Reproducible software
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Zámerom štúdie bolo empiricky overiť reliabilitu autorského fotogrametrického softwaru na meranie uhlov v rôznych polohách kĺbu a porovnať ju s reliabilitou goniometra štandardne využívaného vo fyzioterapeutickej praxi pri diagnostike rozsahu pohybu v kĺbe. Pilotný komparačný výskumu bol realizovaný na vzorke 27 probantov (študentov fyzioterapie), pričom boli merané uhly v troch kĺboch pomocou softwaru aj goniometra. Opakované meranie uhlu v jednom kĺbe realizovalo 20 probantov s časovým odstupom 2 týždňov od prvého merania. Oba overované aspekty reliability – interrater aj intrarater – sa na základe štatistických ukazovateľov (priemerné odchýlky merania, korelačné koeficienty zhody meraní v čase) javia byť vyššie pri meraní pomocou fotogrametrického softwaru v porovnaní s goniometrom. Klúčové slová: fyzioterapeutická diagnostika, meranie uhlov, rozsah pohybu v kĺbe, fotogrametrický software, goniometer, reliabilita
The aim of the study was to empirically verify the reliability of authors´ photogrammetric software for measuring the angles in various joint positions and to compare it with the reliability of the goniometer standardly used in physiotherapy practice for the diagnostics of range of joint motion. The pilot comparative research was conducted on the sample of 27 probands (physiotherapy students) and the angles were measured in three joints using both the goniometer and the software. Repeated measuring the angle in one joint was realized by 20 probands after two weeks from the first measurement. Both verified aspects of reliability – interrater and intrarater – appear to be higher (based on statistical indicators average deviations and correlation coefficients) when the photogrammetric software was used compared to the using of goniometer.
- Klíčová slova
- fyzioterapeutická diagnostika, fotogrametrický software,
- MeSH
- fotografování * MeSH
- kloubní artrometrie * metody statistika a číselné údaje MeSH
- kolenní kloub MeSH
- lidé MeSH
- loketní kloub MeSH
- pilotní projekty MeSH
- reprodukovatelnost výsledků MeSH
- rozsah kloubních pohybů * MeSH
- software MeSH
- validace softwaru * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- hodnotící studie MeSH
- srovnávací studie MeSH
The spinal cord plays a pivotal role in the central nervous system, providing communication between the brain and the body and containing critical motor and sensory networks. Recent advancements in spinal cord MRI data acquisition and image analysis have shown a potential to improve the diagnostics, prognosis, and management of a variety of pathological conditions. In this review, we first discuss the significance of standardized spinal cord MRI acquisition protocol in multi-center and multi-manufacturer studies. Then, we cover open-access spinal cord MRI datasets, which are important for reproducible science and validation of new methods. Finally, we elaborate on the recent advances in spinal cord MRI data analysis techniques implemented in the open-source software package Spinal Cord Toolbox (SCT).
Image processing in cryogenic electron tomography (cryoET) is currently at a similar state as Single Particle Analysis (SPA) in cryogenic electron microscopy (cryoEM) was a few years ago. Its data processing workflows are far from being well defined and the user experience is still not smooth. Moreover, file formats of different software packages and their associated metadata are not standardized, mainly since different packages are developed by different groups, focusing on different steps of the data processing pipeline. The Scipion framework, originally developed for SPA (de la Rosa-Trevín et al., 2016), has a generic python workflow engine that gives it the versatility to be extended to other fields, as demonstrated for model building (Martínez et al., 2020). In this article, we provide an extension of Scipion based on a set of tomography plugins (referred to as ScipionTomo hereafter), with a similar purpose: to allow users to be focused on the data processing and analysis instead of having to deal with multiple software installation issues and the inconvenience of switching from one to another, converting metadata files, managing possible incompatibilities, scripting (writing a simple program in a language that the computer must convert to machine language each time the program is run), etcetera. Additionally, having all the software available in an integrated platform allows comparing the results of different algorithms trying to solve the same problem. In this way, the commonalities and differences between estimated parameters shed light on which results can be more trusted than others. ScipionTomo is developed by a collaborative multidisciplinary team composed of Scipion team engineers, structural biologists, and in some cases, the developers whose software packages have been integrated. It is open to anyone in the field willing to contribute to this project. The result is a framework extension that combines the acquired knowledge of Scipion developers in close collaboration with third-party developers, and the on-demand design of functionalities requested by beta testers applying this solution to actual biological problems.
BACKGROUND: Proton magnetic resonance spectroscopy is a non-invasive measurement technique which provides information about concentrations of up to 20 metabolites participating in intracellular biochemical processes. In order to obtain any metabolic information from measured spectra a processing should be done in specialized software, like jMRUI. The processing is interactive and complex and often requires many trials before obtaining a correct result. This paper proposes a jMRUI enhancement for efficient and unambiguous history tracking and file identification. RESULTS: A database storing all processing steps, parameters and files used in processing was developed for jMRUI. The solution was developed in Java, authors used a SQL database for robust storage of parameters and SHA-256 hash code for unambiguous file identification. The developed system was integrated directly in jMRUI and it will be publically available. A graphical user interface was implemented in order to make the user experience more comfortable. The database operation is invisible from the point of view of the common user, all tracking operations are performed in the background. CONCLUSIONS: The implemented jMRUI database is a tool that can significantly help the user to track the processing history performed on data in jMRUI. The created tool is oriented to be user-friendly, robust and easy to use. The database GUI allows the user to browse the whole processing history of a selected file and learn e.g. what processing lead to the results, where the original data are stored, to obtain the list of all processing actions performed on spectra.
Although the likelihood ratio is a well-known statistical technique, commercial off-the-shelf (COTS) software products for its calculation are not sufficiently validated to suit general requirements for the competence of testing and calibration laboratories (EN/ISO/IEC 17025:2005 norm) per se. The software in question can be considered critical as it directly weighs the forensic evidence allowing judges to decide on guilt or innocence or to identify person or kin (i.e.: in mass fatalities). For these reasons, accredited laboratories shall validate likelihood ratio software in accordance with the above norm. To validate software for calculating the likelihood ratio in parentage/kinship scenarios I assessed available vendors, chose two programs (Paternity Index and familias) for testing, and finally validated them using tests derived from elaboration of the available guidelines for the field of forensics, biomedicine, and software engineering. MS Excel calculation using known likelihood ratio formulas or peer-reviewed results of difficult paternity cases were used as a reference. Using seven testing cases, it was found that both programs satisfied the requirements for basic paternity cases. However, only a combination of two software programs fulfills the criteria needed for our purpose in the whole spectrum of functions under validation with the exceptions of providing algebraic formulas in cases of mutation and/or silent allele.
Systems biology aims to understand living organisms through mathematically modeling their behaviors at different organizational levels, ranging from molecules to populations. Modeling involves several steps, from determining the model purpose to developing the mathematical model, implementing it computationally, simulating the model's behavior, evaluating, and refining the model. Importantly, model simulation results must be reproducible, ensuring that other researchers can obtain the same results after writing the code de novo and/or using different software tools. Guidelines to increase model reproducibility have been published. However, reproducibility remains a major challenge in this field. In this paper, we tackle this challenge for physiologically-based pharmacokinetic (PBPK) models, which represent the pharmacokinetics of chemicals following exposure in humans or animals. We summarize recommendations for PBPK model reporting that should apply during model development and implementation, in order to ensure model reproducibility and comprehensibility. We make a proposal aiming to harmonize abbreviations used in PBPK models. To illustrate these recommendations, we present an original and reproducible PBPK model code in MATLAB, alongside an example of MATLAB code converted to Systems Biology Markup Language format using MOCCASIN. As directions for future improvement, more tools to convert computational PBPK models from different software platforms into standard formats would increase the interoperability of these models. The application of other systems biology standards to PBPK models is encouraged. This work is the result of an interdisciplinary collaboration involving the ELIXIR systems biology community. More interdisciplinary collaborations like this would facilitate further harmonization and application of good modeling practices in different systems biology fields.
- MeSH
- biologické modely * MeSH
- farmakokinetika * MeSH
- lidé MeSH
- počítačová simulace MeSH
- reprodukovatelnost výsledků MeSH
- software * MeSH
- systémová biologie * metody MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
The activities of 54Mn and 65Zn have been determined by 4pi(PC)-gamma coincidence counting, with efficiency variation performed by the conventional method of altering the self-absorption in the sources as well as by the computer discrimination method. The standardisation of 65Zn presents some complications requiring optimisation of the gamma-ray energy window settings to achieve a linear efficiency-extrapolation curve. Determination of these optimal settings by the conventional coincidence method is a tedious task. These difficulties have been reduced by the utilisation of a software coincidence counting system that records time and amplitude information of individual pulses from coincidence measurements, where the coincidence parameters are set after the data collection process has completed, facilitating multiple data evaluations on a single data set. The optimal gamma-ray energy window settings for the 65Zn standardisation were derived from the results of the 54Mn standardisation, as well as from studies of the 65Zn data itself. The setting of the PC channel thresholds for K and both (K+L) electrons is also discussed. The results are compared with those attained using conventional coincidence counting.
- MeSH
- algoritmy MeSH
- dávka záření MeSH
- mangan analýza normy MeSH
- radioizotopy zinku analýza normy MeSH
- radionuklidy analýza normy MeSH
- referenční hodnoty MeSH
- referenční standardy MeSH
- reprodukovatelnost výsledků MeSH
- scintilace - počítání metody normy MeSH
- senzitivita a specificita MeSH
- směrnice jako téma MeSH
- software MeSH
- spektrometrie gama metody normy MeSH
- Publikační typ
- hodnotící studie MeSH
- Geografické názvy
- Česká republika MeSH
BACKGROUND:Analysis of ciliary function for assessment of patients suspected of primary ciliary dyskinesia (PCD) and for research studies of respiratory and ependymal cilia requires assessment of both ciliary beat pattern and beat frequency. While direct measurement of beat frequency from high-speed video recordings is the most accurate and reproducible technique it is extremely time consuming. The aim of this study was to develop a freely available automated method of ciliary beat frequency analysis from digital video (AVI) files that runs on open-source software (ImageJ) coupled to Microsoft Excel, and to validate this by comparison to the direct measuring high-speed video recordings of respiratory and ependymal cilia. These models allowed comparison to cilia beating between 3 and 52 Hz. METHODS:Digital video files of motile ciliated ependymal (frequency range 34 to 52 Hz) and respiratory epithelial cells (frequency 3 to 18 Hz) were captured using a high-speed digital video recorder. To cover the range above between 18 and 37 Hz the frequency of ependymal cilia were slowed by the addition of the pneumococcal toxin pneumolysin. Measurements made directly by timing a given number of individual ciliary beat cycles were compared with those obtained using the automated ciliaFA system. RESULTS:The overall mean difference (± SD) between the ciliaFA and direct measurement high-speed digital imaging methods was -0.05 ± 1.25 Hz, the correlation coefficient was shown to be 0.991 and the Bland-Altman limits of agreement were from -1.99 to 1.49 Hz for respiratory and from -2.55 to 3.25 Hz for ependymal cilia. CONCLUSIONS:A plugin for ImageJ was developed that extracts pixel intensities and performs fast Fourier transformation (FFT) using Microsoft Excel. The ciliaFA software allowed automated, high throughput measurement of respiratory and ependymal ciliary beat frequency (range 3 to 52 Hz) and avoids operator error due to selection bias. We have included free access to the ciliaFA plugin and installation instructions in Additional file 1 accompanying this manuscript that other researchers may use.
In the framework of forensic anthropology osteometric techniques are generally preferred over visual examinations due to a higher level of reproducibility and repeatability; qualities that are crucial within a legal context. The use of osteometric methods has been further reinforced by incorporating statistically-based algorithms and large reference samples in a variety of user-friendly software applications. However, the continued increase in admixture of human populations have made the use of osteometric methods for estimation of ancestry much more complex, which confounds one of major requirements of ancestry assessment - intra-population homogeneity. The present paper tests the accuracy of ancestry and sex assessment using four identification software tools, specifically FORDISC 2.0, FORDISC 3.1.293, COLIPR 1.5.2 and 3D-ID 1.0. Software accuracy was tested in a sample of 174 documented human crania of Brazilian origin composed of different ancestral groups (i.e., European Brazilians, Afro-Brazilians, and Japanese Brazilians and of admixed ancestry). The results show that regardless of the software algorithm employed and composition of the reference database, all methods were able to allocate approximately 50% of Brazilian specimens to an appropriate major reference group. Of the three ancestral groups, Afro-Brazilians were especially prone to misclassification. Japanese Brazilians, by contrast, were shown to be relatively easily recognizable as being of Asian descent but at the same time showed a strong affinity towards Hispanic crania, in particularly when the classification based on FDB was carried out in FORDISC. For crania of admixed origin all of the algorithms showed a considerable higher rate of inconsistency with a tendency for misclassification into Asian and American Hispanic groups. Sex assessments revealed an overall modest to poor reliability (60-71% of correctly classified specimens) using the tested software programs with unbalanced individual rates for males and females. The highest and atypically balanced rate of classification for sex assessment was provided by COLIPR software, which reached 78% of correctly assessed crania.
- MeSH
- lidé MeSH
- populační skupiny etnologie MeSH
- software normy MeSH
- soudní antropologie * metody MeSH
- určení pohlaví podle kostry metody MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- validační studie MeSH
- Geografické názvy
- Brazílie MeSH
This study assessed the measurement error of a monitoring system, the Video Manual Motion Tracker 1.0 (VMMT1.0), during time-motion analysis of basketball players. In this study, four reliability parameters were used to assess the measurement error of the system: the systematic bias, the inter-observer reliability, the intra-observer reliability and the absolute reliability. A basketball game video was used for the analysis. To assess the inter-observer reliability, two observers analysed a player's covered distance for 50 different periods of the game. To assess the relative and absolute reliability of the covered distance, the chosen players were monitored three times by 41 qualified observers. The findings did not indicate a significant systematic bias in the measurement error using the VMMT1.0 (one-way ANOVA, P > 0.05). The intra-observer reliability of the monitoring system was rated as very high (intraclass correlation, ICC = 0.999), similar to its inter-observer reliability (Pearson product-moment correlation, r = 0.994). The absolute reliability does not appear to be significant (standard error of measurement, SEM = 0.34 m). The results showed that the measurement error of the VMMT1.0 is acceptable and comparable with that of other time-motion analysis techniques.
