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An introduction to computational tools for differential binding analysis with ChlP-seq data

Frontiers of Electrical and Electronic Engineering in China 2017年第3期5卷 226-235页

作者： Shiqi Tu Zhen Shao CAS Key Laboratory of computational Biology Collaborative Innovation Center for Genetics and Developmental Biology CAS- Max Planck Society Partner Institute for Computational Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China. Graduate university of Chinese Academy of Sciences Beijing 100049 China

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.

关键词： ChIP-seq peak calling differential binding analysis computational tools

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Making Canonical Workflow Building Blocks Interoperable across Workflow Languages

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Data Intelligence 2022年第2期4卷 342-357页

作者： Stian Soiland-Reyes Genis Bayarri Pau Andrio Robin Long Douglas Lowe Ania Niewielska Adam Hospital Paul Groth Department of Computer Science The University of ManchesterManchester M139PLUK Informatics Institute University of AmsterdamAmsterdam 1098 XHThe Netherlands Institute for Research in Biomedicine(IRB Barcelona) The Barcelona Institute of Science and Technology(BIST)Barcelona O8028Spain The Spanish National Bioinformatics Institute(INB) Barcelona Supercomputing Center(BSC)Barcelona 08034Spain Data Science Institute Lancaster UniversityLancasterLancashire LA14YWUK Research IT IT ServicesThe University of ManchesterManchester M139PLUK European Bioinformatics Institute(EMBL-EBI) HinxtonCambridgeshire CB101SDUK

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.

关键词： Scientific workflows Interoperable FAIR computational tools Containers Software packaging FAIR digital object(FDO),BioExcel Building Blocks library(BioBB),Canonical Workflow Frameworks for Research(CWFR)

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Geometry-based graphical methods for solar control in architecture:A digital framework

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Frontiers of Architectural Research 2023年第4期12卷 754-774页

作者： Federico Bertagna Valeria Piccioni Pierluigi D’Acunto Department of Architecture ETH ZurichZurich 8093Switzerland School of Engineering and Design Technical University of MunichMunich 80333Germany

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.

关键词： Solar control Geometry Graphical methods Facade design Passive design computational tools

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