4%). Government agencies (patient 23.5%, clinician 28.9%, implementation 24.1%, evaluation 23.5%) and developers in the UK (patient 18.5%, clinician 25.2%, implementation 27.2%, evaluation 29.1%) were more likely to generate guidelines that offered all four types of GI tools. Professional societies were more likely to generate guidelines that included clinician GI tools.

Conclusions

Many guidelines do not include any GI tools, or a variety of GI tools for different stakeholders that may be more likely to prompt guideline uptake (point-of-care forms or checklists for clinicians, decision-making or self-management tools for patients, implementation and evaluation tools for managers and policy-makers). While this may vary by country and type of organization, and suggests that developers could improve the range of GI tools they develop, further research is needed to identify determinants and potential solutions. Research is also needed to examine the cost-effectiveness of various types of GI tools so that developers know where to direct their efforts and scarce resources.

     

Assessing computational tools for the discovery of small RNA genes in bacteria

Over the past decade, a number of biocomputational tools have been developed to predict small RNA (sRNA) genes in bacterial genomes. In this study, several of the leading biocomputational tools, which use different methodologies, were investigated. The performance of the tools, both individually and in combination, was evaluated on ten sets of benchmark data, including data from a novel RNA-seq experiment conducted in this study. The results of this study offer insight into the utility as well as the limitations of the leading biocomputational tools for sRNA identification and provide practical guidance for users of the tools.     

Anvaya: a workflows environment for automated genome analysis

Anvaya is a workflow environment for automated genome analysis that provides an interface for several bioinformatics tools and databases, loosely coupled together in a coordinated system, enabling the execution of a set of analyses tools in series or in parallel. It is a client-server workflow environment that has an advantage over existing software as it enables extensive pre & post processing of biological data in an efficient manner. "Anvaya" offers the user, novel functionalities to carry out exhaustive comparative analysis via "custom tools," which are tools with new functionality not available in standard tools, and "built-in PERL parsers," which automate data-flow between tools that hitherto, required manual intervention. It also provides a set of 11 pre-defined workflows for frequently used pipelines in genome annotation and comparative genomics ranging from EST assembly and annotation to phylogenetic reconstruction and microarray analysis. It provides a platform that serves as a single-stop solution for biologists to carry out hassle-free and comprehensive analysis, without being bothered about the nuances involved in tool installation, command line parameters, format conversions required to connect tools and manage/process multiple data sets at a single instance.     

Evolution of web services in bioinformatics

Bioinformaticians have developed large collections of tools to make sense of the rapidly growing pool of molecular biological data. Biological systems tend to be complex and in order to understand them, it is often necessary to link many data sets and use more than one tool. Therefore, bioinformaticians have experimented with several strategies to try to integrate data sets and tools. Owing to the lack of standards for data sets and the interfaces of the tools this is not a trivial task. Over the past few years building services with web-based interfaces has become a popular way of sharing the data and tools that have resulted from many bioinformatics projects. This paper discusses the interoperability problem and how web services are being used to try to solve it, resulting in the evolution of tools with web interfaces from HTML/web form-based tools not suited for automatic workflow generation to a dynamic network of XML-based web services that can easily be used to create pipelines.     

Web Resources for Metagenomics Studies

The development of next-generation sequencing(NGS) platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for metagenomics data analysis with respect to their quality and detail of analysis using simulated metagenomics data. There are at least a dozen such software tools presently available in the public domain. Among them, MGRAST, IMG/M, and METAVIR are the most well-known tools according to the number of citations by peer-reviewed scientific media up to mid-2015. Here, we describe 12 online tools with respect to their web link, annotation pipelines, clustering methods, online user support, and availability of data storage. We have also done the rating for each tool to screen more potential and preferential tools and evaluated five best tools using synthetic metagenome. The article comprehensively deals with the contemporary problems and the prospects of metagenomics from a bioinformatics viewpoint.     

Amino acid biophysical properties in the statistical prediction of peptide-MHC class I binding

Background

Peptides derived from endogenous antigens can bind to MHC class I molecules. Those which bind with high affinity can invoke a CD8⁺ immune response, resulting in the destruction of infected cells. Much work in immunoinformatics has involved the algorithmic prediction of peptide binding affinity to various MHC-I alleles. A number of tools for MHC-I binding prediction have been developed, many of which are available on the web.

Results

We hypothesize that peptides predicted by a number of tools are more likely to bind than those predicted by just one tool, and that the likelihood of a particular peptide being a binder is related to the number of tools that predict it, as well as the accuracy of those tools. To this end, we have built and tested a heuristic-based method of making MHC-binding predictions by combining the results from multiple tools. The predictive performance of each individual tool is first ascertained. These performance data are used to derive weights such that the predictions of tools with better accuracy are given greater credence. The combined tool was evaluated using ten-fold cross-validation and was found to signicantly outperform the individual tools when a high specificity threshold is used. It performs comparably well to the best-performing individual tools at lower specificity thresholds. Finally, it also outperforms the combination of the tools resulting from linear discriminant analysis.

Conclusion

A heuristic-based method of combining the results of the individual tools better facilitates the scanning of large proteomes for potential epitopes, yielding more actual high-affinity binders while reporting very few false positives.     

L’industrie du Paléolithique inférieur du site de Wujiagou,Hubei Province,République Populaire de Chine

The site of Wujiagou, Hubei Province in China, dated to just over 800,000 years, in sandy deposits and sandy-silt which covers a river terrace of the end of the Early Pleistocene, delivered a rich lithic industry, mainly composed of pebbles tools. This industry has an archaic aspect, consisted by the abundance of pebbles tools, the presence of hand-axes, and the small amount of small tools. The pebble tools include choppers and picks, in addition of band-axes. Small tools are relatively poor and have few simple retouched scrapers.     

L’analyse des unités techno-fonctionnelles appliquée à l’étude du macro-outillage néolithique

Ground stone tools are lithic tools made on coarse blanks that are not included in the chipped or polished stone studies. During the study of a ground stone tools collection coming from the Campaniform site of Beg ar Loued (Molène island, Finistère, France), the techno-functional unit (TFU) analysis as been adapted to these objects. A TFU is a part of a tool that is technologically independent, having his own part in this tool's overall functioning. The application of this method to ground stone tools needed some adaptations to their characteristics. The aim is to obtain a high level technological analysis for these tools, succeeding to express functional hypothesis. Two concrete examples from Beg ar Loued's collection illustrate the TFU analysis method's application to ground stone tools. This method has the advantage to organize the progress of each piece's analysis. The TFU analysis helps to understand the multifunctional tools by considering each function as a full tool. This allows us to talk about function's hierarchisation and their adaptation to blanks. We also obtain some informations about blank's selection. These many and varied results make the TFU analysis essential for ground stone tool's technological and functional analysis.     

Gene expression profiling in osteoblast biology: bioinformatic tools

This review focuses on using microarray data on a clonal osteoblast cell model to demonstrate how various current and future bioinformatic tools can be used to understand, at a more global or comprehensible level, how cells grow and differentiate. In this example, BMP2 was used to stimulate growth and differentiation of osteoblast to a mineralized matrix. A discussion is included on various methods for clustering gene expression data, statistical evaluation of data, and various new tools that can be used to derive deeper insight into a particular biological problem. How these tools can be obtained is also discussed. New tools for the biologists to compare their datasets with others, as well as examples of future bioinformatic tools that can be used for developing gene networks and pathways for a given set of data are included and discussed.     

河南舞阳贾湖遗址出土石器的微痕分析

石器作为人类物质文化的记录者,在史前人类的生产生活中占据着重要地位,对石器功能和使用方式的探讨是考古学关注的问题之一。目前国内石器研究的主要手段是从器物形态出发,进行类型学的研究,针对石器具体功能及使用方式的实证研究较为缺乏,对磨制石器的研究尤为不足。有鉴于此,本研究以中原地区舞阳贾湖遗址出土的磨制石器为研究对象,利用微痕分析和实验考古的方法,对石器的功能、使用方式及加工对象进行分析和判断。结果表明:石镰的主要功能是收割禾本科植物;石刀主要用于加工禾本科植物、木材和兽骨等;石斧的功能主要是加工木材,另外还可能承担加工兽皮和兽骨的工作;石锛的主要功能与木作有关;石凿在形态上有所区别,但其加工对象主要是木材;石铲的功能以掘土为主。微痕分析的结果使我们对贾湖聚落磨制石器的功能有了客观的认识,可以看出石器的功能并不单一,广泛存在着"一器多用"的现象。本研究从石器使用的角度,揭示了史前人类的生产活动和行为特点,同时也为研究先民的生业经济状况提供了重要材料。     

Stone tool analysis and human origins research: some advice from Uncle Screwtape

The production of purposefully fractured stone tools with functional, sharp cutting edges is a uniquely derived hominin adaptation. In the long history of life on earth, only hominins have adopted this remarkably expedient and broadly effective technological strategy. In the paleontological record, flaked stone tools are irrefutable proof that hominins were present at a particular place and time. Flaked stone tools are found in contexts ranging from the Arctic to equatorial rainforests and on every continent except Antarctica. Paleolithic stone tools show complex patterns of variability, suggesting that they have been subject to the variable selective pressures that have shaped so many other aspects of hominin behavior and morphology. There is every reason to expect that insights gained from studying stone tools should provide vital and important information about the course of human evolution. And yet, one senses that archeological analyses of Paleolithic stone tools are not making as much of a contribution as they could to the major issues in human origins research.     

XML schemas for common bioinformatic data types and their application in workflow systems

Background  

Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats.     

Simulation tools for biochemical networks: evaluation of performance and usability

MOTIVATION: Simulation of dynamic biochemical systems is receiving considerable attention due to increasing availability of experimental data of complex cellular functions. Numerous simulation tools have been developed for numerical simulation of the behavior of a system described in mathematical form. However, there exist only a few evaluation studies of these tools. Knowledge of the properties and capabilities of the simulation tools would help bioscientists in building models based on experimental data. RESULTS: We examine selected simulation tools that are intended for the simulation of biochemical systems. We choose four of them for more detailed study and perform time series simulations using a specific pathway describing the concentration of the active form of protein kinase C. We conclude that the simulation results are convergent between the chosen simulation tools. However, the tools differ in their usability, support for data transfer to other programs and support for automatic parameter estimation. From the experimentalists' point of view, all these are properties that need to be emphasized in the future.     

Plaidoyer pour un outillage lithique de l’Âge du fer : le cas des maillets à gorge de l’Ouest de la France

The attention is turned here to one kind of tools, characterized by a special morphology: the grooved hammer-stones. They are known in Europe and all over the world in various cultures, as Neolithic or Bronze Age remains and generally linked to extraction or mining activity; but, the discovery of several of these tools in western France, within pre-roman archaeological contexts, especially in sites devoted to marine salt production, leads us to a discussion on dating and the function of such tools, and feeds a more general reflexion about the existence of a specialised lithic set of tools during the Iron Age.