Automation tools
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About eight years ago, a new automation approach and flow technique called "Lab-In-Syringe" was proposed. It was derived from previous flow techniques, all based on handling reagent and sample solutions in a flow manifold. To date Lab-In-Syringe has evidently gained the interest of researchers in many countries, with new modifications, operation modes, and technical improvements still popping up. It has proven to be a versatile tool for the automation of sample preparation, particularly, liquid-phase microextraction approaches. This article aims to assist newcomers to this technique in system planning and setup by overviewing the different options for configurations, limitations, and feasible operations. This includes syringe orientation, in-syringe stirring modes, in-syringe detection, additional inlets, and addable features. The authors give also a chronological overview of technical milestones and a critical explanation on the potentials and shortcomings of this technique, calculations of characteristics, and tips and tricks on method development. Moreover, a comprehensive overview of the different operation modes of Lab-In-Syringe automated sample pretreatment is given focusing on the technical aspects and challenges of the related operations. We further deal with possibilities on how to fabricate required or useful system components, in particular by 3D printing technology, with over 20 different elements exemplarily shown. Finally, a short discussion on shortcomings and required improvements is given.
- Klíčová slova
- 3D printing of instrument elements, Lab-In-Syringe, automation of sample pretreatment, potentials and troubles, system setup and operation modes, tips and tricks in method development,
- MeSH
- chemické techniky analytické přístrojové vybavení metody normy MeSH
- injekční stříkačky * MeSH
- laboratorní automatizace * MeSH
- limita detekce MeSH
- reprodukovatelnost výsledků MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Systematic reviews (SRs) are time-consuming and labor-intensive to perform. With the growing number of scientific publications, the SR development process becomes even more laborious. This is problematic because timely SR evidence is essential for decision-making in evidence-based healthcare and policymaking. Numerous methods and tools that accelerate SR development have recently emerged. To date, no scoping review has been conducted to provide a comprehensive summary of methods and ready-to-use tools to improve efficiency in SR production. OBJECTIVE: To present an overview of primary studies that evaluated the use of ready-to-use applications of tools or review methods to improve efficiency in the review process. METHODS: We conducted a scoping review. An information specialist performed a systematic literature search in four databases, supplemented with citation-based and grey literature searching. We included studies reporting the performance of methods and ready-to-use tools for improving efficiency when producing or updating a SR in the health field. We performed dual, independent title and abstract screening, full-text selection, and data extraction. The results were analyzed descriptively and presented narratively. RESULTS: We included 103 studies: 51 studies reported on methods, 54 studies on tools, and 2 studies reported on both methods and tools to make SR production more efficient. A total of 72 studies evaluated the validity (n = 69) or usability (n = 3) of one method (n = 33) or tool (n = 39), and 31 studies performed comparative analyses of different methods (n = 15) or tools (n = 16). 20 studies conducted prospective evaluations in real-time workflows. Most studies evaluated methods or tools that aimed at screening titles and abstracts (n = 42) and literature searching (n = 24), while for other steps of the SR process, only a few studies were found. Regarding the outcomes included, most studies reported on validity outcomes (n = 84), while outcomes such as impact on results (n = 23), time-saving (n = 24), usability (n = 13), and cost-saving (n = 3) were less often evaluated. CONCLUSION: For title and abstract screening and literature searching, various evaluated methods and tools are available that aim at improving the efficiency of SR production. However, only few studies have addressed the influence of these methods and tools in real-world workflows. Few studies exist that evaluate methods or tools supporting the remaining tasks. Additionally, while validity outcomes are frequently reported, there is a lack of evaluation regarding other outcomes.
- Klíčová slova
- Automation tools, Evidence synthesis, Method, Rapid review, Scoping review, Systematic review,
- MeSH
- lidé MeSH
- systematický přehled jako téma * metody MeSH
- výzkumný projekt MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- scoping review MeSH
Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.
- MeSH
- informatika MeSH
- lipidomika * MeSH
- lipidy chemie MeSH
- software MeSH
- výpočetní biologie * metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- Research Support, N.I.H., Extramural MeSH
- Názvy látek
- lipidy MeSH
Three tools for an automated analysis of electron diffraction pattern and crystallographic visualization are presented. Firstly, diffractGUI determines the zone axis from selected area diffraction, convergent beam diffraction or nanodiffraction patterns and allows for indexing of individual reflections. Secondly, ringGUI identifies crystallographic planes corresponding to the depicted rings in the ring diffraction pattern and can select the sample material from a list of candidates. Both diffractGUI and ringGUI employ methods of computer vision for a fast, robust and accurate analysis. Thirdly, cellViewer is an intuitive visualization tool which is also helpful for crystallographic calculations or educational purposes. diffractGUI and cellViewer can be used together during a transmission electron microscopy session to determine the sample holder tilts required to reach a desired zone axis. All the tools offer a graphical user interface. The toolbox is distributed as a standalone application, so it can be installed on the microscope computer and launched directly from DigitalMicrograph (Gatan Inc.).
- Klíčová slova
- automated analysis, electron diffraction, high-resolution transmission electron microscopy, transmission electron microscopy,
- Publikační typ
- časopisecké články MeSH
Continual technological advances associated with the recent automation revolution have tremendously increased the impact of computer technology in the industry. Software development and testing are time-consuming processes, and the current market faces a lack of specialized experts. Introducing automation to this field could, therefore, improve software engineers' common workflow and decrease the time to market. Even though many code-generating algorithms have been proposed in textual-based programming languages, to the best of the authors' knowledge, none of the studies deals with the implementation of such algorithms in graphical programming environments, especially LabVIEW. Due to this fact, the main goal of this study is to conduct a proof-of-concept for a requirement-based automated code-developing system within the graphical programming environment LabVIEW. The proposed framework was evaluated on four basic benchmark problems, encompassing a string model, a numeric model, a boolean model and a mixed-type problem model, which covers fundamental programming scenarios. In all tested cases, the algorithm demonstrated an ability to create satisfying functional and errorless solutions that met all user-defined requirements. Even though the generated programs were burdened with redundant objects and were much more complex compared to programmer-developed codes, this fact has no effect on the code's execution speed or accuracy. Based on the achieved results, we can conclude that this pilot study not only proved the feasibility and viability of the proposed concept, but also showed promising results in solving linear and binary programming tasks. Furthermore, the results revealed that with further research, this poorly explored field could become a powerful tool not only for application developers but also for non-programmers and low-skilled users.
- MeSH
- algoritmy MeSH
- automatizace MeSH
- pilotní projekty MeSH
- programovací jazyk * MeSH
- software * MeSH
- Publikační typ
- časopisecké články MeSH
Animal behaviour can be viewed as a stream of elements, which, once accurately described, can be counted and timed. Data acquisition techniques and tools are reviewed, and some strategies for collection and analysis of data using PC computers are suggested. Automated instruments are not satisfactory for the study of complex behaviour and as such systemic observation remains irreplaceable. IBM PC-type computers, with a wide range of analytical software (e.g., spreadsheets, statistical packages, technical graphics), are practical for data acquisition. Several systems which can satisfy different applications are reviewed. Some systems can communicate with a videorecorder, a facility which remarkably increases the accuracy of measurement; this is essential for meaningful analyses of the internal structure of behavioural streams (sequences, time patterns) or communication processes. The power of new tools enables behavioural measurement with the necessary complexity to allow a whole new set of questions to be addressed. However, it also increases demands for meaningful content and analysis of data.
- MeSH
- chování zvířat účinky léků MeSH
- počítače MeSH
- psychofarmakologie přístrojové vybavení MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
Photosynthesis research employs several biophysical methods, including the detection of fluorescence. Even though fluorescence is a key method to detect photosynthetic efficiency, it has not been applied/adapted to single-cell confocal microscopy measurements to examine photosynthetic microorganisms. Experiments with photosynthetic cells may require automation to perform a large number of measurements with different parameters, especially concerning light conditions. However, commercial microscopes support custom protocols (through Time Controller offered by Olympus or Experiment Designer offered by Zeiss) that are often unable to provide special set-ups and connection to external devices (e.g., for irradiation). Our new system combining an Arduino microcontroller with the Cell⊕Finder software was developed for controlling Olympus FV1000 and FV1200 confocal microscopes and the attached hardware modules. Our software/hardware solution offers (1) a text file-based macro language to control the imaging functions of the microscope; (2) programmable control of several external hardware devices (light sources, thermal controllers, actuators) during imaging via the Arduino microcontroller; (3) the Cell⊕Finder software with ergonomic user environment, a fast selection method for the biologically important cells and precise positioning feature that reduces unwanted bleaching of the cells by the scanning laser. Cell⊕Finder can be downloaded from http://www.alga.cz/cellfinder. The system was applied to study changes in fluorescence intensity in Synechocystis sp. PCC6803 cells under long-term illumination. Thus, we were able to describe the kinetics of phycobilisome decoupling. Microscopy data showed that phycobilisome decoupling appears slowly after long-term (>1 h) exposure to high light.
- Klíčová slova
- automated microscopy, confocal microscopy, photoprotection, photosynthetic membrane, remote controlled microscopy,
- MeSH
- konfokální mikroskopie přístrojové vybavení metody MeSH
- laboratorní automatizace přístrojové vybavení metody MeSH
- osvětlení MeSH
- software MeSH
- Synechocystis chemie ultrastruktura MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The process of manual species identification is a daunting task, so much so that the number of taxonomists is seen to be declining. In order to assist taxonomists, many methods and algorithms have been proposed to develop semi-automated and fully automated systems for species identification. While semi-automated tools would require manual intervention by a domain expert, fully automated tools are assumed to be not as reliable as manual or semiautomated identification tools. Hence, in this study we investigate the accuracy of fully automated and semi-automated models for species identification. We have built fully automated and semi-automated species classification models using the monogenean species image dataset. With respect to monogeneans' morphology, they are differentiated based on the morphological characteristics of haptoral bars, anchors, marginal hooks and reproductive organs (male and female copulatory organs). Landmarks (in the semi-automated model) and shape morphometric features (in the fully automated model) were extracted from four monogenean species images, which were then classified using k-nearest neighbour and artificial neural network. In semi-automated models, a classification accuracy of 96.67 % was obtained using the k-nearest neighbour and 97.5 % using the artificial neural network, whereas in fully automated models, a classification accuracy of 90 % was obtained using the k-nearest neighbour and 98.8 % using the artificial neural network. As for the crossvalidation, semi-automated models performed at 91.2 %, whereas fully automated models performed slightly higher at 93.75 %.
Next-generation sequencing technology has created many new opportunities for clinical diagnostics, but it faces the challenge of functional annotation of identified mutations. Various algorithms have been developed to predict the impact of missense variants that influence oncogenic drivers. However, computational pipelines that handle biological data must integrate multiple software tools, which can add complexity and hinder non-specialist users from accessing the pipeline. Here, we have developed an online user-friendly web server tool PredictONCO that is fully automated and has a low barrier to access. The tool models the structure of the mutant protein in the first step. Next, it calculates the protein stability change, pocket level information, evolutionary conservation, and changes in ionisation of catalytic amino acid residues, and uses them as the features in the machine-learning predictor. The XGBoost-based predictor was validated on an independent subset of held-out data, demonstrating areas under the receiver operating characteristic curve (ROC) of 0.97 and 0.94, and the average precision from the precision-recall curve of 0.99 and 0.94 for structure-based and sequence-based predictions, respectively. Finally, PredictONCO calculates the docking results of small molecules approved by regulatory authorities. We demonstrate the applicability of the tool by presenting its usage for variants in two cancer-associated proteins, cellular tumour antigen p53 and fibroblast growth factor receptor FGFR1. Our free web tool will assist with the interpretation of data from next-generation sequencing and navigate treatment strategies in clinical oncology: https://loschmidt.chemi.muni.cz/predictonco/.
- Klíčová slova
- Automation, Machine learning, Mutation, Next-generation sequencing, Oncogenicity, Precision oncology, Prediction, Treatment, Virtual screening, Webserver,
- Publikační typ
- časopisecké články MeSH
SUMMARY: PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, PDBImages provides a means to generate high-quality images for PDB and AlphaFold DB models. Its unique ability to render and save images directly to files in a browserless mode sets it apart, offering users a streamlined, automated process for macromolecular structure visualization. Here, we detail the implementation of PDBImages, enumerating its diverse image types, and elaborating on its user-friendly setup. This powerful tool opens a new gateway for researchers to visualize, analyse, and share their work, fostering a deeper understanding of bioinformatics. AVAILABILITY AND IMPLEMENTATION: PDBImages is available as an npm package from https://www.npmjs.com/package/pdb-images. The source code is available from https://github.com/PDBeurope/pdb-images.
- MeSH
- molekulární struktura MeSH
- software * MeSH
- výpočetní biologie * metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
