ReviewProteomics2020
Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines.
Review in Proteomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed.
- Artificial intelligence to investigate metabolomics data for precision medicine.Metabolomics : Official journal of the Metabolomic Society · 2026Review
- Frag'n'Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments.BMC bioinformatics · 2026Article
- Nicotine and tar-multiple targets synergize to alter the immune micro-environment to induce prostate cancer.Discover oncology · 2025Article
- UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis.Journal of cheminformatics · 2023Article
- The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.Nucleic acids research · 2022Article
- The META tool optimizes metagenomic analyses across sequencing platforms and classifiers.Frontiers in bioinformatics · 2022Article
- ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis.Scientific data · 2021Article
- Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers.Nature methods · 2021Review
- Cloudy with a Chance of Peptides: Accessibility, Scalability, and Reproducibility with Cloud-Hosted Environments.Journal of proteome research · 2021Article
- BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers.Journal of proteome research · 2021Article
- Proteomic repository data submission, dissemination, and reuse: key messages.Expert review of proteomicsReview
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
The recent improvements in mass spectrometry instruments and new analytical methods are increasing the intersection between proteomics and big data science. In addition, bioinformatics analysis is becoming increasingly complex and convoluted, involving multiple algorithms and tools. A wide variety of methods and software tools have been developed for computational proteomics and metabolomics during recent years, and this trend is likely to continue. However, most of the computational proteomics and metabolomics tools are designed as single-tiered software application where the analytics tasks cannot be distributed, limiting the scalability and reproducibility of the data analysis. In this paper the key steps of metabolomics and proteomics data processing, including the main tools and software used to perform the data analysis, are summarized. The combination of software containers with workflows environments for large-scale metabolomics and proteomics analysis is discussed. Finally, a new approach for reproducible and large-scale data analysis based on BioContainers and two of the most popular workflow environments, Galaxy and Nextflow, is introduced to the proteomics and metabolomics communities.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.