The Repository Chemotion: Infrastructure for Sustainable Research in Chemistry

Tremouilhac, Pierre; Lin, Chia-Lin; Huang, Pei-Chi; Huang, Yu‐Chieh; Nguyẽ̂n, An; Jung, Nicole; Bach, Felix; Ulrich, Robert; Neumair, Bernhard; Streit, Achim; Bräse, Stefan

doi:10.26434/chemrxiv.12195318.v1

Cited by 5 publications

(4 citation statements)

References 2 publications

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“…The stand-alone application supports the visualization and analysis of spectra, but its functions are limited in comparison to an embedded version, as the information stored in the browser exists temporarily and is not persisted permanently. To show the advantages of the ChemSpectra development as an embedded application offering the full available functionality, it was incorporated into the web applications Chemotion ELN and repository, which are developments of our research group reported earlier [ 20 , 21 ]. Examples for further functions are the storage and management of the files that were edited by ChemSpectra.…”

Section: Methodsmentioning

confidence: 99%

ChemSpectra: a web-based spectra editor for analytical data

et al. 2021

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ChemSpectra, a web-based software to visualize and analyze spectroscopic data, integrating solutions for infrared spectroscopy (IR), mass spectrometry (MS), and one-dimensional 1H and 13C NMR (proton and carbon nuclear magnetic resonance) spectroscopy, is described. ChemSpectra serves as web-based tool for the analysis of the most often used types of one-dimensional spectroscopic data in synthetic (organic) chemistry research. It was developed to support in particular processes for the use of open file formats which enable the work according to the FAIR data principles. The software can deal with the open file formats JCAMP-DX (IR, MS, NMR) and mzML (MS) proposing these data file types to gain interoperable data. ChemSpectra can be extended to read also other formats as exemplified by selected proprietary mass spectrometry data files of type RAW and NMR spectra files of type FID. The JavaScript-based editor can be integrated with other software, as demonstrated by integration into the Chemotion electronic lab notebook (ELN) and Chemotion repository, demonstrating the implementation into a digital work environment that offers additional functionality and sustainable research data management options. ChemSpectra supports different functions for working with spectroscopic data such as zoom functions, peak picking and automatic peak detection according to a default or manually defined threshold. NMR specific functions include the definition of a reference signal, the integration of signals, coupling constant calculation and multiplicity assignment. Embedded into a web application such as an ELN or a repository, the editor can also be used to generate an association of spectra to a sample and a file management. The file management supports the storage of the original spectra along with the last edited version and an automatically generated image of the spectra in png format. To maximize the benefit of the spectra editor for e.g. ELN users, an automated procedure for the transfer of the detected or manually chosen signals to the ELN was implemented. ChemSpectra is released under the AGPL license to encourage its re-use and further developments by the community.

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Section: Methodsmentioning

confidence: 99%

ChemSpectra: a web-based spectra editor for analytical data

et al. 2021

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“…To show the advantages of the ChemSpectra development as an embedded application offering the full available functionality, it was incorporated into the web applications Chemotion ELN and repository, which are developments of our research group reported earlier. 20,21 Examples for further functions are the storage and management of the les that were edited by ChemSpectra. Figure 1 gives an overview of the main parts of the ChemSpectra software and the implemented processes for the stand-alone version (green arrows) and the exemplary implementation with the Chemotion applications (work ow given in blue).…”

Section: Methodsmentioning

confidence: 99%

ChemSpectra: A web-based spectra editor for analytical data

Huang

Tremouilhac

Nguyẽ̂n

et al. 2020

Preprint

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ChemSpectra, a web-based software to visualize and analyze spectroscopic data, integrating solutions for IR (infrared spectroscopy), MS (mass spectrometry), and one-dimensional 1 H and 13 C NMR (proton and carbon nuclear magnetic resonance) spectroscopy, is described. ChemSpectra serves as web-based tool for the analysis of the most often used types of one-dimensional spectroscopic data in synthetic (organic) chemistry research. It was developed to support in particular processes for the use of open file formats which enable the work according to the FAIR data principles. The software can deal with the open file formats JCAMP-DX (IR, MS, NMR) and mzML (MS) proposing these data file types to gain interoperable data. ChemSpectra can be extended to read also other formats as exemplified by selected proprietary mass spectrometry data files of type RAW and NMR spectra files of type FID. The JavaScript-based editor can be integrated with other software, as demonstrated by integration into the Chemotion electronic lab notebook (ELN) and Chemotion repository, demonstrating the implementation into a digital work environment that offers additional functionality and sustainable research data management options. ChemSpectra supports different functions for working with spectroscopic data such as zoom functions, peak picking and automatic peak detection according to a default or manually defined threshold. NMR specific functions include the definition of a reference signal, the integration of signals, coupling constant calculation and multiplicity assignment. Embedded into a web application such as an ELN or a repository, the editor can also be used to generate an association of spectra to a sample and a file management. The file management supports the storage of the original spectra along with the last edited version and an automatically generated image of the spectra in png format. To maximize the benefit of the spectra editor for e.g. ELN users, an automated procedure for the transfer of the detected or manually chosen signals to the ELN was implemented. ChemSpectra is released under the AGPL license to encourage its re-use and further developments by the community.

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“…There are commercial (e.g., Reaxys, 181 CAS, 182 etc) and public (e.g., ChemSpider 183 ) chemical databases, however, they do not yet support the fully digital workflow. Very recent proposal to establish the new repository Chemotion offers a potential platform for a fully digital workflow of chemical R&D 184 . Lab information management systems (LIMS) are another powerful tool for automatically collected data; originally conceived for automated data tracking and exchange, they have been further integrated with data mining, analysis, and translation tools, allowing for much wider range of applications 185 .…”

Section: Perspectives and Other Challenges In Formulation Designmentioning

confidence: 99%

Automated robotic platforms in design and development of formulations

2021

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Product design for formulations is an active and challenging area of research. The new challenges of a fast-paced market, products of increasing complexity, and practical translation of sustainability paradigms require to reexamine the existing theoretical frameworks to include the advantages deriving from the new reality of digitalization of business and research. In this work, we review the existing approaches, clearly stating the role of automation and machine-learning-guided optimization in the broader framework. Moving from this, we review the state of the art of automated hardware and software for formulated product design, and identify the open challenges for future research. Perspectives are given on the emerging fields of automated discovery, scale-up, and multistage optimization, and a unitary picture of the existing connections is provided, in the general context of a completely digital R&D workflow.

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The Repository Chemotion: Infrastructure for Sustainable Research in Chemistry

Cited by 5 publications

References 2 publications

ChemSpectra: a web-based spectra editor for analytical data

ChemSpectra: a web-based spectra editor for analytical data

ChemSpectra: A web-based spectra editor for analytical data

Automated robotic platforms in design and development of formulations

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