ZS Discovery
Aim
Develop efficient and scalable workflows to enhance target discovery, optimizing hands-on time and resources to streamline data interpretation.
Challenges
Research institutions frequently develop unique, in-house workflows utilizing internal computational resources, often locked in to specific software and runtime configurations. However, the lack of standardization and portability makes it difficult to share analysis pipelines, thereby obstructing collaboration and widespread adoption. Additionally, owing to updates to pipeline components, authors often encounter difficulties in reproducing their own work. This dependency on specialized computational environments necessitates extensive compatibility testing across diverse platforms, causing significant delays in deployment.
Solution
Containerization with portability
Containerization offers a lightweight solution to these challenges by encapsulating each pipeline step with all software dependencies into self-contained, ready-to-run container images. These images can be instantiated, loaded, and unloaded on demand. Key advantages of containerization in bioinformatics workflow development and execution include:
- Portability: Nextflow workflows developed on personal devices can be easily transferred to cloud or computing clusters without extensive testing in production environments.
- Reproducibility: Workflows produce consistent results regardless of the computing platform, enabling workflows to be seamlessly deployed at new institutions or sites.
- Collaboration: Individual containers and entire workflows can be readily shared online via container registries and code repositories, facilitating collaboration.
“The era and need of shareable and portable workflows across infrastructures is already a reality. Bioinformaticians need technology that helps them focus on making their analyses right, without worrying about porting it to a particular cluster or cloud.” — Felipe Almeida, Senior Bioinformatician
Scalable and adaptable workflows
Nextflow enables bioinformatics workflows to be created and organized with containers. Each container’s output can feed into the next, creating a functional pipeline that maximizes resources through parallelization. This flexible, scalable approach uses a message-passing paradigm to run continuous checkpoints, tracking intermediate results. If interrupted, the pipeline can resume from the last successful step.
Despite complex background processes, Nextflow abstracts complexity, providing users with a straightforward pipeline execution experience. This allows the automatic management of data requests, data placement (across databases or processes), and computing infrastructure. In addition, Nextflow integrates with various computing infrastructures and schedulers, supporting diverse container technologies for seamless pipeline deployment. This enables users to focus on pipeline execution without managing underlying infrastructure details, simplifying the process and enhancing efficiency.
Open-source pipelines and modules
The vast toolbox of high-quality workflows and containers available on Github and nf-core - a community initiative for developing curated open-source Nextflow pipelines and modules shortens the time required to build and deploy a pipeline. Nextflow fosters an Open Science approach through the recycled use of existing modules, scripts for building and prototyping new modules and sharing workflow innovations in the community.
“Remarkably, our streamlined analytics processes have substantially reduced timeframes while considering cost-efficiency. Our expert teams have guided numerous projects with a diverse range of clients to realize the benefits of containerized bioinformatics workflow development. This is made possible by Nextflow’s interoperability and the availability of shared components through the nf-core community.” — Juan Sendoya, Senior Lead Bioinformatician
About ZS
ZS is a management consulting and technology firm focused on transforming global healthcare and beyond. We leverage our leading-edge analytics, plus the power of data, science and products, to help our clients make more intelligent decisions, deliver innovative solutions and improve outcomes for all. Founded in 1983, ZS has more than 13,000 employees in 35 offices worldwide.
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