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MOTIVATION: Accurately assessing contacts between DNA fragments inside the nucleus with Hi-C experiment is crucial for understanding the role of 3D genome organization in gene regulation. This challenging task is due in part to the high sequencing depth of Hi-C libraries required to support high-resolution analyses. Most existing Hi-C data are collected with limited sequencing coverage, leading to poor chromatin interaction frequency estimation. Current computational approaches to enhance Hi-C signals focus on the analysis of individual Hi-C datasets of interest, without taking advantage of the facts that (i) several hundred Hi-C contact maps are publicly available and (ii) the vast majority of local spatial organizations are conserved across multiple cell types. RESULTS: Here, we present RefHiC-SR, an attention-based deep learning framework that uses a reference panel of Hi-C datasets to facilitate the enhancement of Hi-C data resolution of a given study sample. We compare RefHiC-SR against tools that do not use reference samples and find that RefHiC-SR outperforms other programs across different cell types, and sequencing depths. It also enables high-accuracy mapping of structures such as loops and topologically associating domains. AVAILABILITY AND IMPLEMENTATION: https://github.com/BlanchetteLab/RefHiC.
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Núcleo Celular , Bibliotecas , Cromatina/genéticaRESUMEN
The tendency of an amino acid to adopt certain configurations in folded proteins is treated here as a statistical estimation problem. We model the joint distribution of the observed mainchain and sidechain dihedral angles (ãÏ,ψ,χ1,χ2, ã) of any amino acid by a mixture of a product of von Mises probability distributions. This mixture model maps any vector of dihedral angles to a point on a multi-dimensional torus. The continuous space it uses to specify the dihedral angles provides an alternative to the commonly used rotamer libraries. These rotamer libraries discretize the space of dihedral angles into coarse angular bins, and cluster combinations of sidechain dihedral angles (ãχ1,χ2, ã) as a function of backbone ãÏ,ψã conformations. A 'good' model is one that is both concise and explains (compresses) observed data. Competing models can be compared directly and in particular our model is shown to outperform the Dunbrack rotamer library in terms of model complexity (by three orders of magnitude) and its fidelity (on average 20% more compression) when losslessly explaining the observed dihedral angle data across experimental resolutions of structures. Our method is unsupervised (with parameters estimated automatically) and uses information theory to determine the optimal complexity of the statistical model, thus avoiding under/over-fitting, a common pitfall in model selection problems. Our models are computationally inexpensive to sample from and are geared to support a number of downstream studies, ranging from experimental structure refinement, de novo protein design, and protein structure prediction. We call our collection of mixture models as PhiSiCal (Ïψχal). AVAILABILITY AND IMPLEMENTATION: PhiSiCal mixture models and programs to sample from them are available for download at http://lcb.infotech.monash.edu.au/phisical.
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Compresión de Datos , Bibliotecas , Aminoácidos , Biblioteca de Genes , Teoría de la InformaciónRESUMEN
SUMMARY: Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. This update describes new features and enhancements introduced over many new versions from 2015 to 2022. AVAILABILITY AND IMPLEMENTATION: Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Gráficos por Computador , Bibliotecas , Programas Informáticos , Navegador Web , DocumentaciónRESUMEN
MOTIVATION: Annotation of the mass signals is still the biggest bottleneck for the untargeted mass spectrometry analysis of complex mixtures. Molecular networks are being increasingly adopted by the mass spectrometry community as a tool to annotate large-scale experiments. We have previously shown that the process of propagating annotations from spectral library matches on molecular networks can be automated using Network Annotation Propagation (NAP). One of the limitations of NAP is that the information for the spectral matches is only propagated locally, to the first neighbor of a spectral match. Here, we show that annotation propagation can be expanded to nodes not directly connected to spectral matches using random walks on graphs, introducing the ChemWalker python library. RESULTS: Similarly to NAP, ChemWalker relies on combinatorial in silico fragmentation results, performed by MetFrag, searching biologically relevant databases. Departing from the combination of a spectral network and the structural similarity among candidate structures, we have used MetFusion Scoring function to create a weight function, producing a weighted graph. This graph was subsequently used by the random walk to calculate the probability of 'walking' through a set of candidates, departing from seed nodes (represented by spectral library matches). This approach allowed the information propagation to nodes not directly connected to the spectral library match. Compared with NAP, ChemWalker has a series of improvements, on running time, scalability and maintainability and is available as a standalone python package. AVAILABILITY AND IMPLEMENTATION: ChemWalker is freely available at https://github.com/computational-chemical-biology/ChemWalker. CONTACT: ridasilva@usp.br. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Bibliotecas , Bases de Datos Factuales , Biblioteca de Genes , Espectrometría de Masas , ProbabilidadRESUMEN
SUMMARY: 'PascalX' is a Python library providing fast and accurate tools for mapping SNP-wise GWAS summary statistics. Specifically, it allows for scoring genes and annotated gene sets for enrichment signals based on data from, both, single GWAS and pairs of GWAS. The gene scores take into account the correlation pattern between SNPs. They are based on the cumulative density function of a linear combination of χ2 distributed random variables, which can be calculated either approximately or exactly to high precision. Acceleration via multithreading and GPU is supported. The code of PascalX is fully open source and well suited as a base for method development in the GWAS enrichment test context. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/BergmannLab/PascalX and archived under doi://10.5281/zenodo.4429922. A user manual with usage examples is available at https://bergmannlab.github.io/PascalX/.
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Estudio de Asociación del Genoma Completo , Bibliotecas , Biblioteca de Genes , Programas Informáticos , Polimorfismo de Nucleótido SimpleRESUMEN
MOTIVATION: Analysis of allele-specific expression is strongly affected by the technical noise present in RNA-seq experiments. Previously, we showed that technical replicates can be used for precise estimates of this noise, and we provided a tool for correction of technical noise in allele-specific expression analysis. This approach is very accurate but costly due to the need for two or more replicates of each library. Here, we develop a spike-in approach which is highly accurate at only a small fraction of the cost. RESULTS: We show that a distinct RNA added as a spike-in before library preparation reflects technical noise of the whole library and can be used in large batches of samples. We experimentally demonstrate the effectiveness of this approach using combinations of RNA from species distinguishable by alignment, namely, mouse, human, and Caenorhabditis elegans. Our new approach, controlFreq, enables highly accurate and computationally efficient analysis of allele-specific expression in (and between) arbitrarily large studies at an overall cost increase of â¼5%. AVAILABILITY AND IMPLEMENTATION: Analysis pipeline for this approach is available at GitHub as R package controlFreq (github.com/gimelbrantlab/controlFreq).
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Caenorhabditis elegans , Bibliotecas , Humanos , Animales , Ratones , Alelos , Caenorhabditis elegans/genética , Biblioteca de Genes , ARN/genéticaRESUMEN
BACKGROUND: Public libraries in the United States have experienced increases in opioid-related substance use in their communities and on their premises. This includes fatal and non-fatal overdose events. Some libraries have adopted response measures in their branches to deter substance use or prevent overdose. A small number of libraries around the nation have decided to stock the opioid antagonist naloxone (Narcan) for staff to administer to patrons who experience overdose. This response measure has generated extensive media attention. Although Ohio ranks fourth in age-adjusted drug mortality rate in the United States, there has been no investigation of whether Ohio libraries are observing opioid-related transactions, consumption, and/or overdose events, or which measures they have adopted in response to these activities. We conducted a multimethod survey with Ohio public library directors to identify the response measures they have adopted. We present descriptive findings from the quantitative and qualitative items in our survey. METHODS: We conducted a cross-sectional 54-item multimethod survey of public library system directors (one per system) in Ohio. Directors of each of Ohio's public library systems were invited to participate via email. RESULTS: Of 251 library systems, 56 responded (22.3% response rate), with 34 respondents (60.7%) indicating awareness of opioid-related transactions, consumption, and/or overdose on their premises. Most (n = 43, 76.8%) did not stock naloxone in their buildings. Over half (n = 34, 60.7%) reported implementing one or more non-naloxone response measures. These measures focus on improving security for staff and patrons, deterring opioid-related transactions (purchases and exchanges) and consumption, and providing educational events on substance use. Nearly half (n = 25, 47.2%) partner with community organizations to provide opioid response measures. A similar proportion reported adequate funding to respond to opioid-related substance use (n = 23, 45.1%), and most (n = 38, 74.5%) reported adequate support from their boards and communities. Few respondents have implemented evaluations of their response measures. CONCLUSIONS: Ohio public libraries are responding to evidence of opioid-related transactions, consumption, and/or overdose on their premises with a range of measures that focus on substance use prevention and deterrence. Most Ohio library systems do not stock naloxone. Respondents indicated they prefer to call 911 and let first responders handle overdose events. The majority of respondents indicated their library systems have political capacity to respond to evidence of opioid-related substance use on their premises, but have limited operational and functional capacity. Findings suggest the need to revisit assumptions that public libraries are willing to stock naloxone to respond to overdose events, and that libraries have the resources to respond robustly to opioid-related transactions, consumption, and/or overdose on their premises.
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Naloxona , Trastornos Relacionados con Opioides , Humanos , Ohio , Estudios Transversales , Naloxona/uso terapéutico , Antagonistas de Narcóticos/uso terapéutico , Bibliotecas , Encuestas y Cuestionarios , Femenino , Masculino , Sobredosis de Droga/prevención & control , AdultoRESUMEN
BACKGROUND: Libraries in the UK have evolved from traditional book-lending institutions into dynamic community hubs, This study aims to explore the potential of libraries to act as community hubs to promote mental and physical health and wellbeing of community-dwelling adults, drawing on insights from both library users and library staff in England. DESIGN: A mixed-method, cross-sectional study using online survey and interviews with community-dwelling adults and library staff. METHODS: We collected data using a 14-item electronic survey and interviews with library users and staff to gauge perceptions. Descriptive statistics and thematic analysis were used to identify key trends and emergent themes. RESULTS: We included 605 respondents from the survey and interviewed 12 library users and staff. Libraries remain popular and are considered a 'safe place by members of the community, regardless of their frequency of service usage irrespective of whether they are frequent users of services. However, a lack of awareness among library users about community-facing services could act as a hurdle to improving community health and wellbeing. Targeted engagement with residents is needed to increase awareness of libraries' services, including community interventions to help tackle loneliness and inequalities in digital and health literacy. Library staff often did not feel involved in important decision-making. Various barriers, drivers and practical recommendations were identified to leverage libraries as hubs to promote community health and wellbeing. CONCLUSION: Libraries already offer a variety of resources that directly or indirectly support the health and wellbeing of community-dwelling adults and young people. However, public awareness of these services is limited. As we navigate post-pandemic recovery, libraries can serve as platforms for community engagement, fostering resilience, mental health support and reducing social isolation. Recognising libraries' untapped potential can lead to healthier communities and improved wellbeing.
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Vida Independiente , Bibliotecas , Humanos , Estudios Transversales , Masculino , Adulto , Femenino , Persona de Mediana Edad , Inglaterra , Adulto Joven , Salud Pública , Anciano , Promoción de la Salud , Encuestas y Cuestionarios , Adolescente , COVID-19/epidemiología , COVID-19/psicologíaRESUMEN
This paper discusses the design and implementation of the H5P image hotspots and describes additional use cases for library instruction in order to teach learners from across the country on how different spaces can be used to create private, accessible areas where patrons can conduct telehealth appointments. The Network of the National Library of Medicine created an online class using H5P image hotspots to allow learners to virtually explore a physical space. The class used Moodle, an open-source learning platform, and H5P image hotspots to demonstrate how libraries implemented telehealth programs.
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Instrucción por Computador , Bibliotecas , Estados Unidos , National Library of Medicine (U.S.) , AprendizajeRESUMEN
SUMMARY: Third-generation genome sequencing technologies have led to a sharp increase in the number of high-quality genome assemblies. This allows the comparison of multiple assembled genomes of individual species and demands new tools for visualizing their structural properties. Here, we present plotsr, an efficient tool to visualize structural similarities and rearrangements between genomes. It can be used to compare genomes on chromosome level or to zoom in on any selected region. In addition, plotsr can augment the visualization with regional identifiers (e.g. genes or genomic markers) or histogram tracks for continuous features (e.g. GC content or polymorphism density). AVAILABILITY AND IMPLEMENTATION: plotsr is implemented as a python package and uses the standard matplotlib library for plotting. It is freely available under the MIT license at GitHub (https://github.com/schneebergerlab/plotsr) and bioconda (https://anaconda.org/bioconda/plotsr). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Bibliotecas , Programas Informáticos , GenomaRESUMEN
SUMMARY: Analysis of intra- and extracellular dynamic like vesicles transport involves particle tracking algorithms. The design of a particle tracking pipeline is a routine but tedious task. Therefore, particle dynamics analysis is often performed by combining several pieces of software (filtering, detection, tracking, etc.) requiring many manual operations, and thus leading to poorly reproducible results. Given the new segmentation tools based on deep learning, modularity and interoperability between software have become essential in particle tracking algorithms. A good synergy between a particle detector and a tracker is of paramount importance. In addition, a user-friendly interface to control the quality of estimated trajectories is necessary. To address these issues, we developed STracking, a Python library that allows combining algorithms into standardized particle tracking pipelines. AVAILABILITY AND IMPLEMENTATION: STracking is available as a Python library using 'pip install' and the source code is publicly available on GitHub (https://github.com/sylvainprigent/stracking). A graphical interface is available using two napari plugins: napari-stracking and napari-tracks-reader. These napari plugins can be installed via the napari plugins menu or using 'pip install'. The napari plugin source codes are available on GitHub (https://github.com/sylvainprigent/napari-tracks-reader, https://github.com/sylvainprigent/napari-stracking). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Bibliotecas , Programas Informáticos , Algoritmos , Biblioteca de GenesRESUMEN
SUMMARY: Single-molecule localization microscopy has become an important part of the super-resolution microscopy toolbox in biomedical research. Software platforms for applying analytical methods to the point-based data structures are needed that offer both routine application and flexible customization of analysis procedures. We present a python library called LOCAN that consists of well-defined data structures and analysis methods for analyzing localization data in a script or computable notebook. AVAILABILITY AND IMPLEMENTATION: The package source code is released open-source under a BSD-3 license at https://github.com/super-resolution/Locan. It can be installed from the Python Package Index at https://pypi.org/project/locan. Documentation is available at https://locan.readthedocs.io.
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Bibliotecas , Microscopía , Programas Informáticos , DocumentaciónRESUMEN
SUMMARY: Mathematical models are effective in studying cancer development at different scales from metabolism to tissue. Phase Field Models (PFMs) have been shown to reproduce accurately cancer growth and other related phenomena, including expression of relevant molecules, extracellular matrix remodeling and angiogenesis. However, implementations of such models are rarely published, reducing access to these techniques. To reduce this gap, we developed Mocafe, a modular open-source Python package that implements some of the most important PFMs reported in the literature. Mocafe is designed to handle both PFMs purely based on differential equations and hybrid agent-based PFMs. Moreover, Mocafe is meant to be extensible, allowing the inclusion of new models in future releases. AVAILABILITY AND IMPLEMENTATION: Mocafe is a Python package based on FEniCS, a popular computing platform for solving partial differential equations. The source code, extensive documentation and demos are provided on GitHub at URL: https://github.com/BioComputingUP/mocafe. Moreover, we uploaded on Zenodo an archive of the package, which is available at https://doi.org/10.5281/zenodo.6366052.
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Bibliotecas , Neoplasias , Humanos , Programas Informáticos , DocumentaciónRESUMEN
SUMMARY: Information regarding pathways through voids in biomolecules and their roles in ligand transport is critical to our understanding of the function of many biomolecules. Recently, the advent of high-throughput molecular dynamics simulations has enabled the study of these pathways, and of rare transport events. However, the scale and intricacy of the data produced requires dedicated tools in order to conduct analyses efficiently and without excessive demand on users. To fill this gap, we developed the TransportTools, which allows the investigation of pathways and their utilization across large, simulated datasets. TransportTools also facilitates the development of custom-made analyses. AVAILABILITY AND IMPLEMENTATION: TransportTools is implemented in Python3 and distributed as pip and conda packages. The source code is available at https://github.com/labbit-eu/transport_tools. Data are available in a repository and can be accessed via a link: https://doi.org/10.5281/zenodo.5642954. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Bibliotecas , Programas Informáticos , Ligandos , Biblioteca de Genes , Simulación de Dinámica MolecularRESUMEN
SUMMARY: RNA 3D architectures are stabilized by sophisticated networks of (non-canonical) base pair interactions, which can be conveniently encoded as multi-relational graphs and efficiently exploited by graph theoretical approaches and recent progresses in machine learning techniques. RNAglib is a library that eases the use of this representation, by providing clean data, methods to load it in machine learning pipelines and graph-based deep learning models suited for this representation. RNAglib also offers other utilities to model RNA with 2.5 D graphs, such as drawing tools, comparison functions or baseline performances on RNA applications. AVAILABILITY AND IMPLEMENTATION: The method is distributed as a pip package, RNAglib. Data are available in a repository and can be accessed on rnaglib's web page. The source code, data and documentation are available at https://rnaglib.cs.mcgill.ca. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Bibliotecas , Programas Informáticos , Aprendizaje Automático , Documentación , Biblioteca de GenesRESUMEN
MOTIVATION: Pangenome graphs representing aligned genome assemblies are being shared in the text-based Graphical Fragment Assembly format. As the number of assemblies grows, there is a need for a file format that can store the highly repetitive data space efficiently. RESULTS: We propose the GBZ file format based on data structures used in the Giraffe short-read aligner. The format provides good compression, and the files can be efficiently loaded into in-memory data structures. We provide compression and decompression tools and libraries for using GBZ graphs, and we show that they can be efficiently used on a variety of systems. AVAILABILITY AND IMPLEMENTATION: C++ and Rust implementations are available at https://github.com/jltsiren/gbwtgraph and https://github.com/jltsiren/gbwt-rs, respectively. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Compresión de Datos , Bibliotecas , Secuenciación de Nucleótidos de Alto Rendimiento , Programas InformáticosRESUMEN
MOTIVATION: As pan-genome approaches are largely employed for bacterial comparative genomics and evolution analyses, but still difficult to be carried out by non-bioinformatician biologists, there is a need for an innovative tool facilitating the exploration of bacterial pan-genomes. RESULTS: PanExplorer is a web application providing various genomic analyses and reports, giving intuitive views that enable a better understanding of bacterial pan-genomes. As an example, we produced the pan-genome for 121 Anaplasmataceae strains (including 30 Ehrlichia, 15 Anaplasma, 68 Wolbachia). AVAILABILITY AND IMPLEMENTATION: PanExplorer is written in Perl CGI and relies on several JavaScript libraries for visualization (hotmap.js, MauveViewer, CircosJS). It is freely available at http://panexplorer.southgreen.fr. The source code has been released in a GitHub repository https://github.com/SouthGreenPlatform/PanExplorer. A documentation section is available on PanExplorer website.
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Genoma Bacteriano , Bibliotecas , Genómica , Programas Informáticos , InternetRESUMEN
MOTIVATION: With continually improved instrumentation, Fourier transform infrared (FTIR) microspectroscopy can now be used to capture thousands of high-resolution spectra for chemical characterization of a sample. The spatially resolved nature of this method lends itself well to histological profiling of complex biological specimens. However, current software can make joint analysis of multiple samples challenging and, for large datasets, computationally infeasible. RESULTS: To overcome these limitations, we have developed Photizo-an open-source Python library enabling high-throughput spectral data pre-processing, visualization and downstream analysis, including principal component analysis, clustering, macromolecular quantification and mapping. Photizo can be used for analysis of data without a spatial component, as well as spatially resolved data, obtained e.g. by scanning mode IR microspectroscopy and IR imaging by focal plane array detector. AVAILABILITY AND IMPLEMENTATION: The code underlying this article is available at https://github.com/DendrouLab/Photizo with access to example data available at https://zenodo.org/record/6417982#.Yk2O9TfMI6A.
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Bibliotecas , Programas Informáticos , Espectroscopía Infrarroja por Transformada de Fourier/métodos , Biblioteca de Genes , Análisis de Componente PrincipalRESUMEN
Public libraries in the United States (U.S.) are important sources of health information. Immigrants comprise a large portion of the U.S. population, and research suggests that public libraries help immigrants adjust to life in a new country. Public libraries help immigrants access information directly related to health and provide programs that have indirect impacts on health outcomes, including learning a new language and forging social ties. The purpose of this paper was to examine perspectives from librarians related to interactions with immigrant patrons and how their library supports them in this role. Public librarians (n = 205) from two selected U.S. states completed an online survey focusing on how comfortable they were in helping immigrants with inquiries related to health and the role of the public library in supporting librarians in this endeavor. Respondents generally reported high levels of comfort interacting with immigrants, although there was limited interaction on potentially sensitive topics (i.e., immigration, health). Library staff perceived that libraries overall were not effective in meeting the needs of immigrant populations and that librarians were infrequently offered professional training related to cultural competency and diversity. The findings echo previous studies that demonstrate the need for professional development to ensure that librarians are aware of library resources available to assist immigrant patrons. Findings from this study suggest opportunities for public health professionals and public librarians to collaborate to ensure the provision of reliable resources, health information, and referrals to community-based services.