ArticleBMC bioinformatics2011
openBIS: a flexible framework for managing and analyzing complex data in biology research.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed.
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- Accelerating discovery across scientific disciplines through reproducible workflows with AiiDAlab.Digital discovery · 2026Article
- Workflow‑Based Information Management Framework for Multicenter Research Studies: Design and Development.Online journal of public health informatics · 2026Article
- Change in the chondroitin/dermatan structure in distal lung tissue from COPD patients.Scientific reports · 2026Article
- Digital transformation in laboratory documentation: Insights from an eLabFTW case study and a survey-informed onboarding framework.PloS one · 2026Article
- Immuno-acoustic trapping for extracellular vesicle subpopulations.Scientific reports · 2025Article
- Proteomic Profiling of Acoustically Isolated Extracellular Vesicles from Blood Plasma during Murine Bacterial Sepsis.Journal of proteome research · 2025Article
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- Affording reusable data: recommendations for researchers from a data-intensive project.Scientific data · 2025Article
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- Simplifying Multimodal Clinical Research Data Management: Introducing an Integrated and User-friendly Database Concept.Applied clinical informatics · 2024Article
- Current state of data stewardship tools in life science.Frontiers in big data · 2024Review
- dtool and dserver: A flexible ecosystem for findable data.PloS one · 2024Article
- Simple analysis of gel images with IOCBIO Gel.BMC biology · 2023Article
- Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis.Nature communications · 2023Article
- A pharmacoproteomic landscape of organotypic intervention responses in Gram-negative sepsis.Nature communications · 2023Article
12 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors.
Funding
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Abstract
backgroundModern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it.
resultsWe have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies.
conclusionsopenBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain.
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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.