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Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach.

ABSTRACT: BACKGROUND:Bioinformatics has pervaded all fields of biology and has become an indispensable tool for almost all research projects. Although teaching bioinformatics has been incorporated in all traditional life science curricula, practical hands-on experiences in tight combination with wet-lab experiments are needed to motivate students. RESULTS:We present a tutorial that starts from a practical problem: finding novel enzymes from marine environments. First, we introduce the idea of metagenomics, a recent approach that extends biotechnology to non-culturable microbes. We presuppose that a probe for the screening of metagenomic cosmid library is needed. The students start from the chemical structure of the substrate that should be acted on by the novel enzyme and end with the sequence of the probe. To attain their goal, they discover databases such as BRENDA and programs such as BLAST and Clustal Omega. Students' answers to a satisfaction questionnaire show that a multistep tutorial integrated into a research wet-lab project is preferable to conventional lectures illustrating bioinformatics tools. CONCLUSION:Experimental biologists can better operate basic bioinformatics if a problem-solving approach is chosen.

SUBMITTER: Liguori L

PROVIDER: S-EPMC7447578 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach.

Liguori Ludovica L Monticelli Maria M Allocca Mariateresa M Cubellis Maria Vittoria MV Hay Mele Bruno B

BMC bioinformatics 20200821 Suppl 10

<h4>Background</h4>Bioinformatics has pervaded all fields of biology and has become an indispensable tool for almost all research projects. Although teaching bioinformatics has been incorporated in all traditional life science curricula, practical hands-on experiences in tight combination with wet-lab experiments are needed to motivate students.<h4>Results</h4>We present a tutorial that starts from a practical problem: finding novel enzymes from marine environments. First, we introduce the idea ...[more]

PMID: 32838733

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Project description:Novel cancer therapies are associated with survival patterns that differ from established therapies, which may include survival curves that plateau after a certain follow-up time point. A fraction of the patient population is then considered statistically cured and subject to the same mortality experience as the cancer-free general population. Mixture cure models have been developed to account for this characteristic. As compared to standard survival analysis, mixture cure models can often lead to profoundly different estimates of long-term survival, required for health economic evaluations. This tutorial is designed as a practical introduction to mixture cure models. Step-by-step instructions are provided for the entire implementation workflow, i.e., from gathering and combining data from different sources to fitting models using maximum likelihood estimation and model results interpretation. Two mixture cure models were developed to illustrate (1) an "uninformed" approach where the cure fraction is estimated from trial data and (2) an "informed" approach where the cure fraction is obtained from an external source (e.g., real-world data) used as an input to the model. These models were implemented in the statistical software R, with the freely available code on GitHub. The cure fraction can be estimated as an output from ("uninformed" approach) or used as an input to ("informed" approach) a mixture cure model. Mixture cure models suggest presumed estimates of long-term survival proportions, especially in instances where some fraction of patients is expected to be statistically cured. While this type of model may initially seem complex, it is straightforward to use and interpret. Mixture cure models have the potential to improve the accuracy of survival estimates for treatments associated with statistical cure, and the present tutorial outlines the interpretation and implementation of mixture cure models in R. This type of model will likely become more widely used in health economic analyses as novel cancer therapies enter the market.

Dataset Information

Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach.

Publications

Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach.

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