ArticlePDA journal of pharmaceutical science and technology
Biocompute Objects-A Step towards Evaluation and Validation of Biomedical Scientific Computations.
Article in PDA journal of pharmaceutical science and technology. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
24 citing papers in PubMed.
- GlyGen: a knowledgebase linking glycan data with protein and gene data to reveal novel biological connections.Research square · 2026Article
- The Common Fund Data Ecosystem (CFDE).bioRxiv : the preprint server for biology · 2026Article
- GxP-Ready Single-Cell RNA-seq and Spatial Transcriptomics End-to-End Pipeline for Clinical Research.Computational and structural biotechnology journal · 2026Article
- BioWorkflow: Retrieving comprehensive bioinformatics workflows from publications.Briefings in bioinformatics · 2025Article
- Playbook workflow builder: Interactive construction of bioinformatics workflows.PLoS computational biology · 2025Article
- Building Portable and Reproducible Cancer Informatics Workflows for Scalable Data Analysis: An RNA Sequencing Tutorial.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A data science roadmap for open science organizations engaged in early-stage drug discovery.Nature communications · 2024Review
- Multi-omics approaches to studying gastrointestinal microbiome in the context of precision medicine and machine learning.Frontiers in molecular biosciences · 2023Review
- Software pipelines for RNA-Seq, ChIP-Seq and germline variant calling analyses in common workflow language (CWL).Frontiers in bioinformatics · 2023Article
- Modeling and integration of N-glycan biomarkers in a comprehensive biomarker data model.Glycobiology · 2022Article
- Enhancing the interoperability of glycan data flow between ChEBI, PubChem and GlyGen.Glycobiology · 2021Article
- Orchestrating and sharing large multimodal data for transparent and reproducible research.Nature communications · 2021Article
- The role of metadata in reproducible computational research.Patterns (New York, N.Y.) · 2021Review
- Bioinformatics tools developed to support BioCompute Objects.Database : the journal of biological databases and curation · 2021Article
- A Quantitative Evaluation of COVID-19 Epidemiological Models.medRxiv : the preprint server for health sciences · 2021Article
- Towards the Development of Digital Twins for the Bio-manufacturing Industry.Advances in biochemical engineering/biotechnology · 2021Article
- Data Management and Modeling in Plant Biology.Frontiers in plant science · 2021Review
- OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data.JCO clinical cancer informatics · 2020Article
- Comparative genomics in infectious disease.Current opinion in microbiology · 2020Review
- BCO App: tools for generating BioCompute Objects from next-generation sequencing workflows and computations.F1000Research · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
The unpredictability of actual physical, chemical, and biological experiments due to the multitude of environmental and procedural factors is well documented. What is systematically overlooked, however, is that computational biology algorithms are also affected by multiplicity of parameters and have no lesser volatility. The complexities of computation protocols and interpretation of outcomes is only a part of the challenge: There are also virtually no standardized and industry-accepted metadata schemas for reporting the computational objects that record the parameters used for computations together with the results of computations. Thus, it is often impossible to reproduce the results of a previously performed computation due to missing information on parameters, versions, arguments, conditions, and procedures of application launch. In this article we describe the concept of biocompute objects developed specifically to satisfy regulatory research needs for evaluation, validation, and verification of bioinformatics pipelines. We envision generalized versions of biocompute objects called
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.