scholarly journals PhactorTM – a High Throughput Experimentation Management System

2020 ◽  
Author(s):  
Tim Cernak ◽  
Babak Mahjour
Keyword(s):  
Chemical Synthesis ◽  
High Throughput ◽  
Chemical Laboratory ◽  
Liquid Handling ◽  
High Throughput Experimentation ◽  
Series Of Experiments ◽  
Machine Readable ◽  
Liquid Handling Robot ◽  
Readable Format ◽  
Machine Readable Format

<p>High throughput experimentation (HTE) is an increasingly important tool in the study of chemical synthesis. While the hardware for running HTE in the synthesis lab has evolved significantly in recent years, there remains a need for software solutions to navigate data rich experiments. We have developed the software, phactor™, to facilitate the performance and analysis of HTE in a chemical laboratory. phactor™ allows experimentalists to rapidly design arrays of chemical reactions in 24, 96, 384, or 1,536 wellplates. Users can access online reagent data, such as a lab inventory, to populate wells with experiments and produce instructions to perform the screen manually, or with the assistance of a liquid handling robot. After completion of the screen, analytical results can be uploaded for facile evaluation, and to guide the next series of experiments. All chemical data, metadata, and results are stored in a machine-readable format.</p>

scholarly journals PhactorTM – a High Throughput Experimentation Management System

2020 ◽  
Author(s):  
Tim Cernak ◽  
Babak Mahjour
Keyword(s):  
Chemical Synthesis ◽  
High Throughput ◽  
Chemical Laboratory ◽  
Liquid Handling ◽  
High Throughput Experimentation ◽  
Series Of Experiments ◽  
Machine Readable ◽  
Liquid Handling Robot ◽  
Readable Format ◽  
Machine Readable Format

<p>High throughput experimentation (HTE) is an increasingly important tool in the study of chemical synthesis. While the hardware for running HTE in the synthesis lab has evolved significantly in recent years, there remains a need for software solutions to navigate data rich experiments. We have developed the software, phactor™, to facilitate the performance and analysis of HTE in a chemical laboratory. phactor™ allows experimentalists to rapidly design arrays of chemical reactions in 24, 96, 384, or 1,536 wellplates. Users can access online reagent data, such as a lab inventory, to populate wells with experiments and produce instructions to perform the screen manually, or with the assistance of a liquid handling robot. After completion of the screen, analytical results can be uploaded for facile evaluation, and to guide the next series of experiments. All chemical data, metadata, and results are stored in a machine-readable format.</p>

scholarly journals CFTR Lifecycle Map—A Systems Medicine Model of CFTR Maturation to Predict Possible Active Compound Combinations

2021 ◽  
Vol 22 (14) ◽  
pp. 7590
Author(s):  
Liza Vinhoven ◽  
Frauke Stanke ◽  
Sylvia Hafkemeyer ◽  
Manuel Manfred Nietert
Keyword(s):  
Large Scale ◽  
Synergistic Effects ◽  
Small Scale ◽  
Systems Medicine ◽  
Promising Candidate ◽  
Cftr Mutations ◽  
Machine Readable ◽  
High Throughput Screens ◽  
Readable Format ◽  
Machine Readable Format

Different causative therapeutics for CF patients have been developed. There are still no mutation-specific therapeutics for some patients, especially those with rare CFTR mutations. For this purpose, high-throughput screens have been performed which result in various candidate compounds, with mostly unclear modes of action. In order to elucidate the mechanism of action for promising candidate substances and to be able to predict possible synergistic effects of substance combinations, we used a systems biology approach to create a model of the CFTR maturation pathway in cells in a standardized, human- and machine-readable format. It is composed of a core map, manually curated from small-scale experiments in human cells, and a coarse map including interactors identified in large-scale efforts. The manually curated core map includes 170 different molecular entities and 156 reactions from 221 publications. The coarse map encompasses 1384 unique proteins from four publications. The overlap between the two data sources amounts to 46 proteins. The CFTR Lifecycle Map can be used to support the identification of potential targets inside the cell and elucidate the mode of action for candidate substances. It thereby provides a backbone to structure available data as well as a tool to develop hypotheses regarding novel therapeutics.

scholarly journals High-Throughput Molecular Testing of Ticks Using a Liquid-Handling Robot

2005 ◽  
Vol 42 (6) ◽  
pp. 1063-1067 ◽  
Author(s):  
John R. Moriarity ◽  
Amanda D. Loftis ◽  
Gregory A. Dasch
Keyword(s):  
High Throughput ◽  
Molecular Testing ◽  
Liquid Handling ◽  
Liquid Handling Robot

scholarly journals Linked Data and Metadata

2021 ◽  
pp. 79-90
Author(s):  
Christian Zinke-Wehlmann ◽  
Amit Kirschenbaum ◽  
Raul Palma ◽  
Soumya Brahma ◽  
Karel Charvát ◽  
...  
Keyword(s):  
Linked Data ◽  
Machine Readable ◽  
Readable Format ◽  
Machine Readable Format

AbstractData is the basis for creating information and knowledge. Having data in a structured and machine-readable format facilitates the processing and analysis of the data. Moreover, metadata—data about the data, can help discovering data based on features as, e.g., by whom they were created, when, or for which purpose. These associated features make the data more interpretable and assist in turning it into useful information. This chapter briefly introduces the concepts of metadata and Linked Data—highly structured and interlinked data, their standards and their usages, with some elaboration on the role of Linked Data in bioeconomy.

scholarly journals OSD2F: An Open-Source Data Donation Framework

2021 ◽  
Author(s):  
Theo Araujo ◽  
Jef Ausloos ◽  
Wouter van Atteveldt ◽  
Felicia Loecherbach ◽  
Judith Moeller ◽  
...  
Keyword(s):  
Current State ◽  
Open Source Data ◽  
Source Data ◽  
Data Ownership ◽  
Recent Developments ◽  
Development Goals ◽  
Commercial Organizations ◽  
Machine Readable ◽  
Readable Format ◽  
Machine Readable Format

The digital traces that people leave through their use of various online platforms provide tremendous opportunities for studying human behavior. However, the collection of these data is hampered by legal, ethical and technical challenges. We present a framework and tool for collecting these data through a data donation platform where consenting participants can securely submit their digital traces. This approach leverages recent developments in data rights that have given people more control over their own data, such as legislation that now mandates companies to make digital trace data available on request in a machine-readable format. By transparently requesting access to specific parts of this data for clearly communicated academic purposes, the data ownership and privacy of participants is respected and researchers are less dependent on commercial organizations that store this data in proprietary archives. In this paper we outline the general design principles, the current state of the tool, and future development goals.

scholarly journals Semi-automated high-throughput substrate screening assay for nucleoside kinases

2021 ◽  
Author(s):  
Katja Hellendahl ◽  
Maryke Fehlau ◽  
Sebastian Hans ◽  
Peter Neubauer ◽  
Anke Kurreck
Keyword(s):  
High Throughput ◽  
Viral Infections ◽  
Screening Assay ◽  
Liquid Handling ◽  
Wide Range ◽  
High Throughput Assay ◽  
Liquid Handling Robot

Nucleoside kinases (NKs) are key enzymes involved in the in vivo phosphorylation of nucleoside analogues used as drugs to treat cancer or viral infections. Having different specificities, the characterization of NKs is essential for drug design and the production of nucleotide analogues in an in vitro enzymatic process. Therefore, a fast and reliable substrate screening assay for NKs is of great importance. Here, we report the validation of a well-known luciferase-based assay for the detection of NK activity in 96-well plate format. The assay was semi-automated using a liquid handling robot. A good linearity was demonstrated (r² >0.98) in the range of 0 to 500 µM ATP, and it was shown that also alternative phosphate donors like dATP or CTP were accepted by the luciferase. The developed high-throughput assay revealed comparable results to HPLC analysis. The assay was exemplary used for the comparison of the substrate spectra of four nucleoside kinases using 20 (8 natural and 12 modified) substrates. The screening results correlated well with literature data and, additionally, previously unknown substrates were identified for three of the NKs studied. Our results demonstrate that the developed semi-automated high-throughput assay is suitable to identify best performing NKs for a wide range of substrates.

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