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Beginning Backdrop CMS
Learn what Backdrop CMS is and how it fulfills the role of a content management system, along with how to install and configure it. This book teaches how to create and manage content, taxonomy, users, page layouts, and menus to get the best site possible. You'll also see how to install on shared hosting - which is a focus of the Backdrop CMS team - to make hosting your website affordable. Backdrop has a very strong community, and Beginning Backdrop CMS shows you how to leverage Backdrop's repository of contributed modules and themes to expand the functionality and look of your site, along with how to contribute your own material to the community. Beginning Backdrop CMS focuses on the user who is responsible for building, maintaining, and managing an organization's website and who is interested in Backdrop's ability to meet their site's requirements. It covers why you should consider using a content management system when building a new web site. By reading this book, you will: Understand why you should use Backdrop CMS and the power of the platform. Build confidence in your ability to use Backdrop CMS. Gain the knowledge necessary to build, deploy, and manage web sites of moderate complexity on Backdrop. Understand the process for migrating a Drupal 6 or 7 site to Backdrop CMS.
Book
Investigation of 2D Seismic DDA Method for Numerical Simulation of Shaking Table Test of Rock Mass Engineering
Since the basic theory of the discontinue deformation analysis (DDA) method was proposed, the DDA open source has gone through a long development process. At present, different kinds of programs have been widely applied in rock mass engineering such as slope, dam, and tunnel. This paper introduces the solution principle of DDA motion equations in detail, as well as the development status of the 2D open-source program. Numerical simulation of shaking table test of rock mass engineering using 2D DDA program is highlighted, and investigations of seismic wave pre-processing and seismic input method are carried out. First, based on the Newmark integration scheme, the integration algorithms of synthetic or measured seismic wave time history, correction function of seismic wave, and DDA simulation are unified. Then, three seismic input methods are implanted in the DDA program, and the applicability of various seismic input methods is discussed. On this basis, using the improved seismic 2D DDA program, a shaking table test of typical rock mass engineering is simulated. Through the comparison between the theoretical/test data and simulation results, the reliability of the improved DDA program in seismic response analysis is verified; the large mass method and the large stiffness method are more suitable for rigid foundation, such as shaking table test; the propagation of the seismic wave presents a significant amplification effect due to the reflection, refraction, and diffraction in the tunnel. The research results provide DDA theory and an open-source program for analyzing the seismic response of rock mass engineering.
Journal Article
An image J plugin for the high throughput image analysis of in vitro scratch wound healing assays
In vitro scratch wound healing assay, a simple and low-cost technique that works along with other image analysis tools, is one of the most widely used 2D methods to determine the cellular migration and proliferation in processes such as regeneration and disease. There are open-source programs such as imageJ to analyze images of in vitro scratch wound healing assays, but these tools require manual tuning of various parameters, which is time-consuming and limits image throughput. For that reason, we developed an optimized plugin for imageJ to automatically recognize the wound healing size, correct the average wound width by considering its inclination, and quantify other important parameters such as: area, wound area fraction, average wound width, and width deviation of the wound images obtained from a scratch/ wound healing assay. Our plugin is easy to install and can be used with different operating systems. It can be adapted to analyze both individual images and stacks. Additionally, it allows the analysis of images obtained from bright field, phase contrast, and fluorescence microscopes. In conclusion, this new imageJ plugin is a robust tool to automatically standardize and facilitate quantification of different in vitro wound parameters with high accuracy compared with other tools and manual identification.
Journal Article
PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing an appropriate partitioning scheme is an important step in most analyses because it can affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit statistical justification. Here, we describe two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models. These methods allow millions of partitioning schemes to be compared in realistic time frames and so permit the objective selection of partitioning schemes even for large multilocus DNA data sets. We demonstrate that these methods significantly outperform previous approaches, including both the ad hoc selection of partitioning schemes (e.g., partitioning by gene or codon position) and a recently proposed hierarchical clustering method. We have implemented these methods in an open-source program, PartitionFinder. This program allows users to select partitioning schemes and substitution models using a range of information-theoretic metrics (e.g., the Bayesian information criterion, akaike information criterion [AIC], and corrected AIC). We hope that PartitionFinder will encourage the objective selection of partitioning schemes and thus lead to improvements in phylogenetic analyses. PartitionFinder is written in Python and runs under Mac OSX 10.4 and above. The program, source code, and a detailed manual are freely available from www.robertlanfear.com/partitionfinder.
Journal Article
Kubernetes best practices : blueprints for building successful applications on Kubernetes
\"In this practical guide, four Kubernetes professionals with deep experience in distributed systems, enterprise application development, and open source will guide you through the process of building applications with this container orchestration system. Based on the experiences of companies that are running Kubernetes in production successfully, many of the methods are also backed by concrete code examples. This book is ideal for those already familiar with basic Kubernetes concepts who want to learn common best practices. You'll learn exactly what you need to know to build your best app with Kubernetes the first time.\"-- Provided by publisher
Book
Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction
RNAs are fundamental in living cells and perform critical functions determined by their tertiary architectures. However, accurate modeling of 3D RNA structure remains a challenging problem. We present a novel method, DRfold, to predict RNA tertiary structures by simultaneous learning of local frame rotations and geometric restraints from experimentally solved RNA structures, where the learned knowledge is converted into a hybrid energy potential to guide RNA structure assembly. The method significantly outperforms previous approaches by >73.3% in TM-score on a sequence-nonredundant dataset containing recently released structures. Detailed analyses showed that the major contribution to the improvements arise from the deep end-to-end learning supervised with the atom coordinates and the composite energy function integrating complementary information from geometry restraints and end-to-end learning models. The open-source DRfold program with fast training protocol allows large-scale application of high-resolution RNA structure modeling and can be further improved with future expansion of RNA structure databases.
Here the authors developed an open-source program (DRfold) for RNA tertiary structure prediction from sequence. Through a unique combination of end-to-end learning and geometry restraint guided simulations, the method demonstrates advantage over peer methods.
Journal Article
Programming Kubernetes : developing cloud-native applications
If you're looking to develop native applications in Kubernetes, this is your guide. Developers and AppOps administrators will learn how to build Kubernetes-native applications that interact directly with the API server to query or update the state of resources. AWS developer advocate Michael Hausenblas and Red Hat principal software engineer Stefan Schmanski explain the characteristics of these apps and show you how to program Kubernetes to build them. You'll explore the basic building blocks of Kubernetes, including the client-go API library and custom resources. All you need to get started is a rudimentary understanding of development and system administration tools and practices, such as package management, the Go programming language, and Git.
Book
NGmerge: merging paired-end reads via novel empirically-derived models of sequencing errors
Background
Advances in Illumina DNA sequencing technology have produced longer paired-end reads that increasingly have sequence overlaps. These reads can be merged into a single read that spans the full length of the original DNA fragment, allowing for error correction and accurate determination of read coverage. Extant merging programs utilize simplistic or unverified models for the selection of bases and quality scores for the overlapping region of merged reads.
Results
We first examined the baseline quality score - error rate relationship using sequence reads derived from PhiX. In contrast to numerous published reports, we found that the quality scores produced by Illumina were not substantially inflated above the theoretical values, once the reference genome was corrected for unreported sequence variants. The PhiX reads were then used to create empirical models of sequencing errors in overlapping regions of paired-end reads, and these models were incorporated into a novel merging program, NGmerge. We demonstrate that NGmerge corrects errors and ambiguous bases better than other merging programs, and that it assigns quality scores for merged bases that accurately reflect the error rates. Our results also show that, contrary to published analyses, the sequencing errors of paired-end reads are not independent.
Conclusions
We provide a free and open-source program, NGmerge, that performs better than existing read merging programs. NGmerge is available on GitHub (
https://github.com/harvardinformatics/NGmerge
) under the MIT License; it is written in C and supported on Linux.
Journal Article