Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacteri...Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft(partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.展开更多
Background： Gene transcription in eukaryotie cells is collectively controlled by a large panel of ehromatin associated proteins and ChIP-seq is now widely used to locate their binding sites along the whole genome. In...Background： Gene transcription in eukaryotie cells is collectively controlled by a large panel of ehromatin associated proteins and ChIP-seq is now widely used to locate their binding sites along the whole genome. Inferring the differential binding sites of these proteins between biological conditions by comparing the corresponding ChIP-seq samples is of general interest, yet it is still a computationally challenging task. Results： Here, we briefly review the computationhl tools developed in recent years for differential binding analysis with ChIP-seq data. The methods are extensively classified by their strategy of statistical modeling and s＇cope of application. Finally, a decision tree is presented for choosing proper tools based on the specific dataset. Conclusions： Computational tools for differential binding analysis with ChIP-seq data vary significantly with respect to their applicability and performance. This review can serve as a practical guide for readers to select appropriate tools for their own datasets.展开更多
Robotic hands grasp and manipulate objects through the contact forces between the fingers and the objects. The determination of contact forces in grasping is discussed in this paper. To systematically investigate the ...Robotic hands grasp and manipulate objects through the contact forces between the fingers and the objects. The determination of contact forces in grasping is discussed in this paper. To systematically investigate the characteristics of different grasps, the vector space of contact forces is decomposed into four subspaces and their basis is found by an efficient computational method. The vector of contact forces is then formulated into four components: active and passive grasping forces, controllable and uncontrollable internal forces. The dimensions of the subspaces identify uncontrollable internal forces. The contact force is further expressed into an explicit function of the external wrench and the joint torques. The resulting formulation simplifies the computation in the optimization of contact forces and makes the optimal variables controllable. Two numerical cases are given to show the simplicity and validity of the method.展开更多
The form of a building is among the most critical design aspects concerning building energy consumption.Form-based passive design strategies,like solar control,can significantly reduce heating and cooling demands if i...The form of a building is among the most critical design aspects concerning building energy consumption.Form-based passive design strategies,like solar control,can significantly reduce heating and cooling demands if implemented early in the design process.In this sense,there is an evident need for tools that can adequately support designers in their decisions.This paper aims to illustrate how geometry-based graphical methods(GGM)can provide effective support in the conceptual design stage.The paper introduces a novel digital framework for designing and analysing shading devices that leverages geometrical models and graphical methods.The digital implementation of GGM allows extending their applicability to threedimensional and non-planar geometries.A comprehensive review of existing methods and tools for the design of shading devices lays the ground for the proposed digital framework,which is then demonstrated through two case studies.The results show that the diagrammatic nature of GGM facilitates a better and more direct understanding of the relationship between form and performance.展开更多
We introduce the concept of Canonical Workflow Building Blocks(CWBB),a methodology of describing and wrapping computational tools,in order for them to be utilised in a reproducible manner from multiple workflow langua...We introduce the concept of Canonical Workflow Building Blocks(CWBB),a methodology of describing and wrapping computational tools,in order for them to be utilised in a reproducible manner from multiple workflow languages and execution platforms.The concept is implemented and demonstrated with the BioExcel Building Blocks library(BioBB),a collection of tool wrappers in the field of computational biomolecular simulation.Interoperability across different workflow languages is showcased through a protein Molecular Dynamics setup transversal workflow,built using this library and run with 5 different Workflow Manager Systems(WfMS).We argue such practice is a necessary requirement for FAIR Computational Workflows and an element of Canonical Workflow Frameworks for Research(CWFR)in order to improve widespread adoption and reuse of computational methods across workflow language barriers.展开更多
With the continuing development and improvement of genome-wide techniques, a great number of candidate genes are discovered. How to identify the most likely disease genes among a large number of candidates becomes a f...With the continuing development and improvement of genome-wide techniques, a great number of candidate genes are discovered. How to identify the most likely disease genes among a large number of candidates becomes a fundamental challenge in human health. A common view is that genes related to a specific or similar disease tend to reside in the same neighbourhood of biomolecular networks. Recently, based on such observations,many methods have been developed to tackle this challenge. In this review, we firstly introduce the concept of disease genes, their properties, and available data for identifying them. Then we review the recent computational approaches for prioritizing candidate disease genes based on Protein-Protein Interaction（PPI） networks and investigate their advantages and disadvantages. Furthermore, some pieces of existing software and network resources are summarized. Finally, we discuss key issues in prioritizing candidate disease genes and point out some future research directions.展开更多
With many cores driven by high memory bandwidth, today＇s graphics processing unit （GPU） has involved into an absolute computing workhorse. More and more scientists, researchers and software developers are using GPU...With many cores driven by high memory bandwidth, today＇s graphics processing unit （GPU） has involved into an absolute computing workhorse. More and more scientists, researchers and software developers are using GPUs to accelerate their algorithms and ap- plications. Developing complex programs and software on the GPU, however, is still far from easy with ex- isting tools provided by hardware vendors. This article introduces our recent research efforts to make GPU soft- ware development much easier. Specifically, we designed BSGP, a high-level programming language for general- purpose computation on the GPU. A BSGP program looks much the same as a sequential C program, and is thus easy to read, write and maintain. Its performance on the GPU is guaranteed by a well-designed compiler that converts the program to native GPU code. We also developed an effective debugging system for BSGP pro- grams based on the GPU interrupt, a unique feature of BSGP that allows calling CPU functions from inside GPU code. Moreover, using BSGP, we developed GPU algorithms for constructing several widely-used spatial hierarchies for high-performance graphics applications.展开更多
基金Supported by Coordenao de Aperfeioamento de Pessoal de Nível Superior(CAPES)in Brazil,processes BEX 12954-12-8 and 11517-12-3,to Barbosa EGV and Aburjaile FF
文摘Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft(partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.
文摘Background： Gene transcription in eukaryotie cells is collectively controlled by a large panel of ehromatin associated proteins and ChIP-seq is now widely used to locate their binding sites along the whole genome. Inferring the differential binding sites of these proteins between biological conditions by comparing the corresponding ChIP-seq samples is of general interest, yet it is still a computationally challenging task. Results： Here, we briefly review the computationhl tools developed in recent years for differential binding analysis with ChIP-seq data. The methods are extensively classified by their strategy of statistical modeling and s＇cope of application. Finally, a decision tree is presented for choosing proper tools based on the specific dataset. Conclusions： Computational tools for differential binding analysis with ChIP-seq data vary significantly with respect to their applicability and performance. This review can serve as a practical guide for readers to select appropriate tools for their own datasets.
基金National Natural Science Foundation of China(59985001)
文摘Robotic hands grasp and manipulate objects through the contact forces between the fingers and the objects. The determination of contact forces in grasping is discussed in this paper. To systematically investigate the characteristics of different grasps, the vector space of contact forces is decomposed into four subspaces and their basis is found by an efficient computational method. The vector of contact forces is then formulated into four components: active and passive grasping forces, controllable and uncontrollable internal forces. The dimensions of the subspaces identify uncontrollable internal forces. The contact force is further expressed into an explicit function of the external wrench and the joint torques. The resulting formulation simplifies the computation in the optimization of contact forces and makes the optimal variables controllable. Two numerical cases are given to show the simplicity and validity of the method.
文摘The form of a building is among the most critical design aspects concerning building energy consumption.Form-based passive design strategies,like solar control,can significantly reduce heating and cooling demands if implemented early in the design process.In this sense,there is an evident need for tools that can adequately support designers in their decisions.This paper aims to illustrate how geometry-based graphical methods(GGM)can provide effective support in the conceptual design stage.The paper introduces a novel digital framework for designing and analysing shading devices that leverages geometrical models and graphical methods.The digital implementation of GGM allows extending their applicability to threedimensional and non-planar geometries.A comprehensive review of existing methods and tools for the design of shading devices lays the ground for the proposed digital framework,which is then demonstrated through two case studies.The results show that the diagrammatic nature of GGM facilitates a better and more direct understanding of the relationship between form and performance.
基金The National Key Basic Research Program of China(2013CB910203)the National Natural Science Foundation of China(31270760)+1 种基金the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB08030102)the Specialized Research Fund for the Doctoral Program of Higher Education(20113402120013)
基金a project funded by the European Union contracts H2020-INFRAEDI-02-2018823830,and H2020-EINFRA-2015-1675728funded through EOSC-Life(https://www.eosc-life.eu)contract H2020-INFRAEOSC-2018-2824087ELIXIR-CONVERGE(https://elixir-europe.org)contract H2020-INFRADEV-2019-2871075.
文摘We introduce the concept of Canonical Workflow Building Blocks(CWBB),a methodology of describing and wrapping computational tools,in order for them to be utilised in a reproducible manner from multiple workflow languages and execution platforms.The concept is implemented and demonstrated with the BioExcel Building Blocks library(BioBB),a collection of tool wrappers in the field of computational biomolecular simulation.Interoperability across different workflow languages is showcased through a protein Molecular Dynamics setup transversal workflow,built using this library and run with 5 different Workflow Manager Systems(WfMS).We argue such practice is a necessary requirement for FAIR Computational Workflows and an element of Canonical Workflow Frameworks for Research(CWFR)in order to improve widespread adoption and reuse of computational methods across workflow language barriers.
文摘With the continuing development and improvement of genome-wide techniques, a great number of candidate genes are discovered. How to identify the most likely disease genes among a large number of candidates becomes a fundamental challenge in human health. A common view is that genes related to a specific or similar disease tend to reside in the same neighbourhood of biomolecular networks. Recently, based on such observations,many methods have been developed to tackle this challenge. In this review, we firstly introduce the concept of disease genes, their properties, and available data for identifying them. Then we review the recent computational approaches for prioritizing candidate disease genes based on Protein-Protein Interaction（PPI） networks and investigate their advantages and disadvantages. Furthermore, some pieces of existing software and network resources are summarized. Finally, we discuss key issues in prioritizing candidate disease genes and point out some future research directions.
文摘With many cores driven by high memory bandwidth, today＇s graphics processing unit （GPU） has involved into an absolute computing workhorse. More and more scientists, researchers and software developers are using GPUs to accelerate their algorithms and ap- plications. Developing complex programs and software on the GPU, however, is still far from easy with ex- isting tools provided by hardware vendors. This article introduces our recent research efforts to make GPU soft- ware development much easier. Specifically, we designed BSGP, a high-level programming language for general- purpose computation on the GPU. A BSGP program looks much the same as a sequential C program, and is thus easy to read, write and maintain. Its performance on the GPU is guaranteed by a well-designed compiler that converts the program to native GPU code. We also developed an effective debugging system for BSGP pro- grams based on the GPU interrupt, a unique feature of BSGP that allows calling CPU functions from inside GPU code. Moreover, using BSGP, we developed GPU algorithms for constructing several widely-used spatial hierarchies for high-performance graphics applications.
