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This article recounts, from my perspective of four decades in this field, evolving paradigms of primary cell wall structure and the mechanism of surface enlargement of growing cell walls. Updates of the structures, physical interactions, and roles of cellulose, xyloglucan, and pectins are presented. This leads to an example of how a conceptual depiction of wall structure can be translated into an explicit quantitative model based on molecular dynamics methods. Comparison of the model's mechanical behavior with experimental results provides insights into the molecular basis of complex mechanical behaviors of primary cell wall and uncovers the dominant role of cellulose-cellulose interactions in forming a strong yet extensible network.

Abstract. With the eddy covariance (EC) technique, net fluxes of carbon dioxide (CO2) and other trace gases as well as water and energy fluxes can be measured at the ecosystem level. These flux measurements are a main source for understanding biosphere–atmosphere interactions and feedbacks through cross-site analysis, model–data integration, and upscaling. The raw fluxes measured with the EC technique require extensive and laborious data processing. While there are standard tools1 available in an open-source environment for processing high-frequency (10 or 20 Hz) data into half-hourly quality-checked fluxes, there is a need for more usable and extensible tools for the subsequent post-processing steps. We tackled this need by developing the REddyProc package in the cross-platform language R that provides standard CO2-focused post-processing routines for reading (half-)hourly data from different formats, estimating the u* threshold, as well as gap-filling, flux-partitioning, and visualizing the results. In addition to basic processing, the functions are extensible and allow easier integration in extended analysis than current tools. New features include cross-year processing and a better treatment of uncertainties. A comparison of REddyProc routines with other state-of-the-art tools resulted in no significant differences in monthly and annual fluxes across sites. Lower uncertainty estimates of both u* and resulting gap-filled fluxes by 50 % with the presented tool were achieved by an improved treatment of seasons during the bootstrap analysis. Higher estimates of uncertainty in daytime partitioning (about twice as high) resulted from a better accounting for the uncertainty in estimates of temperature sensitivity of respiration. The provided routines can be easily installed, configured, and used. Hence, the eddy covariance community will benefit from the REddyProc package, allowing easier integration of standard post-processing with extended analysis. 1http://fluxnet.fluxdata.org/2017/10/10/toolbox-a-rolling-list-of-softwarepackages-for-flux-related-data-processing/, last access: 17 August 2018

The Point-to-Point Protocol (PPP) [1] provides a standard method for transporting multi-protocol datagrams over point-to-point links.PPP also defines an extensible Link Control Protocol, which allows negotiation of an Authentication Protocol for authenticating its peer before allowing Network Layer protocols to transmit over the link.This document defines the PPP Extensible Authentication Protocol.

We present TrackMate, an open source Fiji plugin for the automated, semi-automated, and manual tracking of single-particles. It offers a versatile and modular solution that works out of the box for end users, through a simple and intuitive user interface. It is also easily scriptable and adaptable, operating equally well on 1D over time, 2D over time, 3D over time, or other single and multi-channel image variants. TrackMate provides several visualization and analysis tools that aid in assessing the relevance of results. The utility of TrackMate is further enhanced through its ability to be readily customized to meet specific tracking problems. TrackMate is an extensible platform where developers can easily write their own detection, particle linking, visualization or analysis algorithms within the TrackMate environment. This evolving framework provides researchers with the opportunity to quickly develop and optimize new algorithms based on existing TrackMate modules without the need of having to write de novo user interfaces, including visualization, analysis and exporting tools. The current capabilities of TrackMate are presented in the context of three different biological problems. First, we perform Caenorhabditis-elegans lineage analysis to assess how light-induced damage during imaging impairs its early development. Our TrackMate-based lineage analysis indicates the lack of a cell-specific light-sensitive mechanism. Second, we investigate the recruitment of NEMO (NF-κB essential modulator) clusters in fibroblasts after stimulation by the cytokine IL-1 and show that photodamage can generate artifacts in the shape of TrackMate characterized movements that confuse motility analysis. Finally, we validate the use of TrackMate for quantitative lifetime analysis of clathrin-mediated endocytosis in plant cells.

The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

Summary: FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The dashboard groups samples in dropdowns for navigation among the data sets, utilizes human-readable configuration files to manipulate the pages and tabs, and is extensible with CSV data. Availability and Implementation: FQC is implemented in Python 3 and Javascript, and is maintained under an MIT license. Documentation and source code is available at: https://github.com/pnnl/fqc . Contact: joseph.brown@pnnl.gov.

sdm is an object‐oriented, reproducible and extensible, platform for species distribution modelling. It uses individual species and community‐based approaches, enabling ensembles of models to be fitted and evaluated, to project species potential distributions in space and time. It provides a standardized and unified structure for handling species distributions data and modelling techniques, and supports markedly different modelling approaches, including correlative, process‐based (mechanistic), agent‐based, and cellular automata. The object‐oriented design of software is such that scientists can modify existing methods, extend the framework by developing new methods or modelling procedures, and share them to be reproduced by other scientists. sdm can handle spatial and temporal data for single or multiple species and uses high performance computing solutions to speed up modelling and simulations. The framework is implemented in R, providing a flexible and easy‐to‐use GUI interface.

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GenX is a versatile program using the differential evolution algorithm for fitting X-ray and neutron reflectivity data. It utilizes the Parratt recursion formula for simulating specular reflectivity. The program is easily extensible, allowing users to incorporate their own models into the program. This can be useful for fitting data from other scattering experiments, or for any other minimization problem which has a large number of input parameters and/or contains many local minima, where the differential evolution algorithm is suitable. In addition, GenX manages to fit an arbitrary number of data sets simultaneously. The program is released under the GNU General Public License.

SRILM is a collection of C++ libraries, executable programs, and helper scripts designed to allow both production of and experimen-tation with statistical language models for speech recognition and other applications. SRILM is freely available for noncommercial purposes. The toolkit supports creation and evaluation of a vari-ety of language model types based on N-gram statistics, as well as several related tasks, such as statistical tagging and manipu-lation of N-best lists and word lattices. This paper summarizes the functionality of the toolkit and discusses its design and imple-mentation, highlighting ease of rapid prototyping, reusability, and combinability of tools. 1.

OpenMM is a software toolkit for performing molecular simulations on a range of high performance computing architectures. It is based on a layered architecture: the lower layers function as a reusable library that can be invoked by any application, while the upper layers form a complete environment for running molecular simulations. The library API hides all hardware-specific dependencies and optimizations from the users and developers of simulation programs: they can be run without modification on any hardware on which the API has been implemented. The current implementations of OpenMM include support for graphics processing units using the OpenCL and CUDA frameworks. In addition, OpenMM was designed to be extensible, so new hardware architectures can be accommodated and new functionality (e.g., energy terms and integrators) can be easily added.

Recently, both industry and academia have proposed many different roadmaps for the future of DRAM. Consequently, there is a growing need for an extensible DRAM simulator, which can be easily modified to judge the merits of today's DRAM standards as well as those of tomorrow. In this paper, we present Ramulator, a fast and cycle-accurate DRAM simulator that is built from the ground up for extensibility. Unlike existing simulators, Ramulator is based on a generalized template for modeling a DRAM system, which is only later infused with the specific details of a DRAM standard. Thanks to such a decoupled and modular design, Ramulator is able to provide out-of-the-box support for a wide array of DRAM standards: DDR3/4, LPDDR3/4, GDDR5, WIO1/2, HBM, as well as some academic proposals (SALP, AL-DRAM, TL-DRAM, RowClone, and SARP). Importantly, Ramulator does not sacrifice simulation speed to gain extensibility: according to our evaluations, Ramulator is 2.5× faster than the next fastest simulator. Ramulator is released under the permissive BSD license.

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Open source software encourages innovation by allowing users to extend the functionality of existing applications. Treeview is a popular application for the visualization of microarray data, but is closed-source and platform-specific, which limits both its current utility and suitability as a platform for further development. Java Treeview is an open-source, cross-platform rewrite that handles very large datasets well, and supports extensions to the file format that allow the results of additional analysis to be visualized and compared. The combination of a general file format and open source makes Java Treeview an attractive choice for solving a class of visualization problems. An applet version is also available that can be used on any website with no special server-side setup.

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Myle Ott, Sergey Edunov, Alexei Baevski, Angela Fan, Sam Gross, Nathan Ng, David Grangier, Michael Auli. Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics (Demonstrations). 2019.

Most security attacks exploit instances of well-known classes of implementation flaws. Developers could detect and eliminate many of these flaws before deploying the software, yet these problems persist with disturbing frequency-not because the security community doesn't sufficiently understand them but because techniques for preventing them have not been integrated into the software development process. This article describes an extensible tool that uses lightweight static analysis to detect common security vulnerabilities (including buffer overflows and format string vulnerabilities).

Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. Several sophisticated software packages (e.g., AFNI, BrainVoyager, FSL, FreeSurfer, Nipy, R, SPM) are used to process and analyze large and often diverse (highly multi-dimensional) data. However, this heterogeneous collection of specialized applications creates several issues that hinder replicable, efficient, and optimal use of neuroimaging analysis approaches: (1) No uniform access to neuroimaging analysis software and usage information; (2) No framework for comparative algorithm development and dissemination; (3) Personnel turnover in laboratories often limits methodological continuity and training new personnel takes time; (4) Neuroimaging software packages do not address computational efficiency; and (5) Methods sections in journal articles are inadequate for reproducing results. To address these issues, we present Nipype (Neuroimaging in Python: Pipelines and Interfaces; http://nipy.org/nipype), an open-source, community-developed, software package, and scriptable library. Nipype solves the issues by providing Interfaces to existing neuroimaging software with uniform usage semantics and by facilitating interaction between these packages using Workflows. Nipype provides an environment that encourages interactive exploration of algorithms, eases the design of Workflows within and between packages, allows rapid comparative development of algorithms and reduces the learning curve necessary to use different packages. Nipype supports both local and remote execution on multi-core machines and clusters, without additional scripting. Nipype is Berkeley Software Distribution licensed, allowing anyone unrestricted usage. An open, community-driven development philosophy allows the software to quickly adapt and address the varied needs of the evolving neuroimaging community, especially in the context of increasing demand for reproducible research.

To investigate the interactions of extensibility and parallelism in database query processing, we have developed a new dataflow query execution system called Volcano. The Volcano effort provides a rich environment for research and education in database systems design, heuristics for query optimization, parallel query execution, and resource allocation. Volcano uses a standard interface between algebra operators, allowing easy addition of new operators and operator implementations. Operations on individual items, e.g., predicates, are imported into the query processing operators using support functions. The semantics of support functions is not prescribed; any data type including complex objects and any operation can be realized. Thus, Volcano is extensible with new operators, algorithms, data types, and type-specific methods. Volcano includes two novel meta-operators. The choose-plan meta-operator supports dynamic query evaluation plans that allow delaying selected optimization decisions until run-time, e.g., for embedded queries with free variables. The exchange meta-operator supports intra-operator parallelism on partitioned datasets and both vertical and horizontal inter-operator parallelism, translating between demand-driven dataflow within processes and data-driven dataflow between processes. All operators, with the exception of the exchange operator, have been designed and implemented in a single-process environment, and parallelized using the exchange operator. Even operators not yet designed can be parallelized using this new operator if they use and provide the interator interface. Thus, the issues of data manipulation and parallelism have become orthogonal, making Volcano the first implemented query execution engine that effectively combines extensibility and parallelism.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>