TY - GEN A1 - Lisec, Jan T1 - CorMID - Correct Mass Isotopologue Distribution Vectors N2 - The investigation of metabolic fluxes and metabolite distributions within cells by means of tracer molecules is a valuable tool to unravel the complexity of biological systems. Technological advances in mass spectrometry (MS) technology such as atmospheric pressure chemical ionization (APCI) coupled with high resolution (HR), not only allows for highly sensitive analyses but also broadens the usefulness of tracer-based experiments, as interesting signals can be annotated de novo when not yet present in a compound library. However, several effects in the APCI ion source, i.e., fragmentation and rearrangement, lead to superimposed mass isotopologue distributions (MID) within the mass spectra, which need to be corrected during data evaluation as they will impair enrichment calculation otherwise. Here, we present and evaluate a novel software tool to automatically perform such corrections. We discuss the different effects, explain the implemented algorithm, and show its application on several experimental datasets. This adjustable tool is available as an R package from CRAN. KW - Mass Spectrometry KW - Software KW - R package KW - Mass Isotopomer Distribution KW - Flux Analysis PY - 2022 UR - https://github.com/cran/CorMID/ PB - GitHub CY - San Francisco, CA, USA AN - OPUS4-56442 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Lisec, Jan T1 - IsoCor N2 - Despite numerous advantages offered by hyphenation of chromatography and electrokinetic separation methods with multicollector (MC) ICP-MS for isotope analysis, the main limitation of such systems is the decrease in precision and increase in uncertainty due to generation of short transient signals. To minimize this limitation, most authors compare several isotope ratio calculation methods and establish a multi-step data processing routine based on the precision and accuracy of the methods. However, to the best of our knowledge, there is no universal data processing tool available that incorporates all important steps of the treatment of the transient signals. Thus, we introduce a data processing application (App) IsoCor that facilitates automatic calculation of isotope ratios from transient signals and eases selection of the most suitable method. The IsoCor App performs baseline subtraction, peak detection, mass bias correction, isotope ratio calculation and delta calculation. The feasibility and reliability of the App was proven by reproducing the results from isotope analysis of three elements (neodymium, mercury and sulfur) measured on-line via hyphenated systems. The IsoCor App provides trackability of the results to ensure quality control of the analysis. KW - Shiny-App KW - ICP-MS KW - Software PY - 2022 UR - https://github.com/cran/IsoCor/ PB - GitHub CY - San Francisco, CA, USA AN - OPUS4-56307 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Liehr, Sascha T1 - ANNforPAT - Artificial Neural Networks for Process Analytical Technology N2 - This code accompanies the paper "Artificial neural networks for quantitative online NMR spectroscopy" published in Analytical and Bioanalytical Chemistry (2020). KW - Artificial neural networks KW - Automation KW - Online NMR spectroscopy KW - Process industry KW - Real-time process monitoring PY - 2020 UR - https://github.com/BAMresearch/ANNforPAT PB - GitHub CY - San Francisco AN - OPUS4-54481 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Pauw, Brian Richard A1 - Hörmann, Anja T1 - Trinamic TMCL IOC for exposing Trinamics motor controllers to EPICS CA N2 - Trinamic TMCL IOC is a Python package designed for controlling stepper motors connected to a Trinamic board using the TMCL language (all boards supported by PyTrinamic should now work, has been tested on the TMCM 6110 and the TMCM 6214). Since it is implementing the TMCL protocol, it should be easy to adapt to other Trinamic motor controller boards. This package assumes the motor controller is connected over a machine network via a network-to-serial converter, but the underlying PyTrinamic package allows for other connections too. This allows the control of attached motors via the EPICS Channel-Access virtual communications bus. If EPICS is not desired, plain Pythonic control via motion_control should also be possible. An example for this will be provided in the example.ipynb Jupyter notebook. This package leverages Caproto for EPICS IOCs and a modified PyTrinamic library for the motor board control, and interfaces between the two via an internal set of dataclasses. Configuration for the motors and boards are loaded from YAML files (see tests/testdata/example_config.yaml). The modifications to PyTrinamic involved extending their library with a socket interface. This was a minor modification that should eventually find its way into the official package (a pull request has been submitted). KW - Instrumentation KW - Motor controller KW - EPICS KW - Channel access KW - Instrument control KW - Laboratory automation PY - 2024 DO - https://doi.org/10.5281/zenodo.10792593 PB - Zenodo CY - Geneva AN - OPUS4-59624 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Pauw, Brian Richard A1 - Smales, Glen Jacob A1 - Moeez, A. A1 - Hörmann, Anja A1 - Breßler, Ingo T1 - Example configurations and test cases for the Python HDF5Translator framework. N2 - This is a set of use examples for the HDF5Translator framework. This framework lets you translate measurement files into a different (e.g. NeXus-compatible) structure, with some optional checks and conversions on the way. For an in-depth look at what it does, there is a blog post here. The use examples provided herein are each accompanied by the measurement data necessary to test and replicate the conversion. The README.md files in each example show the steps necessary to do the conversion for each. We encourage those who have used or adapted one or more of these exampes to create their own conversion, to get in touch with us so we may add your example to the set. KW - Measurement data conversion KW - Data conversion KW - HDF5 KW - NeXus KW - NXsas KW - Framework KW - Python PY - 2024 DO - https://doi.org/10.5281/zenodo.10925971 PB - Zenodo CY - Geneva AN - OPUS4-59796 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Kern, Simon A1 - Liehr, Sascha A1 - Wander, Lukas A1 - Bornemann-Pfeiffer, Martin A1 - Müller, S. A1 - Maiwald, Michael A1 - Kowarik, Stefan T1 - Training data of quantitative online NMR spectroscopy for artificial neural networks N2 - Data set of low-field NMR spectra of continuous synthesis of nitro-4’-methyldiphenylamine (MNDPA). 1H spectra (43 MHz) were recorded as single scans. Two different approaches for the generation of artificial neural networks training data for the prediction of reactant concentrations were used: (i) Training data based on combinations of measured pure component spectra and (ii) Training data based on a spectral model. Synthetic low-field NMR spectra First 4 columns in MAT-files represent component areas of each reactant within the synthetic mixture spectrum. Xi (“pure component spectra dataset”) Xii (“spectral model dataset”) Experimental low-field NMR spectra from MNDPA-Synthesis This data set represents low-field NMR-spectra recorded during continuous synthesis of nitro-4’-methyldiphenylamine (MNDPA). Reference values from high-field NMR results are included. KW - NMR spectroscopy KW - Real-time process monitoring KW - Artificial neural networks KW - Online NMR spectroscopy KW - Automation KW - Process industry PY - 2020 DO - https://doi.org/10.5281/zenodo.3677139 PB - Zenodo CY - Geneva AN - OPUS4-50456 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Kern, Simon A1 - Wander, Lukas A1 - Meyer, Klas A1 - Guhl, Svetlana A1 - Gottu Mukkula, A. R. A1 - Holtkamp, M. A1 - Salge, M. A1 - Fleischer, C. A1 - Weber, N. A1 - Engell, S. A1 - Paul, Andrea A1 - King, R. A1 - Maiwald, Michael T1 - Raw data of pilot plant runs for CONSENS project (Case study 1) N2 - In case study one of the CONSENS project, two aromatic substances were coupled by a lithiation reaction, which is a prominent example in pharmaceutical industry. The two aromatic reactants (Aniline and o-FNB) were mixed with Lithium-base (LiHMDS) in a continuous modular plant to produce the desired product (Li-NDPA) and a salt (LiF). The salt precipitates which leads to the formation of particles. The feed streams were subject to variation to drive the plant to its optimum. The uploaded data comprises the results from four days during continuous plant operation time. Each day is denoted from day 1-4 and represents the dates 2017-09-26, 2017-09-28, 2017-10-10, 2017-10-17. In the following the contents of the files are explained. KW - Process Analytical Technology KW - Multivariate Data Analysis KW - Nuclear Magnetic Resonance KW - Near Infrared Spectroscopy KW - Continuous Manufacturing KW - CONSENS PY - 2018 DO - https://doi.org/10.5281/zenodo.1438233 PB - Zenodo CY - Geneva AN - OPUS4-48063 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -