Computational platforms and environments articles within Nature Communications

Featured

  • Article
    | Open Access

    In this work, the authors report NMR lipids Databank to promote decentralised sharing of biomolecular molecular dynamics (MD) simulation data with an overlay design. Programmatic access enables analyses of rare phenomena and advances the training of machine learning models.

    • Anne M. Kiirikki
    • , Hanne S. Antila
    •  & O. H. Samuli Ollila

  • Article
    | Open Access

    Reproducibility is essential for the progress of research, yet achieving it remains elusive even in computational fields. Here, authors develop the rworkflows suite, making robust CI/CD workflows easy and freely accessible to all R package developers.

    • Brian M. Schilder
    • , Alan E. Murphy
    •  & Nathan G. Skene

  • Article
    | Open Access

    Spatial visualization of metabolites in tissues via mass spectrometry imaging can be prone to user perception bias. Here, the authors report the computational framework moleculaR that introduces probabilistic data-dependent molecular mapping of nonrandom spatial patterns of metabolite signals.

    • Denis Abu Sammour
    • , James L. Cairns
    •  & Carsten Hopf

  • Article
    | Open Access

    The analysis of longitudinal bulk and single-cell multi-omics data is a highly complex task. Here, the authors introduce PALMO, a software platform with five modules to analyse longitudinal bulk and single-cell multi-omics data, which is extensively tested in external datasets that include multiple omics modalities.

    • Suhas V. Vasaikar
    • , Adam K. Savage
    •  & Xiao-jun Li

  • Article
    | Open Access

    The extensive information capacity of DNA makes it an attractive alternative to traditional data storage. DNA-Aeon is a DNA data storage solution that can correct all error types commonly observed in DNA storage, while encoding data into sequences that meet user-defined constraints such as GC content, homopolymer length, and no undesired motifs.

    • Marius Welzel
    • , Peter Michael Schwarz
    •  & Dominik Heider

  • Article
    | Open Access

    Traditional bulk sequencing data lack information about cell-type-specific gene expression. Here, the authors develop a Tissue-AdaPtive autoEncoder (TAPE), a deep learning method connecting bulk RNA-seq and single-cell RNA-seq, and apply it to analyze the cell type fractions and cell-type-specific gene expression in clinical data.

    • Yanshuo Chen
    • , Yixuan Wang
    •  & Yu Li

  • Article
    | Open Access

    Automated design and build processes can rapidly accelerate work in synthetic biology and metabolic engineering. Here the authors present Galaxy-SynBioCAD, a toolshed for synthetic biology, metabolic engineering, and industrial biotechnology that they use to build and execute Galaxy scientific workflows from pathway design to strain engineering through the automated generation of scripts driving robotic workstations.

    • Joan Hérisson
    • , Thomas Duigou
    •  & Jean-Loup Faulon

  • Article
    | Open Access

    There are only a few platforms that integrate multiple omics data types, bioinformatics tools, and interfaces for integrative analyses and visualization that do not require programming skills. Here the authors present an integrative web-based platform for analysis of omics data and signatures of cellular perturbations.

    • Marcin Pilarczyk
    • , Mehdi Fazel-Najafabadi
    •  & Mario Medvedovic

  • Comment
    | Open Access

    Diversity is a creative force that broadens views and enhances ideas; it increases productivity as well as the impact of our science, making our respective organisations more agile and timely. Equality of opportunity is a key to success for any research organisation. Here we argue that every research organisation, whether in academia or in industry, needs to have better inclusion policies to harness the benefits of diversity in research. Drawing from our personal experiences and perspectives as women in science, we share our suggestions on how to promote inclusion in academia and create a better research culture for all. Our shared experiences highlight the many hurdles women in science face on a daily basis. We stress that rules and regulations, as well as education for awareness, will play critical role in this much needed shift from a male-dominated scientific culture that dates from Victorian times to a modern focus on gender equality in science. The key ingredients of this new culture will be flexibility, transparency, fairness and thoughtfulness.

    • Sarah A. Teichmann
    • , Muzlifah Haniffa
    •  & Jasmin Fisher

  • Article
    | Open Access

    Cellular contexts such as disease state, organismal life stage and tissue microenvironment, shape intercellular communication, and ultimately affect an organism’s phenotypes. Here, the authors present Tensor-cell2cell, an unsupervised method for deciphering context-driven intercellular communication.

    • Erick Armingol
    • , Hratch M. Baghdassarian
    •  & Nathan E. Lewis

  • Article
    | Open Access

    Small-scale bioreactors are increasingly used in quantitative biology. Here, the authors report ReacSight, a software solution to connect reactor arrays with sensitive measurement devices using low-cost pipetting robots and provide applications leveraging optogenetic control in yeast.

    • François Bertaux
    • , Sebastián Sosa-Carrillo
    •  & Gregory Batt

  • Article
    | Open Access

    Studies of circular RNAs have often been limited to the tissue or organism level. Here, authors investigate the comprehensive expression landscape of circRNAs in human and mouse at single-cell resolution, revealing highly specific and dynamic changes of circRNAs during multiple biological processes.

    • Wanying Wu
    • , Jinyang Zhang
    •  & Fangqing Zhao

  • Article
    | Open Access

    This paper describes the ‘4DN Data Portal’ that hosts data generated by the 4D Nucleome network, including Hi-C and other chromatin conformation capture assays, as well as various sequencing-based and imaging-based assays. Raw data have been uniformly processed to increase comparability and the portal is implemented with visualization tools to browse the data without download.

    • Sarah B. Reiff
    • , Andrew J. Schroeder
    •  & Peter J. Park

  • Article
    | Open Access

    In microscopy, applications in which reactiveness is needed are multifarious. Here the authors report MicroMator, a Python software package for reactive experiments, which they use for applications requiring real-time tracking and light-targeting at the single-cell level.

    • Zachary R. Fox
    • , Steven Fletcher
    •  & Gregory Batt

  • Article
    | Open Access

    Here the authors introduce Cellar, an interactive webserver for analyzing single-cell omics data. They show that Cellar supports all aspects of the analysis and modeling process and can be used to integrate different types of single cell omics and spatial data.

    • Euxhen Hasanaj
    • , Jingtao Wang
    •  & Ziv Bar-Joseph

  • Article
    | Open Access

    “Mapping the dark matter of metabolism remains an open challenge that can be addressed globally and systematically by existing computational solutions. Here the authors present ATLASx, a repository of known and predicted enzymatic reaction, connecting millions of compounds to help synthetic biologists and metabolic engineers to design and explore metabolic pathways.”

    • Homa MohammadiPeyhani
    • , Jasmin Hafner
    •  & Vassily Hatzimanikatis

  • Article
    | Open Access

    The interpretation of somatic variants in cancer is challenging due to the scale and complexity of sequencing data. Here, the authors present PORI, an open-source framework for interpreting somatic variants in cancer using graph knowledge base tools, automated reporting, and manual curation.

    • Caralyn Reisle
    • , Laura M. Williamson
    •  & Steven J. M. Jones

  • Article
    | Open Access

    It is no secret that a significant part of scientific research is difficult to reproduce. Here, the authors present a cloud-computing platform called ORCESTRA that facilitates reproducible processing of multimodal biomedical data using customizable pipelines and well-documented data objects.

    • Anthony Mammoliti
    • , Petr Smirnov
    •  & Benjamin Haibe-Kains

  • Article
    | Open Access

    The increasing scale and scope of biomedical data is generating tremendous opportunities for improving health outcomes, but also raises new challenges ranging from data acquisition and storage to data analysis and utilization. To meet these challenges, the authors develop the Personal Health Dashboard, which provides an end-to-end solution for deep biomedical data analytics.

    • Amir Bahmani
    • , Arash Alavi
    •  & Michael P. Snyder

  • Article
    | Open Access

    The authors present flDPnn, a computational tool for disorder and disorder function predictions from protein sequences. flDPnn was assessed with the data from the “Critical Assessment of Protein Intrinsic Disorder Prediction” experiment and on an independent and low-similarity test dataset, which show that flDPnn offers accurate predictions of disorder, fully disordered proteins and four common disorder functions.

    • Gang Hu
    • , Akila Katuwawala
    •  & Lukasz Kurgan

  • Article
    | Open Access

    Deep learning algorithms trained on data streamed temporally from different clinical sites and from a multitude of physiological sensors are generally affected by a degradation in performance. To mitigate this, the authors propose a continual learning strategy that employs a replay buffer.

    • Dani Kiyasseh
    • , Tingting Zhu
    •  & David Clifton

  • Article
    | Open Access

    Whole genome sequencing data are increasingly becoming routinely available but generating actionable insights is challenging. Here, the authors describe Pathogenwatch, a web tool for genomic surveillance of S. Typhi, and demonstrate its use for antimicrobial resistance assignment and strain risk assessment.

    • Silvia Argimón
    • , Corin A. Yeats
    •  & David M. Aanensen

  • Article
    | Open Access

    Data-rich networks can be difficult to interpret beyond a certain size. Here, the authors introduce a platform that uses virtual reality to allow the visual exploration of large networks, while interfacing with data repositories and other analytical methods to improve the interpretation of big data.

    • Sebastian Pirch
    • , Felix Müller
    •  & Jörg Menche

  • Article
    | Open Access

    The Danish health system has been collecting health-related data on the entire Danish population for years. Here the authors present the Danish Disease Trajectory Browser (DTB), which allows users to explore population-wide disease progression patterns from data collected between 1994 and 2018.

    • Troels Siggaard
    • , Roc Reguant
    •  & Søren Brunak

  • Article
    | Open Access

    The computational prediction of protein allostery can guide experimental studies of protein function and cellular activity. Here, the authors develop a network-based method to detect allosteric coupling within proteins solely based on their structures, and set up a webserver for allostery prediction.

    • Jian Wang
    • , Abha Jain
    •  & Nikolay V. Dokholyan

  • Article
    | Open Access

    Deep learning is becoming a popular approach for understanding biological processes but can be hard to adapt to new questions. Here, the authors develop Janggu, a python library that aims to ease data acquisition and model evaluation and facilitate deep learning applications in genomics.

    • Wolfgang Kopp
    • , Remo Monti
    •  & Altuna Akalin

  • Article
    | Open Access

    Taxonomy classification of amplicon sequences is an important step in investigating microbial communities in microbiome analysis. Here, the authors show incorporating environment-specific taxonomic abundance information can lead to improved species-level classification accuracy across common sample types.

    • Benjamin D. Kaehler
    • , Nicholas A. Bokulich
    •  & Gavin A. Huttley

  • Article
    | Open Access

    The Scalable Precision Medicine Oriented Knowledge Engine (SPOKE) is a heterogeneous knowledge network that integrates information from 29 public databases. Here, Nelson et al. extend SPOKE to embed clinical data from electronic health records to create medically meaningful barcodes for each medical variable.

    • Charlotte A. Nelson
    • , Atul J. Butte
    •  & Sergio E. Baranzini

  • Article
    | Open Access

    Most morphological visualization platforms are not designed to share research data, or are limited to data visualization. Here the authors present MorphoNet, an open-source, web-based tool for interactive visualization and sharing of complex morphodynamic datasets, onto which users can project their own data.

    • Bruno Leggio
    • , Julien Laussu
    •  & Emmanuel Faure

  • Article
    | Open Access

    Adaptive immunity from both B and T cells critically controls the rejection or survival of transplanted organs. Here the authors show, by analyzing human B cell receptor repertoire in longitudinal studies of patients receiving kidney transplants, that repertoire diversity is positively associated with the incidence of kidney rejection.

    • Silvia Pineda
    • , Tara K. Sigdel
    •  & Minnie M. Sarwal

  • Article
    | Open Access

    Imputation can effectively augment marker density in existing genetic datasets and enable integration across germplasm resources. Here Wang et al. present a public imputation server for rice using a diverse reference panel to facilitate imputation in the rice genetics community.

    • Diane R. Wang
    • , Francisco J. Agosto-Pérez
    •  & Susan R. McCouch

  • Article
    | Open Access

    Availability of computing power can limit computational analysis of large genetic and genomic datasets. Here, Canela-Xandri, et al. describe a software called DISSECT that is capable of analyzing large-scale genetic data by distributing the work across thousands of networked computers.

    • Oriol Canela-Xandri
    • , Andy Law
    •  & Albert Tenesa

Browse broader subjects

Browse Computational platforms and environments across other nature.com journals