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Docker: lightweight Linux containers for consistent development and deployment
Abstract
Docker promises the ability to package applications and their dependencies into lightweight containers that move easily between different distros, start up quickly and are isolated from each other.
... Secure.inc utilizes a containerized infrastructure to isolate potentially harmful files within a controlled execution space. By executing files inside these secured containers, the system ensures that any malicious activity remains confined, preventing it from spreading to other parts of the device or compromising user data [1], [5]. This containment strategy adds a critical layer of protection that conventional mobile security tools, which lack such granularity, often cannot provide [6], [11]. ...
... Secure.inc addresses this by executing each file within an isolated container environment, effectively safeguarding the core system from exposure to malicious behavior [1], [10]. ...
The widespread adoption of mobile platforms for data exchange and file management has introduced heightened concerns regarding malware and overall system security. To address this, the cross-platform mobile solution Secure.inc has been developed. It implements container- based isolation to assess and analyze files within a secure virtual environment prior to user access, thereby minimizing the risk of infection [1], [2]. Built using Flutter for the frontend, with backend services supported by Node.js and Express.js, the system also utilizes Firebase for real-time database operations. Files are processed within a cloud- hosted container, allowing for proactive threat detection and isolation. This approach enhances system resilience while maintaining performance, offering users a robust defense mechanism without degrading device efficiency [3], [4], [10]. Keywords— Containerization, Malware Detection, Secure File Handling, Mobile Security, Flutter, Node.js, Firebase
... The aim is to offer the product as an easily accessible open platform, where organizations can create and transform their own datasets. We also offer the solution as a Docker file [25] with a Linux-based OS, which can be used by organizations with their own infrastructure. In this way, the proposed solution can be used both as an industrial data platform -only trusted organizations can join it -and as a public data marketplace, in terms of B2B data sharing tools classification [26]. ...
Our paper focuses on Linked Data Lineage as the collection of modeled organizational data, enabling continuous integration and modern governance in Business-to-Business (B2B) sharing. We first explore approaches organizations adopt to enhance B2B data integration. Next, we highlight key B2B and Business-to-Government (B2G) linked data use cases and strategies for governance frameworks. We review software tools supporting data governance and propose a systemic method for defining organizational integration flows. This is demonstrated through a system enabling businesses to design linked data pipelines, leveraging Semantic Web technologies for continuous integration and governance. Insights and recommendations for improving data sharing processes are provided.
... The genome assembly and evaluation pipelines were developed using the nf-core tooling 37 , using MultiQC 38 , and making extensive use of the Conda package manager, the Bioconda initiative 39 , the Biocontainers infrastructure 40 , and the Docker 41 and Singularity 42 containerisation solutions. ...
The Southern Corroboree frog ( Pseudophryne corroboree ; Anura; Myobatrachidae) is a Critically Endangered amphibian, according to the IUCN, and is endemic to the Snowy Mountains region of Kosciuszko National Park in New South Wales, Australia. This species has been driven to functional extinction by the introduction of the fungal disease, chytridiomycosis. Here we provide the first reference genome for P. corroboree . Using PacBio HiFi sequencing, Arima Hi-C, and Bionano optical mapping, we produced a chromosome-level genome assembly. Additionally, we generated a reference transcriptome based on multiple tissues from both male and female individuals to support genome annotation. The resulting genome spans 8.87 Gb across 12 chromosomes, with a contig N50 of 6.8 Mb. This research provides a phased, annotated genome assembly along with transcriptomic resources to facilitate future conservation genomic studies of P. corroboree . Furthermore, the genome offers an invaluable resource for taxonomic and evolutionary research, particularly given the nearest available chromosome-level reference genome is from Mixophyes fleayi , a species that last shared a common ancestor with P. corroboree 80 million years ago.
... Sandboxing: Code execution is isolated using Docker containers [23], with each session assigned a ephemeral container to prevent cross-contamination. Containers are preconfigured with a minimal Alpine Linux image and Python 3.11 to reduce startup latency. ...
This is the study that presents an AI-Python-based chatbot that helps students to learn programming by demonstrating solutions to such problems as debugging errors, solving syntax problems or converting abstract theoretical concepts to practical implementations. Traditional coding tools like Integrated Development Environments (IDEs) and static analyzers do not give robotic help while AI-driven code assistants such as GitHub Copilot focus on getting things done. To close this gap, our chatbot combines static code analysis, dynamic execution tracing, and large language models (LLMs) to provide the students with relevant and practical advice, hence promoting the learning process. The chatbot's hybrid architecture employs CodeLlama for code embedding, GPT-4 for natural language interactions, and Docker-based sandboxing for secure execution. Evaluated through a mixed-methods approach involving 1,500 student submissions, the system demonstrated an 85% error resolution success rate, outperforming standalone tools like pylint (62%) and GPT-4 (73%). Quantitative results revealed a 59.3% reduction in debugging time among users, with pre-and post-test assessments showing a 34% improvement in coding proficiency, particularly in recursion and exception handling. Qualitative feedback from 120 students highlighted the chatbot's clarity, accessibility, and confidence-building impact, though critiques included occasional latency and restrictive code sanitization. Emphasizing the ethical aspects of the project, the bias principle led to the discrimination of gendered reasons for 83% and the GDPR-iPad-like procedures to anonymity were followed. The chatbot's productivity points to its ability to make coding education available to everyone and to give 24/7 aid to students in some not well-funded schools. Future work will expand multilingual support through localized datasets and culturally adapted examples, integrate gamification to enhance engagement, and develop collaborative learning features. By balancing technical innovation with pedagogical empathy, this research provides a blueprint for AI tools that prioritize educational equity and long-term skill retention over mere code completion. The chatbot exemplifies how AI can augment human instruction, fostering deeper conceptual understanding in programming education.
... The blobtoolkit pipeline was developed using nf-core tooling (Ewels et al., 2020) and MultiQC (Ewels et al., 2016), relying on the Conda package manager, the Bioconda initiative (Grüning et al., 2018), the Biocontainers infrastructure (da Veiga Leprevost et al., 2017), as well as the Docker (Merkel, 2014) and Singularity (Kurtzer et al., 2017) containerisation solutions. Table 3 contains a list of relevant software tool versions and sources. ...
We present a genome assembly from an individual Lucinisca nassula (the woven lucine; Mollusca; Bivalvia; Lucinida; Lucinidae). The genome sequence is 2,926.50 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.1 kilobases in length. The genome sequence of a bacterial endosymbiont, Ca . Thiodiazotropha sp. was also assembled.
... By reducing manual input and enhancing reproducibility, the pipeline is particularly well-suited for large-scale, multi-center studies where standardization and scalability are essential. The segmentation tools implemented leverage machine learning and deep learning methods that have demonstrated such as Docker [39], to encapsulate applications and their dependencies into portable containers. This method allows for consistent deployment across various environments, including cloud platforms, local servers, and edge devices [40]. ...
Accurate, reproducible body composition analysis from abdominal computed tomography (CT) images is critical for both clinical research and patient care. We present a fully automated, artificial intelligence (AI)-based pipeline that streamlines the entire process—from data normalization and anatomical landmarking to automated tissue segmentation and quantitative biomarker extraction. Our methodology ensures standardized inputs and robust segmentation models to compute volumetric, density, and cross-sectional area metrics for a range of organs and tissues. Additionally, we capture selected DICOM header fields to enable downstream analysis of scan parameters and facilitate correction for acquisition-related variability. By emphasizing portability and compatibility across different scanner types, image protocols, and computational environments, we ensure broad applicability of our framework. This toolkit is the basis for the Opportunistic Screening Consortium in Abdominal Radiology (OSCAR) and has been shown to be robust and versatile, critical for large multi-center studies.
Graphical abstract
... Genome sequences with no hits are chunked with seqtk and aligned to the NT database with blastn(Altschul et al., 1990). The blobtools suite combines all these outputs into a blobdir for visualisation.The blobtoolkit pipeline was developed using nf-core tooling(Ewels et al., 2020) andMultiQC (Ewels et al., 2016), relying on the Conda package manager, the Bioconda initiative(Grüning et al., 2018), the Biocontainers infrastructure(da Veiga Leprevost et al., 2017), as well as the Docker(Merkel, 2014) andSingularity (Kurtzer et al., 2017) containerisation solutions. ...
We present a genome assembly from a specimen of Tamarix gallica (Tamarisk; Streptophyta; Magnoliopsida; Caryophyllales; Tamaricaceae). The assembly contains two haplotypes with total lengths of 1,404.82 megabases and 1,536.15 megabases. Most of haplotype 1 (98.66%) is scaffolded into 12 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial and plastid genome assemblies have lengths of 483.72 kilobases and 156.16 kilobases, respectively.
... The blobtoolkit pipeline was developed using nf-core tooling (Ewels et al., 2020) and MultiQC (Ewels et al., 2016), relying on the Conda package manager, the Bioconda initiative (Grüning et al., 2018), the Biocontainers infrastructure (da Veiga Leprevost et al., 2017), as well as the Docker (Merkel, 2014) and Singularity (Kurtzer et al., 2017) containerisation solutions. Table 4 contains a list of relevant software tool versions and sources. ...
We present a genome assembly from a female specimen of Podarcis filfolensis (Maltese wall lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The assembly contains two haplotypes with total lengths of 1,506.95 megabases and 1,404.02 megabases. Most of haplotype 1 (98.73%) is scaffolded into 20 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.23 kilobases.
... The whole application is distributed as Docker images and deployed in Docker containers [34], according to the scheme in Fig. 3. The platform is composed of three modules: 1) User Interface (UI) module: the component is written in Typescript and uses Bootstrap as a frontend toolkit, Stencil, a reusable web components compiler, and Plotly.js ...
Renewable Energy Communities (RECs) are envisaged as a key enabler for a citizen-driven energy transition. The pooling of renewable energy resources at a local level and the active involvement of public entities, Small and Medium-sized Enterprises (SMEs) and private customers can lower the energy costs of end-consumers and increase public acceptance of renewable projects. At the same time, the RECs can support power system operation by leveraging their flexibility and providing ancillary services to the grid. While a significant amount of research has focused on optimizing the operation of existing RECs to maximize their performance and economic benefits, fewer studies have analysed the forecast of future REC performance to support the planning of new communities. The present paper tackles this research gap by developing a novel tool for the forecast of techno-economic performance of REC. The tool relies on two different techniques (based on statistical random sampling and neural networks, respectively) to predict the energy behaviour of RECs on the basis of their fundamental planning parameters (type/number of members, installed generation, geographical location). In order to reach a larger audience of practitioners, a web-based open-source implementation of the tool has been developed and made available to the general public, designing a graphical interface that facilitates the use of the tool by non-technical experts.
... Manager) and supports modular extensions (R-4). To simplify the setup and usage, as well as to ensure cross-platform consistency, configuration is centralized and a Docker [27] workflow is provided for development and deployment (R-5). ...
Teleoperation is a key enabler for future mobility, supporting Automated Vehicles in rare and complex scenarios beyond the capabilities of their automation. Despite ongoing research, no open source software currently combines Remote Driving, e.g., via steering wheel and pedals, Remote Assistance through high-level interaction with automated driving software modules, and integration with a real-world vehicle for practical testing. To address this gap, we present a modular, open source teleoperation software stack that can interact with an automated driving software, e.g., Autoware, enabling Remote Assistance and Remote Driving. The software features standardized interfaces for seamless integration with various real-world and simulation platforms, while allowing for flexible design of the human-machine interface. The system is designed for modularity and ease of extension, serving as a foundation for collaborative development on individual software components as well as realistic testing and user studies. To demonstrate the applicability of our software, we evaluated the latency and performance of different vehicle platforms in simulation and real-world. The source code is available on GitHub.
... Any entity requesting a certificate from the root CA that is not listed in the root CA's record is denied service. The services are written in Node.js [20] and configured as Docker [15] images, making the implementation transferable and lightweight. ...
This work explores the performance and scalability of a hierarchical certificate authority framework with automated certificate issuance employing post-quantum cryptographic (PQC) signature algorithms. The system is designed for compatibility with both classical and PQC algorithms, promoting crypto-agility while ensuring robust security against quantum-based threats. The proposed framework design expects minimal cryptographic requirements from potential clients, protects certificates of high importance against cross-dependent chains-of-trust and allows for prompt switching between classical and PQC algorithms. Finally, we evaluate SPHINCS, Falcon, and Dilithium variants in various configurations of certificate issuance and verification accommodating a large client base, underlining the trade-offs in balancing performance, scalability, and security.
The growth of IoT devices has generated an increasing demand for effective, agile, and scalable deployment frameworks. Traditional IoT architectures are generally strained by interoperability, real-time responsiveness, and resource optimization due to inherent complexity in managing heterogeneous devices and large-scale deployments. While containerization and dynamic API frameworks are seen as solutions, current methodologies are founded primarily on static API architectures that cannot be adapted in real time with evolving data structures and communication needs. Dynamic routing has been explored, but current solutions lack database schema flexibility and endpoint management. This work presents a Dockerized framework that integrates Dynamic RESTful APIs with containerization to achieve maximum flexibility and performance in IoT configurations. With the use of FastAPI for asynchronous processing, the framework dynamically scales API schemas as per real-time conditions, achieving maximum device interaction efficiency. Docker provides guaranteed consistent, portable deployment across different environments. An emulated IoT environment was used to measure significant performance parameters, including functionality, throughput, response time, and scalability. The evaluation shows that the framework maintains high throughput, with an error rate of 3.11% under heavy loads and negligible latency across varying traffic conditions, ensuring fast response times without compromising system integrity. The framework demonstrates significant advantages in IoT scenarios requiring the addition of new parameters or I/O components where dynamic endpoint generation enables immediate monitoring without core application changes. Architectural decisions involving RESTful paradigms, microservices, and containerization are also discussed in this paper to ensure enhanced flexibility, modularity, and performance. The findings provide a valuable addition to dynamic IoT API framework design, illustrating how dynamic, Dockerized RESTful APIs can improve the efficiency and flexibility of IoT systems.
The growing demand for reproducible research is based on the expectation that publishing research in this form will enable its reuse and the generation of new knowledge. However, reproducibility alone does not guarantee these benefits. Users still need to make considerable efforts to understand the data and analysis code before they can reuse these components in other contexts. To address this challenge, we introduce the Data-to-Knowledge Package (D2K-Package), a collection of research materials including source code and open FAIR data, virtual labs, web API services, and computational workflows. The D2K-Package’s core is the reproducible basis composed of the data and source code on which an analysis is based. This core is designed such that the other components can be derived from it. The main goal of the package is to help researchers generate new knowledge by facilitating the understanding and encouraging the reuse of reproducible research. We demonstrate the applicability of the D2K-Package with a hydrological use case which can be also used for testing, and discuss its seamless integration into the research cycle.
StructMAn is a method for protein structural annotation. It describes each position of a protein sequence or specific variants in it in terms of their importance for the three-dimensional (3D) structure of the protein and its interactions with other molecules. StructMAn maps, aligns, and aggregates data from experimentally resolved and predicted 3D structures of proteins and their homologs for any given protein sequence and/or a combination of mutations in it. The results provide structural annotation for every amino acid position allowing a detailed structural analysis. Furthermore, StructMAn enables generation of a wide variety of position-specific high-quality structural features that can be leveraged in machine learning applications. With the new web server StructMAn 2.0 Web, we provide a user-friendly way to use StructMAn offering an easy-to-use input interface and a comprehensive visualization for the various results of StructMAn. StructMAn 2.0 Web is available at https://tools.helmholtz-hips.de/structman.
During development, dynamic changes in gene expression and chromatin architecture drive the transition from progenitors to specialised cell types. Here we use single cell ATAC sequencing (scATAC-seq) to investigate changes in chromatin accessibility as neural plate border cells segregate into neural, neural crest and placode cells. We developed a Nextflow pipeline, single cell Advanced Chromatin Exploration (scACE), which integrates scATAC-seq and scRNA-seq data to identify cell state specific accessibility profiles and groups of chromatin regions with coordinated dynamic behaviour, termed accessibility modules (AMs). We find that progenitors are characterised by broadly open chromatin, reflecting their broad potential to generate any ectodermal derivative. As development proceeds, cell-type-specific chromatin signatures are established. Inferring an enhancer-centric gene regulatory network, we predict Foxk2 as new regulator for placode specification and verify this prediction experimentally. Foxk2 target enhancers are open in placodal, but not any other ectodermal cells. This finding suggests that on a regulatory level, cells can use different strategies to control fate choice: differential accessibility of enhancers and broad accessibility controlled by differentially expressed transcription factors.
The need for computational resources grows as computational algorithms gain popularity in different sectors of the scientific community. Sequential codes need to be converted to parallel versions to optimize the use of these resources. Maintaining a local infrastructure for the execution of distributed computing, through desktop grids, for example, has been replaced in favor of cloud platforms that abstract the complexity of these local infrastructures. Unfortunately, the cost of accessing these resources could leave out various studies that could be carried by a simpler infrastructure. In this article, we present a platform for distributing computer simulations on resources available on a local network using container virtualization that abstracts the complexity needed to configure these execution environments and allows any user can benefit from this infrastructure. Simulations could be developed in any programming language (such as Python, Java, C, and R) and with specific execution needs within reach of the scientific community in a general way. We will present results obtained in running simulations that required more than 1000 runs with different initial parameters and various other experiments that benefited from using the platform.
We present a genome assembly from a specimen of Galeopsis tetrahit (the common hemp-nettle; Streptophyta; Magnoliopsida; Lamiales; Lamiaceae). The genome sequence has a total length of 1,430.70 megabases. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules, supporting the specimen being an allotetraploid (2 n = 4 x = 32). The plastid genome and 10 multipartite mitochondrial sequences were also assembled. Gene annotation of this assembly on Ensembl identified 42,915 protein-coding genes.
We present a genome assembly from a male specimen of Agonopterix alstromeriana (Brown-spot Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence has a total length of 491.16 megabases. Most of the assembly (99.59%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.32 kilobases.
We present a genome assembly from a haploid male specimen of Bombus vestalis (Vestal Cuckoo Bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence has a total length of 280.01 megabases. Most of the assembly (91.96%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,600 protein-coding genes.
We present a genome assembly from a specimen of Barbarea vulgaris (winter-cress or yellow rocket; Streptophyta; Magnoliopsida; Brassicales; Brassicaceae). The genome sequence has a total length of 246.25 megabases. Most of the assembly (99.45%) is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 364.65 kilobases and 154.59 kilobases, respectively. Gene annotation of this assembly at Ensembl identified 24,516 protein-coding genes.
We present a genome assembly from a specimen of Euphorbia peplus (petty spurge; Streptophyta; Magnoliopsida; Malpighiales; Euphorbiaceae). The genome sequence has a total length of 277.10 megabases. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. We also assembled six multipartite mitochondrial molecules and one plastid genome.
We present a genome assembly from a female specimen of Nomada lathburiana (Lathbury's Nomad Bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence has a total length of 269.68 megabases. Most of the assembly (90.08%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 29.04 kilobases. Gene annotation of this assembly by Ensembl identified 11,607 protein-coding genes.
We present a genome assembly from a female specimen of Podarcis erhardii (Erhard's wall lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The assembly contains two haplotypes with total lengths of 1,495.98 megabases and 1,477.75 megabases. Most of haplotype 1 (99.28%) is scaffolded into 20 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.14 kilobases.
We present a genome assembly from a female specimen of Pyrrhia umbra (Bordered Sallow; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 433.58 megabases. Most of the assembly (99.99%) is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 15.36 kilobases.
We present a genome assembly from a specimen of Alisma plantago-aquatica (common water plantain; Streptophyta; Magnoliopsida; Alismatales; Alismataceae). The genome sequence has a total length of 9,377.97 megabases. Most of the assembly (99.53%) is scaffolded into 7 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 250.4 kilobases and 159.88 kilobases, respectively.
We present a genome assembly from a male specimen of Scoparia ambigualis (Common Grey; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a total length of 1,040.83 megabases. Most of the assembly (99.56%) is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.33 kilobases.
We present a genome assembly from a male specimen of Plagodis pulveraria (American Barred Umber; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 931.73 megabases. Most of the assembly (99.83%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.98 kilobases.
We present a genome assembly from a male specimen of Scotopteryx chenopodiata (Shaded Broad-bar; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 337.86 megabases. Most of the assembly (98.85%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.65 kilobases.
We present a genome assembly from a female specimen of Nomada ferruginata (Yellow-shouldered Nomad Bee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence has a total length of 310.50 megabases. Most of the assembly (90.75%) is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 26.13 kilobases. Gene annotation of this assembly on Ensembl identified 11,828 protein-coding genes.
We present a genome assembly from a female Humulus lupulus plant (Common hop, Hops; Streptophyta; Magnoliopsida; Rosales; Cannabaceae). The genome sequence has a total length of 2,488.10 megabases. Most of the assembly (99.39%) is scaffolded into 10 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial and plastid genome assemblies have lengths of 400.02 kilobases and 153.77 kilobases, respectively. Gene annotation of this assembly by Ensembl identified 32,487 protein-coding genes.
The MTBseq pipeline, published in 2018, was designed to address bioinformatics challenges in tuberculosis research using whole-genome sequencing data. It was the first publicly available pipeline on Github to perform full analysis of WGS data for M. tuberculosis encompassing quality control through mapping, variant calling for lineage classification, drug resistance prediction, and phylogenetic inference. However, the pipeline's architecture is not optimal for high-performance computing or cloud computing environments, which often require large datasets. To optimize the pipeline, a Nextflow wrapper MTBseq-nf, was created which offers shorter execution times through the parallel mode along with multiple other thematic improvements. The MTBseq-nf wrapper, as opposed to the linear batched analysis of samples in TBfull step of MTBseq pipeline, can execute multiple instances of the same step in parallel and therefore makes full use of the provided computational resources. For evaluation of scalability and reproducibility, we used 90 M. tuberculosis genomes (ENA accession PRJEB7727) for the benchmarking analysis on a dedicated computing server. In our experiments the execution time of MTBseq-nf parallel analysis mode is at least twice as fast as the standard MTBseq pipeline for more than 20 samples. Furthermore, the MTBseq-nf wrapper facilitates reproducibility using the nf-core, bioconda, and biocontainers projects for platform independence. The proposed MTBseq-nf wrapper pipeline is a user-friendly pipeline optimized for hardware efficiency, scalability for larger datasets, and improved reproducibility.
We present a genome assembly from a female specimen of Ditula angustiorana (Red-barred Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 468.36 megabases. Most of the assembly (99.83%) is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 16.19 kilobases.
We present a genome assembly from a specimen of Amphibalanus improvisus (Bay barnacle; Arthropoda; Thecostraca; Balanomorpha; Balanidae). The genome sequence has a total length of 763.27 megabases. Most of the assembly (91.83%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 15.34 kilobases.
We present a genome assembly from a male specimen of Hoplodrina octogenaria (Uncertain moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 476.65 megabases. Most of the assembly (99.98%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.93 kilobases.
This research presents a novel framework and experimental results that combine zero-knowledge proofs (ZKPs) with private blockchain technology to safeguard whistleblower privacy while ensuring secure digital evidence submission and verification. For example, whistleblowers involved in corporate fraud cases can submit sensitive financial records anonymously while maintaining the credibility of the evidence. The proposed framework introduces several key innovations, including a private blockchain implementation utilising proof-of-work (PoW) consensus to ensure immutable storage and thorough scrutiny of submitted evidence, with mining difficulty dynamically aligned to the sensitivity of the data. It also features an adaptive difficulty mechanism that automatically adjusts computational requirements based on the sensitivity of the evidence, providing tailored protection levels. In addition, a unique two-phase validation process is incorporated, which generates a digital signature from the evidence alongside random challenges, significantly improving security and authenticity. The integration of ZKPs enables iterative hash-based verification between parties (Prover and Verifier) while maintaining the complete privacy of the source data. This research investigates the whistleblower’s niche in traditional digital evidence management systems (DEMSs), prioritising privacy without compromising evidence integrity. Experimental results demonstrate the framework’s effectiveness in preserving anonymity while assuring the authenticity of the evidence, making it useful for judicial systems and organisations handling sensitive disclosures. This paper signifies notable progress in secure whistleblowing systems, offering a way to juggle transparency with informant confidentiality.
Writing code is becoming essential for psychology and neuroscience research, supporting increasingly advanced experimental designs, processing of ever-larger datasets and easy reproduction of scientific results. Despite its critical role, coding remains challenging for many researchers, as it is typically not part of formal academic training. We present a range of practices tailored to different levels of programming experience, from beginners to advanced users. Our ten principles help researchers streamline and automate their projects, reduce human error, and improve the quality and reusability of their code. For principal investigators, we highlight the benefits of fostering a collaborative environment that values code sharing. Maintaining basic standards for code quality, reusability, and shareability is critical for increasing the trustworthiness and reliability of research in experimental psychology and cognitive neuroscience.
We present a genome assembly of the diplonemid Diplonema japonicum YPF1604 (Discoba; Euglenozoa; Diplonemea; Diplonemidae). The genome sequence is 62.30 megabases in span. Most of the assembly is scaffolded into 118 chromosomal pseudomolecules. The multipartite mitochondrial genome was also assembled. The genome sequences of two bacterial endosymbionts, Ca . Cytomitobacter primus and Ca. Cytomitobacter primus, were also assembled.
We present a genome assembly from a specimen of Narthecium ossifragum (Bog Asphodel; Streptophyta; Magnoliopsida; Dioscoreales; Nartheciaceae). The genome sequence has a total length of 378.87 megabases. Most of the assembly (98.91%) is scaffolded into 13 chromosomal pseudomolecules. Two mitochondrial multipartite genomes of 309.19 and 100.78 kilobases, and a plastid genome of 155.31 kilobases were assembled.
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