DALI is a popular resource for comparing protein structures. The software is based on distance‐matrix alignment. The associated web server provides tools to navigate, integrate and organize some data ...pushed out by genomics and structural genomics. The server has been running continuously for the past 25 years. Structural biologists routinely use DALI to compare a new structure against previously known protein structures. If significant similarities are discovered, it may indicate a distant homology, that is, that the structures are of shared origin. This may be significant in determining the molecular mechanisms, as these may remain very similar from a distant predecessor to the present day, for example, from the last common ancestor of humans and bacteria. Meta‐analysis of independent reference‐based evaluations of alignment accuracy and fold discrimination shows DALI at top rank in six out of 12 studies. The web server and standalone software are available from http://ekhidna2.biocenter.helsinki.fi/dali.
Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated ...into meta-analyses. This makes it possible to generate new hypotheses by finding features that are reproducible across biospecimens and data layers. Qiita dramatically accelerates such integration tasks in a web-based microbiome-comparison platform, which we demonstrate with Human Microbiome Project and Integrative Human Microbiome Project (iHMP) data.
Research summary: Building on the problem-solving perspective, we study behaviors related to projects and the communication-based antecedents of such behaviors in the free open-source software (FOSS) ...community. We examine two kinds of problem/project-behaviors: Individuals can set up projects around the formulation of new problems or join existing projects and define and/or work on subproblems within an existing problem. The choice between these two behaviors is influenced by the mode of communication. A communication mode with little a priori structure is the best mode for communicating about new problems (i.e., formulating a problem); empirically, it is associated with project launching behaviors. In contrast, more structured communication fits subproblems better and is related to project joining behaviors. Our hypotheses derive support from data from the FOSS community. Managerial summary: We study how the way in which individuals communicate influence the project-behaviors they engage in. We find that relatively unstructured communication is associated with the setting up new projects, while communication that is structured around an artifact is associated with joining projects. Our findings hold implications for understanding how management may influence project behaviors and problem-solving: Firms that need to concentrate on more incremental problem-solving efforts (e.g., because a sufficient number of attractive problems have already been defined) should create environments in which interaction is undertaken mainly via artifacts. On the other hand, if firms seek to generate new problems (e.g., new strategic opportunities), they should create environments in which open-ended, verbal conversation is relatively more important than artifact-based communication.
Standardization serves a as a means to improve overall quality of life through the economies of scale gained from the pervasive adoption of technical solutions. It enables competition by facilitating ...interoperability between products of different vendors. The wider open source community develops free and open source software (FOSS) in a global upstream/downstream model that similarly benefits society as a public good. FOSS and standards setting organizations (SSOs) are both instruments causing standardizing effects. Innovators and policy-makers assume that a mutually beneficial collaboration between them is desirable. However, their exact relationship is not fully understood, especially when and how FOSS and SSOs complement each other, or displace each other as competitors. To be able to compare FOSS and SSOs, our study develops a phase model of standardization that is applicable to both approaches, and applies this model to compare the strengths and weaknesses of FOSS and SSOs against common opportunities and threats in the ICT sector. Based on qualitative expert interviews with FOSS and SSO representatives, the synthesis of the separate results support conclusions from a product, a process and a societal perspective. The study identifies cost of change as a key determinant for the efficacy of each approach. It concludes that FOSS and SSOs create complementary products, compete for efficiency of the standardization process, and are both independent and complementary standardization instruments available to industry and influenceable by policy-makers. The paper closes with a discussion of possible implications relevant to businesses, the wider open source community, SSOs and policy-makers.
orbitize! is an open-source, object-oriented software package for fitting the orbits of directly imaged objects. It packages the Orbits for the Impatient (OFTI) algorithm and a parallel-tempered ...Markov Chain Monte Carlo (MCMC) algorithm into a consistent and intuitive Python API. orbitize! makes it easy to run standard astrometric orbit fits; in less than 10 lines of code, users can read in data, perform one fit using OFTI and another using MCMC, and make two publication-ready figures. Extensive pedagogical tutorials, intended to be navigable by both orbit-fitting novices and seasoned experts, are available on our documentation page. We have designed the orbitize! API to be flexible and easy to use/modify for unique cases. orbitize! was designed by members of the exoplanet imaging community to be a central repository for algorithms, techniques, and know-how developed by this community. We intend for it to continue to expand and change as the field progresses and new techniques are developed, and call for community involvement in this process. Complete and up-to-date documentation is available at orbitize.info, and the source code is available at github.com/sblunt/orbitize.
Publication of the Belle II Software Kuhr, Thomas; Bianchi, Fabizio; De Pietro, Giacomo ...
EPJ Web of Conferences,
2024, Volume:
295
Journal Article, Conference Proceeding
Peer reviewed
Open access
The Belle II software was developed by a few hundred individual contributors over several years. Following the rising desire of making it publicly available, the collaboration established open source ...software policies and procedures. The political and technical challenges and their solutions at Belle II are discussed in this article. With the publication of the Belle II software, basf2, on GitHub and Zenodo in 2021 an important milestone towards open science was reached.
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Crystal Plasticity (CP) modeling is a powerful and well established computational materials science tool to investigate mechanical structure–property relations in crystalline ...materials. It has been successfully applied to study diverse micromechanical phenomena ranging from strain hardening in single crystals to texture evolution in polycrystalline aggregates. However, when considering the increasingly complex microstructural composition of modern alloys and their exposure to—often harsh—environmental conditions, the focus in materials modeling has shifted towards incorporating more constitutive and internal variable details of the process history and environmental factors into these structure–property relations. Technologically important fields of application of enhanced CP models include phase transformations, hydrogen embrittlement, irradiation damage, fracture, and recrystallization. A number of niche tools, containing multi-physics extensions of the CP method, have been developed to address such topics. Such implementations, while being very useful from a scientific standpoint, are, however, designed for specific applications and substantial efforts are required to extend them into flexible multi-purpose tools for a general end-user community. With the Düsseldorf Advanced Material Simulation Kit (DAMASK) we, therefore, undertake the effort to provide an open, flexible, and easy to use implementation to the scientific community that is highly modular and allows the use and straightforward implementation of different types of constitutive laws and numerical solvers. The internal modular structure of DAMASK follows directly from the hierarchy inherent to the employed continuum description. The highest level handles the partitioning of the prescribed field values on a material point between its underlying microstructural constituents and the subsequent homogenization of the constitutive response of each constituent. The response of each microstructural constituent is determined, at the intermediate level, from the time integration of the underlying constitutive laws for elasticity, plasticity, damage, phase transformation, and heat generation among other coupled multi-physical processes of interest. Various constitutive laws based on evolving internal state variables can be implemented to provide this response at the lowest level. DAMASK already contains various CP-based models to describe metal plasticity as well as constitutive models to incorporate additional effects such as heat production and transfer, damage evolution, and athermal transformations. Furthermore, the implementation of additional constitutive laws and homogenization schemes, as well as the integration of a wide class of suitable boundary and initial value problem solvers, is inherently considered in its modular design.
A fully open source software program for automated two‐dimensional and one‐dimensional data reduction and preliminary analysis of isotropic small‐angle X‐ray scattering (SAXS) data is presented. The ...program is freely distributed, following the open‐source philosophy, and does not rely on any commercial software packages. BioXTAS RAW is a fully automated program that, via an online feature, reads raw two‐dimensional SAXS detector output files and processes and plots data as the data files are created during measurement sessions. The software handles all steps in the data reduction. This includes mask creation, radial averaging, error bar calculation, artifact removal, normalization and q calibration. Further data reduction such as background subtraction and absolute intensity scaling is fast and easy via the graphical user interface. BioXTAS RAW also provides preliminary analysis of one‐dimensional data in terms of the indirect Fourier transform using the objective Bayesian approach to obtain the pair‐distance distribution function, PDDF, and is thereby a free and open‐source alternative to existing PDDF estimation software. Apart from the TIFF input format, the program also accepts ASCII‐format input files and is currently compatible with one‐dimensional data files from SAXS beamlines at a number of synchrotron facilities. BioXTAS RAW is written in Python with C++ extensions.
A developer's field-guide to designing scalable services using Kubernetes Key Features * Develop and run your software using containers within a Kubernetes environment * Get hands-on experience of ...using Kubernetes with DevOps concepts such as continuous integration, benchmark testing, monitoring, and so on * Pragmatic example-based approach showing how to use Kubernetes in the development process Book Description Kubernetes is documented and typically approached from the perspective of someone running software that has already been built. Kubernetes may also be used to enhance the development process, enabling more consistent testing and analysis of code to help developers verify not only its correctness, but also its efficiency. This book introduces key Kubernetes concepts, coupled with examples of how to deploy and use them with a bit of Node.js and Python example code, so that you can quickly replicate and use that knowledge. You will begin by setting up Kubernetes to help you develop and package your code. We walk you through the setup and installation process before working with Kubernetes in the development environment. We then delve into concepts such as automating your build process, autonomic computing, debugging, and integration testing. This book covers all the concepts required for a developer to work with Kubernetes. By the end of this book, you will be in a position to use Kubernetes in development ecosystems. What you will learn * Build your software into containers * Deploy and debug software running in containers within Kubernetes * Declare and add configuration through Kubernetes * Define how your application fits together, using internal and external services * Add feedback to your code to help Kubernetes manage your services * Monitor and measure your services through integration testing and in production deployments Who this book is for If you are a full-stack or back-end software developers interested, curious, or being asked to test as well as run the code you're creating, you can leverage Kubernetes to make that process simpler and consistent regardless of where you deploy. If you're looking for developer focused examples in NodeJS and Python for how to build, test, deploy, and run your code with Kubernetes, this is perfect for you.
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