Computational platforms and environments articles from across Nature Portfolio

Computational platforms and environments are platforms of integrated software that have user-friendly interfaces and that can be used by researchers to properly analyse data, such as large datasets, and answer research questions.

Latest Research and Reviews

Research
08 June 2023 | Open Access

Investigating the novel-binding site of RPA2 on Menin and predicting the effect of point mutation of Menin through protein–protein interactions
- Gurjeet Kaur
- , Manisha Prajapat
- & Bikash Medhi
Scientific Reports 13, 9337
Research
24 May 2023 | Open Access

ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species

RNA-sequencing data analysis is difficult for non-model species that have no reference genome. ExpressAnalyst enables RNA-sequencing analysis for any eukaryotic species in less than 24 h, on a laptop, and without any programming.
- Peng Liu
- , Jessica Ewald
- & Jianguo Xia
Nature Communications 14, 2995
Research
24 May 2023 | Open Access

Prediction of protein subplastid localization and origin with PlastoGram
- Katarzyna Sidorczuk
- , Przemysław Gagat
- & Michał Burdukiewicz
Scientific Reports 13, 8365
Research
24 May 2023 | Open Access

Deep learning for multi-class semantic segmentation enables colorectal cancer detection and classification in digital pathology images
- John-Melle Bokhorst
- , Iris D. Nagtegaal
- & Francesco Ciompi
Scientific Reports 13, 8398
Research
18 May 2023 | Open Access

The Cell Tracking Challenge: 10 years of objective benchmarking

This updated analysis of the Cell Tracking Challenge explores how algorithms for cell segmentation and tracking in both 2D and 3D have advanced in recent years, pointing users to high-performing tools and developers to open challenges.
- Martin Maška
- , Vladimír Ulman
- & Carlos Ortiz-de-Solórzano
Nature Methods, 1-11
Research
17 May 2023 | Open Access

A randomized clinical trial assessing the effect of automated medication-targeted alerts on acute kidney injury outcomes

In a multicenter randomized trial, researchers found that electronic alerts increased the rate of discontinuation of potential nephrotoxins. This did not translate into improved clinical outcomes, except among those exposed to proton-pump inhibitors.
- F. Perry Wilson
- , Yu Yamamoto
- & Ugochukwu Ugwuowo
Nature Communications 14, 2826

All Research & Reviews

News and Comment

Correspondence | 05 June 2023

Distributed-Something: scripts to leverage AWS storage and computing for distributed workflows at scale
- Erin Weisbart
- & Beth A. Cimini
Nature Methods, 1-2
Correspondence | 10 April 2023

The scverse project provides a computational ecosystem for single-cell omics data analysis
- Isaac Virshup
- , Danila Bredikhin
- & Fabian J. Theis
Nature Biotechnology 41, 604-606
Comments & Opinion
06 March 2023 | Open Access

Ten lessons for data sharing with a data commons

A data commons is a cloud-based data platform with a governance structure that allows a community to manage, analyze and share its data. Data commons provide a research community with the ability to manage and analyze large datasets using the elastic scalability provided by cloud computing and to share data securely and compliantly, and, in this way, accelerate the pace of research. Over the past decade, a number of data commons have been developed and we discuss some of the lessons learned from this effort.
- Robert L. Grossman
Scientific Data 10, 120
Correspondence | 03 March 2023

PoCA: a software platform for point cloud data visualization and quantification
- Florian Levet
- & Jean-Baptiste Sibarita
Nature Methods 20, 629-630
News & Views | 16 February 2023

Spatial Omics DataBase (SODB): increasing accessibility to spatial omics data

SODB is a large-scale platform providing rich data resources, efficient data exporting, and interactive analytical modules for spatial omics research.

Nature Methods 20, 359-360
Correspondence | 21 October 2022

ShareLoc — an open platform for sharing localization microscopy data
- Wei Ouyang
- , Jiachuan Bai
- & Christophe Zimmer
Nature Methods 19, 1331-1333

All News & Comment

Computational platforms and environments articles from across Nature Portfolio

Latest Research and Reviews

Investigating the novel-binding site of RPA2 on Menin and predicting the effect of point mutation of Menin through protein–protein interactions

ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species

Prediction of protein subplastid localization and origin with PlastoGram

Deep learning for multi-class semantic segmentation enables colorectal cancer detection and classification in digital pathology images

The Cell Tracking Challenge: 10 years of objective benchmarking

A randomized clinical trial assessing the effect of automated medication-targeted alerts on acute kidney injury outcomes

News and Comment

Distributed-Something: scripts to leverage AWS storage and computing for distributed workflows at scale

The scverse project provides a computational ecosystem for single-cell omics data analysis

Ten lessons for data sharing with a data commons

PoCA: a software platform for point cloud data visualization and quantification

Spatial Omics DataBase (SODB): increasing accessibility to spatial omics data

ShareLoc — an open platform for sharing localization microscopy data

Search

Quick links