Approaches for containerized scientific workflows in cloud environments with applications in life science

Containers are gaining popularity in life science research as they provide a solution for encompassing dependencies of provisioned tools, simplify software installations for end users and offer a form of isolation between processes. Scientific workflows are ideal for chaining containers into data analysis pipelines to aid in creating reproducible analyses. In this article, we review a number of approaches to using containers as implemented in the workflow tools Nextflow, Galaxy, Pachyderm, Argo, Kubeflow, Luigi and SciPipe, when deployed in cloud environments. A particular focus is placed on the workflow tool’s interaction with the Kubernetes container orchestration framework.

Understanding the BLAST (Basic Local Alignment Search Tool) Program and a Step-by-step Guide for its use in Life Science Research

Bioinformatics is the new branch of science which deals with the acquisition, storage, analysis and dissemination of biological data with the help of computer science and information technology. It has the enormous ability to analyze a vast quantity of biological data quickly and cost-effectively. In the past decades, enormous sequence information has been generated due to the advances in DNA and protein sequencing techniques. Estimating similarities between biological sequences is becoming necessary to obtain hidden information present within the sequence and to trace evolutionary relationship exist within the sequences. This sequence comparison can be achieved by basic local alignment search tool (BLAST). So BLAST has become a fundamental tools of life science research. Hence it is essential to know how to do sequence comparison using BLAST and how to accurately interpret the BLAST output data. The present article aims to familiarize the biologists and researchers with different BLAST programs and their use in research program.

The need for standardisation in life science research - an approach to excellence and trust.

Today, academic researchers benefit from the changes driven by digital technologies and the enormous growth of knowledge and data, on globalisation, enlargement of the scientific community, and the linkage between different scientific communities and the society. To fully benefit from this development, however, information needs to be shared openly and transparently. Digitalisation plays a major role here because it permeates all areas of business, science and society and is one of the key drivers for innovation and international cooperation. To address the resulting opportunities, the EU promotes the development and use of collaborative ways to produce and share knowledge and data as early as possible in the research process, but also to appropriately secure results with the European strategy for Open Science (OS). It is now widely recognised that making research results more accessible to all societal actors contributes to more effective and efficient science; it also serves as a boost for innovation in the public and private sectors. However for research data to be findable, accessible, interoperable and reusable the use of standards is essential. At the metadata level, considerable efforts in standardisation have already been made (e.g. Data Management Plan and FAIR Principle etc.), whereas in context with the raw data these fundamental efforts are still fragmented and in some cases completely missing. The CHARME consortium, funded by the European Cooperation in Science and Technology (COST) Agency, has identified needs and gaps in the field of standardisation in the life sciences and also discussed potential hurdles for implementation of standards in current practice. Here, the authors suggest four measures in response to current challenges to ensure a high quality of life science research data and their re-usability for research and innovation.

From intent to implementation: Factors affecting public involvement in life science research

Public involvement is key to closing the gap between research production and research use, and the only way to achieving ultimate transparency in science. The majority of life science research is not public-facing, but is funded by the public and impacts communities. We undertook an exploratory survey of researchers within the life sciences to better understand their views and perceived challenges to involving the public in their research. As survey response rate could not be determined, interpretation of the results must be cautious. We had a valid response cohort of n = 110 researchers, of whom 90% were primarily laboratory based. Using a mixed methods approach, we demonstrate that a top-down approach is key to motivate progression of life scientists from feeling positive towards public involvement to actually engaging in it. Researchers who viewed public involvement as beneficial to their research were more likely to have direct experience of doing it. We demonstrate that the systemic flaws in the way life sciences research enterprise is organised, including the promotion system, hyper-competition, and time pressures are major barriers to involving the public in the scientific process. Scientists are also apprehensive of being involuntarily involved in the current politicized climate; misinformation and publicity hype surrounding science nowadays makes them hesitant to share their early and in-progress research. The time required to deliberate study design and relevance, plan and build relationships for sustained involvement, provide and undertake training, and improve communication in the current research environment is often considered nonpragmatic, particularly for early career researchers. In conclusion, a top-down approach involving institutional incentives and infrastructure appears most effective at transitioning researchers from feeling positive towards public involvement to actually implementing it.

A guide to accurate reporting in digital image processing – can anyone reproduce your quantitative analysis?

ABSTRACTConsiderable attention has been recently paid to improving replicability and reproducibility in life science research. This has resulted in commendable efforts to standardize a variety of reagents, assays, cell lines and other resources. However, given that microscopy is a dominant tool for biologists, comparatively little discussion has been offered regarding how the proper reporting and documentation of microscopy relevant details should be handled. Image processing is a critical step of almost any microscopy-based experiment; however, improper, or incomplete reporting of its use in the literature is pervasive. The chosen details of an image processing workflow can dramatically determine the outcome of subsequent analyses, and indeed, the overall conclusions of a study. This Review aims to illustrate how proper reporting of image processing methodology improves scientific reproducibility and strengthens the biological conclusions derived from the results.

Research Integrity: A primer on research involving animals

This document seeks to highlight the abundance of information regarding good practice, responsible conduct and integrity that relates to animal use in research. General awareness of these across the Life Science research community is highly variable. However, many of the documents referenced here offer useful tools to assist in the review of training, support and/or mentoring to equip students and staff with the necessary knowledge and skills that they will need to achieve, or work towards achieving, the expectations described above.

Life and Biology

This chapter examines Heidegger’s understanding of life by analysing his appraisal of early twentieth-century biology. The chapter places this appraisal into the context of Heidegger’s overall aim of identifying the lineage that runs from the ancient conception of the human’s status within physis, through the physis/ēthos division in Plato’s Academy, into modern articulations of the life/spirit opposition. Heidegger pursues this aim in The Fundamental Concepts of Metaphysics by exploring biology, the discipline that explicitly seeks to examine one side of the life/spirit divide, and assessing what the landscape of this discipline looks like in the contemporary situation. The chapter argues that, given the broader context, it is acceptable that Heidegger summarises the contents of life-science research in a way that expresses metaphysical prejudices, for his claim is that we must first understand the delusions of thinking, and how we ourselves came to be deluded, in order to retrieve and rearticulate more essential knowledge.