Advances in Smart Digital Tools for Research and Development

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 3253

Special Issue Editors


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Guest Editor
Institute of Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
Interests: multivariate analysis; digitalization and modeling of industrial biotechnological and chemical processes; biosimilar monoclonal antibody;

E-Mail Website
Guest Editor
Institute of Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
Interests: pattern recognition; wastewater treatment; biotechnology; chemical processes; water treatment; instrumentation; chemical engineering; environmental biotechnology; process development; bioprocess engineering and fermentation technology; industrial biotechnology; nitrogen; bioprocess technology; Escherichia coli; denitrification; nitrification; cell culture techniques; bioenergy; design of experiments; bioreactors; bioprocess development; industrial microbiology; enzyme immobilization; ammonia; nitrite; cell polarity; bioprocess

Special Issue Information

Dear Colleagues,

The landscape of R&D in biotechnology is rapidly changing. Innovations are supported not only by advanced technologies to access versatile information of living systems but also by increasingly automated and parallelized operations in robots as well as by more efficient and self-learning computational approaches. A major pillar unifying these trends is the potential for rapidly generated large datasets with the associated challenge to store, standardize, and process such data. From gene sequencing, through drug screening, to simulation of the dynamic behavior of industrial bioreactors, new methods and tools are being developed, enabling improved understanding, confidence, and decision support. This Special Issue is devoted to the impact of computer-aided methods on the diverse stages of development and manufacture of biopharmaceutical drugs. The focus is set on computer methods that support the different stages and scales in R&D: bioinformatics (gene-level modeling), molecular dynamics simulation, cell-level modeling including MFA and FBA, reactor-scale modeling such as CFD and model-based process control, system-level modeling for high-throughput and sequential experimental design and operation, as well as modeling approaches supporting the regulatory PAT (e.g., soft sensors) and QbD approaches (e.g., process design and optimization).

Possible topics of interest of this Special Issue include, but are not limited to:

  • Big Data in gene sequencing
  • Genome, metabolic, and flux modeling
  • Big Data in bio-analytics and soft sensors
  • Big Data in high-throughput systems
  • Dynamical modeling of biosystems
  • Computational fluid dynamics for bioreactors
  • Bioprocess design, optimization, and upscaling

Dr. Michael Sokolov
Dr. Mariano Nicolas Cruz Bournazou
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • big data
  • data analytics
  • gene sequencing
  • omics
  • flux balances analysis
  • bioprocess modeling
  • design of experiments
  • multivariate data analysis
  • hybrid modeling
  • computer aided bioprocess engineering
  • bioprocess optimization
  • bioprocess automation

Published Papers (1 paper)

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Research

20 pages, 4276 KiB  
Article
Time Integrated Flux Analysis: Exploiting the Concentration Measurements Directly for Cost-Effective Metabolic Network Flux Analysis
by Rui M. C. Portela, Anne Richelle, Patrick Dumas and Moritz von Stosch
Microorganisms 2019, 7(12), 620; https://doi.org/10.3390/microorganisms7120620 - 27 Nov 2019
Cited by 1 | Viewed by 2979
Abstract
Background: Flux analyses, such as Metabolic Flux Analysis (MFA), Flux Balance Analysis (FBA), Flux Variability Analysis (FVA) or similar methods, can provide insights into the cellular metabolism, especially in combination with experimental data. The most common integration of extracellular concentration data requires the [...] Read more.
Background: Flux analyses, such as Metabolic Flux Analysis (MFA), Flux Balance Analysis (FBA), Flux Variability Analysis (FVA) or similar methods, can provide insights into the cellular metabolism, especially in combination with experimental data. The most common integration of extracellular concentration data requires the estimation of the specific fluxes (/rates) from the measured concentrations. This is a time-consuming, mathematically ill-conditioned inverse problem, raising high requirements for the quality and quantity of data. Method: In this contribution, a time integrated flux analysis approach is proposed which avoids the error-prone estimation of specific flux values. The approach is adopted for a Metabolic time integrated Flux Analysis and (sparse) time integrated Flux Balance/Variability Analysis. The proposed approach is applied to three case studies: (1) a simulated bioprocess case studying the impact of the number of samples (experimental points) and measurements’ noise on the performance; (2) a simulation case to understand the impact of network redundancies and reaction irreversibility; and (3) an experimental bioprocess case study, showing its relevance for practical applications. Results: It is observed that this method can successfully estimate the time integrated flux values, even with relatively low numbers of samples and significant noise levels. In addition, the method allows the integration of additional constraints (e.g., bounds on the estimated concentrations) and since it eliminates the need for estimating fluxes from measured concentrations, it significantly reduces the workload while providing about the same level of insight into the metabolism as classic flux analysis methods. Full article
(This article belongs to the Special Issue Advances in Smart Digital Tools for Research and Development)
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