Modeling Enzyme Kinetics: Current Challenges and Future Perspectives for Biocatalysis DOI
Jürgen Pleiss

Biochemistry, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 26, 2024

Biocatalysis is becoming a data science. High-throughput experimentation generates rapidly increasing stream of biocatalytic data, which the raw material for mechanistic and novel data-driven modeling approaches predictive design improved biocatalysts bioprocesses. The holistic molecular understanding enzymatic reaction systems will enable us to identify overcome kinetic bottlenecks shift thermodynamics reaction. full characterization community effort; therefore, published methods results should be findable, accessible, interoperable, reusable (FAIR), achieved by developing standardized exchange formats, complete reproducible documentation experimentation, collaborative platforms sustainable software analyzing repositories publishing together with data. FAIRification biocatalysis prerequisite highly automated laboratory infrastructures that improve reproducibility scientific reduce time costs required develop synthesis routes.

Language: Английский

Natural language access point to digital metal–organic polyhedra chemistry in The World Avatar DOI Creative Commons
Simon D. Rihm, Dan Tran, Aleksandar Kondinski

et al.

Data-Centric Engineering, Journal Year: 2025, Volume and Issue: 6

Published: Jan. 1, 2025

Abstract Metal–organic polyhedra (MOPs) are discrete, porous metal–organic assemblies known for their wide-ranging applications in separation, drug delivery, and catalysis. As part of The World Avatar (TWA) project—a universal interoperable knowledge model—we have previously systematized MOPs expanded the explorable MOP space with novel targets. Although these data available via a complex query language, more user-friendly interface is desirable to enhance accessibility. To address similar challenge other chemistry domains, natural language question-answering system “Marie” has been developed; however, its scalability limited due reliance on supervised fine-tuning, which hinders adaptability new domains. In this article, we introduce an enhanced database first-of-its-kind tailored chemistry. By augmenting TWA’s geometry data, enable visualization not just empirically verified structures but also machine-predicted ones. addition, renovated Marie’s semantic parser adopt in-context few-shot learning, allowing seamless interaction extensive repository. These advancements significantly improve accessibility versatility TWA, marking important step toward accelerating automating development reticular materials aid digital assistants.

Language: Английский

Citations

0

Humanoid robotics in material and chemistry experiments DOI

Yao Xu,

Wentao Yang, Wenguang Tu

et al.

Science China Materials, Journal Year: 2025, Volume and Issue: unknown

Published: May 28, 2025

Language: Английский

Citations

0

The Digital Lab Facility Manager: Automating operations of research laboratories through “The World Avatar” DOI Creative Commons
Simon D. Rihm, Yong Ren Tan, Wilson Ang

et al.

Deleted Journal, Journal Year: 2024, Volume and Issue: 1(3), P. 100031 - 100031

Published: Aug. 27, 2024

Language: Английский

Citations

3

The digital lab manager: Automating research support DOI Creative Commons
Simon D. Rihm, Yong Ren Tan, Wilson Ang

et al.

SLAS TECHNOLOGY, Journal Year: 2024, Volume and Issue: 29(3), P. 100135 - 100135

Published: May 3, 2024

Laboratory management automation is essential for achieving interoperability in the domain of experimental research and accelerating scientific discovery. The integration resources sharing knowledge across organisations enable discoveries to be accelerated by increasing productivity laboratories, optimising funding efficiency, addressing emerging global challenges. This paper presents a novel framework digitalising automating administration laboratories through World Avatar, an all-encompassing dynamic graph. Digital Framework serves as flexible tool, enabling users efficiently leverage data from diverse systems formats without being confined specific software or protocol. Establishing dedicated ontologies agents combining them with technologies such QR codes, RFID tags, mobile apps, enabled us develop modular applications that tackle some key challenges related lab management. Here, we showcase automated tracking intervention system explosive chemicals well easy-to-use application asset information retrieval. Implementing these, have achieved semantic linking BIM BMS laboratory inventory chemical knowledge. Our approach can capture crucial points reduce processing time. All provenance recorded following FAIR principles, ensuring its accessibility interoperability.

Language: Английский

Citations

2

Reducing education inequalities through cloud-enabled live-cell biotechnology DOI Creative Commons
Samira Vera-Choqqueccota, Baha Eddine Youcef Belmekki, Mohamed‐Slim Alouini

et al.

Trends in biotechnology, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 1, 2024

Biotechnology holds the potential to drive innovations across various fields from agriculture medicine. However, despite numerous interventions, biotechnology education remains highly unequal worldwide. Historically, high costs and exposure hazardous materials have hindered education. Integration of cloud technologies into classrooms has emerged as an alternative solution that is already enabling experiments reach thousands students globally. We describe several collectively facilitate real-time experimentation in remote locations. These advances enable access scientific data live experiments, promote collaborative research, ensure educational inclusivity. propose cloud-enabled live-cell a mechanism for reducing inequalities promoting sustainable development.

Language: Английский

Citations

0

Modeling Enzyme Kinetics: Current Challenges and Future Perspectives for Biocatalysis DOI
Jürgen Pleiss

Biochemistry, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 26, 2024

Biocatalysis is becoming a data science. High-throughput experimentation generates rapidly increasing stream of biocatalytic data, which the raw material for mechanistic and novel data-driven modeling approaches predictive design improved biocatalysts bioprocesses. The holistic molecular understanding enzymatic reaction systems will enable us to identify overcome kinetic bottlenecks shift thermodynamics reaction. full characterization community effort; therefore, published methods results should be findable, accessible, interoperable, reusable (FAIR), achieved by developing standardized exchange formats, complete reproducible documentation experimentation, collaborative platforms sustainable software analyzing repositories publishing together with data. FAIRification biocatalysis prerequisite highly automated laboratory infrastructures that improve reproducibility scientific reduce time costs required develop synthesis routes.

Language: Английский

Citations

0