Concurrent Materials Design, Accelerated by AI
This article references topics presented by Dr. Michael Heiber at Enthought’s 2025 R&D Innovation Summit in Tokyo. Link to video below.Over the last...
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Bioinformatics—used extensively in genomics, pathology, and drug discovery—combines mathematical and computational methods to collect, classify, store, and analyze large and complex biological data. The set of biological data analysis operations executed in a predefined order is commonly referred to as a “bioinformatics pipeline”. In other words, a bioinformatics pipeline is an analysis workflow that takes input data files in unprocessed raw form through a series of transformations to produce output data in a human-interpretable form.
Typically, a bioinformatics pipeline consists of four components: 1) a user interface; 2) a core workflow framework; 3) input and output data; and 4) downstream scientific insights.
The core framework contains a variety of third-party software tools and in-house scripts wrapped into specific workflow steps. The steps are executed in a particular environment via a user interface, taking raw experimental data, reference files, and metadata as inputs. The resulting output data is then used to drive scientific insights through downstream advanced results, visualization, and interpretation.
Despite the existence of highly sophisticated data pipelines, there is a frequent need in R&D to create ad-hoc bioinformatics pipelines either for prototyping and proof-of-concept purposes or to integrate newly published tools and methods since existing pipelines are not easily customizable. As the pipelines grow with additional steps, managing and maintaining the necessary tools becomes more difficult. Moreover, the complex and rapidly changing nature of biological databases, experimental techniques, and analysis tools makes reproducing, extending, and scaling pipelines a significant challenge.
Scientists, bioinformaticians, and lab managers are tasked with designing their pipelines and identifying the gaps within their frameworks. The best approach to prioritizing efforts depends highly on the operational need, the scientific scope, and the state of the bioinformatic pipeline. The very first step, however, is to understand the evolution of a bioinformatics pipeline.
A bioinformatics pipeline evolves through five phases. Pipeline stakeholders first seek to explore and collect the essential components, including raw data, tools, and references (Conception Phase). Then, they automate the analysis steps and investigate pipeline results (Survival Phase). Once satisfied, they move on to seek reproducibility and robustness (Stability Phase), extensibility (Success Phase), and finally scalability (Significance Phase). Below is a figure of the evolution at-a-glance as well as a description of each phase.
With the improved availability and affordability of high-throughput technologies such as Next-Generation Sequencing, the challenge in biology and clinical research has shifted from producing data towards developing efficient and robust bioinformatics data analyses. Integrating, processing, and interpreting the datasets resulting from such advanced technologies inevitably involve multiple analysis steps and a variety of tools resulting in complex analysis pipelines.
The evolution of such pipelines raises serious challenges for effective ways of designing and running them:
To address these issues, life science R&D labs need to invest now in designing and developing reproducible, extensible, and scalable bioinformatics pipelines to avoid playing catch-up later.
Enthought has extensive experience in optimizing complex bioinformatics pipelines leveraging machine learning and AI. Contact us to see how we can help your team.
Learn more about each phase including mini-case studies in the full paper: Optimized Workflows: Towards Reproducible, Extensible and Scalable Bioinformatics Pipelines
This article references topics presented by Dr. Michael Heiber at Enthought’s 2025 R&D Innovation Summit in Tokyo. Link to video below.Over the last...
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