MaD GUI: An Open-Source Python Package for Annotation and Analysis of Time-Series Data

Developing machine learning algorithms for time-series data often requires manual annotation of the data. To do so, graphical user interfaces (GUIs) are an important component. Existing Python packages for annotation and analysis of time-series data have been developed without addressing adaptability, usability, and user experience. Therefore, we developed a generic open-source Python package focusing on adaptability, usability, and user experience. The developed package, Machine Learning and Data Analytics (MaD) GUI, enables developers to rapidly create a GUI for their specific use case. Furthermore, MaD GUI enables domain experts without programming knowledge to annotate time-series data and apply algorithms to it. We conducted a small-scale study with participants from three international universities to test the adaptability of MaD GUI by developers and to test the user interface by clinicians as representatives of domain experts. MaD GUI saves up to 75% of time in contrast to using a state-of-the-art package. In line with this, subjective ratings regarding usability and user experience show that MaD GUI is preferred over a state-of-the-art package by developers and clinicians. MaD GUI reduces the effort of developers in creating GUIs for time-series analysis and offers similar usability and user experience for clinicians as a state-of-the-art package.

A Beginner's Guide to Arterial Spin Labeling (ASL) Image Processing

Arterial spin labeling (ASL) is a non-invasive and cost-effective MRI technique for brain perfusion measurements. While it has developed into a robust technique for scientific and clinical use, its image processing can still be daunting. The 2019 Ann Arbor ISMRM ASL working group established that education is one of the main areas that can accelerate the use of ASL in research and clinical practice. Specifically, the post-acquisition processing of ASL images and their preparation for region-of-interest or voxel-wise statistical analyses is a topic that has not yet received much educational attention. This educational review is aimed at those with an interest in ASL image processing and analysis. We provide summaries of all typical ASL processing steps on both single-subject and group levels. The readers are assumed to have a basic understanding of cerebral perfusion (patho) physiology; a basic level of programming or image analysis is not required. Starting with an introduction of the physiology and MRI technique behind ASL, and how they interact with the image processing, we present an overview of processing pipelines and explain the specific ASL processing steps. Example video and image illustrations of ASL studies of different cases, as well as model calculations, help the reader develop an understanding of which processing steps to check for their own analyses. Some of the educational content can be extrapolated to the processing of other MRI data. We anticipate that this educational review will help accelerate the application of ASL MRI for clinical brain research.

Prediction of Soil Heavy Metal Immobilization by Biochar Using Machine Learning

Biochar application is a promising strategy for the remediation of contaminated soil, while ensuring sustainable waste management. Biochar remediation of heavy metal (HM)-contaminated soil primarily depends on the properties of the soil, biochar, and HM. The optimum conditions for HM immobilization in biochar-amended soils are site-specific and vary among studies. Therefore, a generalized approach to predict HM immobilization efficiency in biochar-amended soils is required. This study employs machine learning (ML) approaches to predict the HM immobilization efficiency of biochar in biochar-amended soils. The nitrogen content in the biochar (0.3-25.9%) and biochar application rate (0.5-10%) were the two most significant features affecting HM immobilization. Causal analysis showed that the empirical categories for HM immobilization efficiency, in the order of importance, were biochar properties > experimental conditions > soil properties > HM properties. Therefore, this study presents new insights into the effects of biochar properties and soil properties on HM immobilization. This approach can help determine the optimum conditions for enhanced HM immobilization in biochar-amended soils.

BlenderPhotonics: an integrated open-source software environment for three-dimensional meshing and photon simulations in complex tissues

SIGNIFICANCE

Rapid advances in biophotonics techniques require quantitative, model-based computational approaches to obtain functional and structural information from increasingly complex and multiscaled anatomies. The lack of efficient tools to accurately model tissue structures and subsequently perform quantitative multiphysics modeling greatly impedes the clinical translation of these modalities.

AIM

Although the mesh-based Monte Carlo (MMC) method expands our capabilities in simulating complex tissues using tetrahedral meshes, the generation of such domains often requires specialized meshing tools, such as Iso2Mesh. Creating a simplified and intuitive interface for tissue anatomical modeling and optical simulations is essential toward making these advanced modeling techniques broadly accessible to the user community.

APPROACH

We responded to the above challenge by combining the powerful, open-source three-dimensional (3D) modeling software, Blender, with state-of-the-art 3D mesh generation and MC simulation tools, utilizing the interactive graphical user interface in Blender as the front-end to allow users to create complex tissue mesh models and subsequently launch MMC light simulations.

RESULTS

Here, we present a tutorial to our Python-based Blender add-on-BlenderPhotonics-to interface with Iso2Mesh and MMC, which allows users to create, configure and refine complex simulation domains and run hardware-accelerated 3D light simulations with only a few clicks. We provide a comprehensive introduction to this tool and walk readers through five examples, ranging from simple shapes to sophisticated realistic tissue models.

CONCLUSIONS

BlenderPhotonics is user friendly and open source, and it leverages the vastly rich ecosystem of Blender. It wraps advanced modeling capabilities within an easy-to-use and interactive interface. The latest software can be downloaded at http://mcx.space/bp.

Prototyping Mobile Storytelling Applications for People with Aphasia

Aphasia is a partial or total loss of the ability to articulate ideas or comprehend spoken language, resulting from brain damage, in a person whose language skills were previously normal. Our goal was to find out how a storytelling app can help people with aphasia to communicate and share daily experiences. For this purpose, the Aphasia Create app was created for tablets, along with Aphastory for the Google Glass device. These applications facilitate social participation and enhance quality of life by using visual storytelling forms composed of photos, drawings, icons, etc., that can be saved and shared. We performed usability tests (supervised by a neuropsychologist) on six participants with aphasia who were able to communicate. Our work contributes (1) evidence that the functions implemented in the Aphasia Create tablet app suit the needs of target users, but older people are often not familiar with tactile devices, (2) reports that the Google Glass device may be problematic for persons with right-hand paresis, and (3) a characterization of the design guidelines for apps for aphasics. Both applications can be used to work with people with aphasia, and can be further developed. Aphasic centers, in which the apps were presented, expressed interest in using them to work with patients. The Aphasia Create app won the Enactus Poland National Competition in 2015.

A comparison of artificial intelligence techniques for predicting hyperforin content in Hypericum perforatum L. in different ecological habitats

Hyperforin, a major bioactive constituent of Hypericum concentration, is impacted by various phenological phases and soil characteristics. We aimed to design a model predicting hyperforin content in Hypericum perforatum based on different ecological and phenological conditions. We employed artificial intelligence modeling techniques including multilayer perceptron (MLP), radial basis function (RBF), and support vector machine (SVM) to examine the factors critical in predicting hyperforin content. We found that the MLP model (R 2 = .9) is the most suitable and precise model compared with RBF (R 2 = .81) and SVM (R 2 = .74) in predicting hyperforin in H. perforatum based on ecological conditions, plant growth, and soil features. Moreover, phenological stages, organic carbon, altitude, and total N are detected in sensitivity analysis as the main factors that have a considerable impact on hyperforin content. We also report that the developed graphical user interface would be adaptable for key stakeholders including producers, manufacturers, analytical laboratory managers, and pharmacognosists.

Daiquiri: a web-based user interface framework for beamline control and data acquisition

Daiquiri is a web-based user interface (UI) framework for control system monitoring and data acquisition designed for synchrotron beamlines. It provides simple, intuitive and responsive interfaces to control and monitor hardware, launch acquisition sequences and manage associated metadata. Daiquiri concerns itself only with the UI layer; it does not provide a scan engine or controls system but can be easily integrated with existing systems.

NEST Desktop, an Educational Application for Neuroscience

Simulation software for spiking neuronal network models matured in the past decades regarding performance and flexibility. But the entry barrier remains high for students and early career scientists in computational neuroscience since these simulators typically require programming skills and a complex installation. Here, we describe an installation-free Graphical User Interface (GUI) running in the web browser, which is distinct from the simulation engine running anywhere, on the student's laptop or on a supercomputer. This architecture provides robustness against technological changes in the software stack and simplifies deployment for self-education and for teachers. Our new open-source tool, NEST Desktop, comprises graphical elements for creating and configuring network models, running simulations, and visualizing and analyzing the results. NEST Desktop allows students to explore important concepts in computational neuroscience without the need to learn a simulator control language before. Our experiences so far highlight that NEST Desktop helps advancing both quality and intensity of teaching in computational neuroscience in regular university courses. We view the availability of the tool on public resources like the European ICT infrastructure for neuroscience EBRAINS as a contribution to equal opportunities.

IRTGUI: An R Package for Unidimensional Item Response Theory Analysis With a Graphical User Interface

In the last decade, many R packages were published to perform item response theory (IRT) analysis. Some researchers and practitioners have difficulty in using these functional tools because of their insufficient coding skills. The IRTGUI package provides these researchers a user-friendly GUI where they can perform unidimensional IRT analysis without coding skills. Using the IRTGUI package, person and item parameters, model and item fit indices can be obtained. Dimensionality and local independence assumptions can be tested. With the IRTGUI package, users can generate dichotomous data sets with customizable conditions. Also, Wright Maps, item characteristics and information curves can be graphically displayed. All outputs can be easily downloaded by users.

HFOApp: A MATLAB Graphical User Interface for High-Frequency Oscillation Marking

Epilepsy affects 3.4 million people in the United States, and, despite the availability of numerous antiepileptic drugs, 36% of patients have uncontrollable seizures, which severely impact quality of life. High-frequency oscillations (HFOs) are a potential biomarker of epileptogenic tissue that could be useful in surgical planning. As a result, research into the efficacy of HFOs as a clinical tool has increased over the last 2 decades. However, detection and identification of these transient rhythms in intracranial electroencephalographic recordings remain time-consuming and challenging. Although automated detection algorithms have been developed, their results are widely inconsistent, reducing reliability. Thus, manual marking of HFOs remains the gold standard, and manual review of automated results is required. However, manual marking and review are time consuming and can still produce variable results because of their subjective nature and the limitations in functionality of existing open-source software. Our goal was to develop a new software with broad application that improves on existing open-source HFO detection applications in usability, speed, and accuracy. Here, we present HFOApp: a free, open-source, easy-to-use MATLAB-based graphical user interface for HFO marking. This toolbox offers a high degree of intuitive and ergonomic usability and integrates interactive automation-assist options with manual marking, significantly reducing the time needed for review and manual marking of recordings, while increasing inter-rater reliability. The toolbox also features simultaneous multichannel detection and marking. HFOApp was designed as an easy-to-use toolbox for clinicians and researchers to quickly and accurately mark, quantify, and characterize HFOs within electrophysiological datasets.

Clinical Utility and Functionality of an Artificial Intelligence-Based App to Predict Mortality in COVID-19: Mixed Methods Analysis

Background

The artificial neural network (ANN) is an increasingly important tool in the context of solving complex medical classification problems. However, one of the principal challenges in leveraging artificial intelligence technology in the health care setting has been the relative inability to translate models into clinician workflow.

Objective

Here we demonstrate the development of a COVID-19 outcome prediction app that utilizes an ANN and assesses its usability in the clinical setting.

Methods

Usability assessment was conducted using the app, followed by a semistructured end-user interview. Usability was specified by effectiveness, efficiency, and satisfaction measures. These data were reported with descriptive statistics. The end-user interview data were analyzed using the thematic framework method, which allowed for the development of themes from the interview narratives. In total, 31 National Health Service physicians at a West London teaching hospital, including foundation physicians, senior house officers, registrars, and consultants, were included in this study.

Results

All participants were able to complete the assessment, with a mean time to complete separate patient vignettes of 59.35 (SD 10.35) seconds. The mean system usability scale score was 91.94 (SD 8.54), which corresponds to a qualitative rating of “excellent.” The clinicians found the app intuitive and easy to use, with the majority describing its predictions as a useful adjunct to their clinical practice. The main concern was related to the use of the app in isolation rather than in conjunction with other clinical parameters. However, most clinicians speculated that the app could positively reinforce or validate their clinical decision-making.

Conclusions

Translating artificial intelligence technologies into the clinical setting remains an important but challenging task. We demonstrate the effectiveness, efficiency, and system usability of a web-based app designed to predict the outcomes of patients with COVID-19 from an ANN.

AIDeveloper: Deep Learning Image Classification in Life Science and Beyond

Artificial intelligence (AI)-based image analysis has increased drastically in recent years. However, all applications use individual solutions, highly specialized for a particular task. Here, an easy-to-use, adaptable, and open source software, called AIDeveloper (AID) to train neural nets (NN) for image classification without the need for programming is presented. AID provides a variety of NN-architectures, allowing to apply trained models on new data, obtain performance metrics, and export final models to different formats. AID is benchmarked on large image datasets (CIFAR-10 and Fashion-MNIST). Furthermore, models are trained to distinguish areas of differentiated stem cells in images of cell culture. A conventional blood cell count and a blood count obtained using an NN are compared, trained on >1.2 million images, and demonstrated how AID can be used for label-free classification of B- and T-cells. All models are generated by non-programmers on generic computers, allowing for an interdisciplinary use.

A graphical user interface (NWUSA) for Raman spectral processing, analysis and feature recognition

It is a practical necessity for non-professional users to interpret biologically derived Raman spectral information for obtaining accurate and reliable analytical results. An integrated Raman spectral analysis software (NWUSA) was developed for spectral processing, analysis, and feature recognition. It provides a user-friendly graphical interface to perform the following preprocessing tasks: spectral range selection, cosmic ray removal, polynomial fitting based background subtraction, Savitzky-Golay smoothing, area-under-curve normalization, mean-centered procedure, as well as multivariate analysis algorithms including principal component analysis (PCA), linear discriminant analysis, partial least squares-discriminant analysis, support vector machine (SVM), and PCA-SVM. A spectral dataset obtained from two different samples was utilized to evaluate the performance of the developed software, which demonstrated that the analysis software can quickly and accurately achieve functional requirements in spectral data processing and feature recognition. Besides, the open-source software can not only be customized with more novel functional modules to suit the specific needs, but also benefit many Raman based investigations, especially for clinical usages.

Stakeholder Perspectives to Support Graphical User Interface Design for Children with Autism Spectrum Disorder: A Qualitative Study

The development of digital supports for people with autism has increased considerably in recent years. Technology designers and developers have interpreted the needs and learning styles of people with autism in different ways. As a result, there are generic, non-specific or heterogeneous guidelines for the design and development of technology for people with autism. This study aims to identify and describe the recommended elements to support graphical user interface design for children with Autism Spectrum Disorder (ASD), considering the stakeholders' perspective, engaged in a computer application development. A qualitative, longitudinal, multicentre study was carried out. A sample of 39 participants belonging to four groups of stakeholders participated: children with autism, family members, professionals with experience in the intervention with children with autism, and professionals with expertise in the design and development of assistive technology. The techniques used to formalise the collection of information from participants were semi-structured interviews and observation. MAXQDA 2020 software (Verbi Software, Berlin, Germany) was used to analyse the data. The result is a guide with suggestions to support an interface design that emerges from the stakeholder perspectives. This study provides useful information to offer alternatives for children with ASD and facilitate the understanding of daily life.

A BCI Based Alerting System for Attention Recovery of UAV Operators

As unmanned aerial vehicles have become popular, the number of accidents caused by an operator's inattention have increased. To prevent such accidents, the operator should maintain an attention status. However, limited research has been conducted on the brain-computer interface (BCI)-based system with an alerting module for the operator's attention recovery of unmanned aerial vehicles. Therefore, we introduce a detection and alerting system that prevents an unmanned aerial vehicle operator from falling into inattention status by using the operator's electroencephalogram signal. The proposed system consists of the following three components: a signal processing module, which collects and preprocesses an electroencephalogram signal of an operator, an inattention detection module, which determines whether an inattention status occurred based on the preprocessed signal, and, lastly, an alert providing module that presents stimulus to an operator when inattention is detected. As a result of evaluating the performance with a real-world dataset, it was shown that the proposed system successfully contributed to the recovery of operator attention in the evaluating dataset, although statistical significance could not be established due to the small number of subjects.

Proposals and Comparisons from One-Sensor EEG and EOG Human-Machine Interfaces

Human-Machine Interfaces (HMI) allow users to interact with different devices such as computers or home elements. A key part in HMI is the design of simple non-invasive interfaces to capture the signals associated with the user's intentions. In this work, we have designed two different approaches based on Electroencephalography (EEG) and Electrooculography (EOG). For both cases, signal acquisition is performed using only one electrode, which makes placement more comfortable compared to multi-channel systems. We have also developed a Graphical User Interface (GUI) that presents objects to the user using two paradigms-one-by-one objects or rows-columns of objects. Both interfaces and paradigms have been compared for several users considering interactions with home elements.

Lossless Decompression Accelerator for Embedded Processor with GUI

The development of the mobile industry brings about the demand for high-performance embedded systems in order to meet the requirement of user-centered application. Because of the limitation of memory resource, employing compressed data is efficient for an embedded system. However, the workload for data decompression causes an extreme bottleneck to the embedded processor. One of the ways to alleviate the bottleneck is to integrate a hardware accelerator along with the processor, constructing a system-on-chip (SoC) for the embedded system. In this paper, we propose a lossless decompression accelerator for an embedded processor, which supports LZ77 decompression and static Huffman decoding for an inflate algorithm. The accelerator is implemented on a field programmable gate array (FPGA) to verify the functional suitability and fabricated in a Samsung 65 nm complementary metal oxide semiconductor (CMOS) process. The performance of the accelerator is evaluated by the Canterbury corpus benchmark and achieved throughput up to 20.7 MB/s at 50 MHz system clock frequency.

Binary and Hybrid Work-Condition Maps for Interactive Exploration of Ergonomic Human Arm Postures

Ergonomics of human workers is one of the key elements in design and evaluation of production processes. Human ergonomics have a major impact on productivity as well as chronic health risks incurred by inappropriate working postures and conditions. In this paper we propose a novel method for estimating and communicating the ergonomic work condition called Binary Work-Condition Map, which provides a visualized feedback about work conditions of different configurations of an arm. The map is of binary nature and is derived by imposing the desired thresholds on considered ergonomic and safety related criteria. Therefore, the suggested arm postures in the map guarantee that all considered criteria are satisfied. This eliminates the ambiguity compared to state-of-the-art maps that uses continuous scales derived from weighted sum of multiple ergonomics criteria. In addition, to combine the advantages of both the binary map and the continuous map, we additionally propose a Hybrid Work-Condition Map that rules out unsuitable workspace with the binary map approach and renders the suitable workspace with the continuous map approach. The proposed approach was tested in simulation for various tasks and conditions. In addition, we conducted subjective evaluation experiments to compare the proposed methods with the state-of-the art method regarding the usability. The results indicated that the binary map is simpler to use, while the hybrid map is a good tradeoff between the binary and the continuous map. In selecting the map, strong points of each map should be considered with respect to the requirements of a specific application and task.

MAELASviewer: An Online Tool to Visualize Magnetostriction

The design of new materials for technological applications is increasingly being assisted by online computational tools that facilitate the study of their properties. In this work, based on modern web application frameworks, the online app MAELASviewer has been developed to visualize and analyze magnetostriction via a user-friendly interactive graphical interface. The features and technical details of this new tool are described in detail. Among other applications, it could potentially be used for the design of magnetostrictive materials for sensors and actuators.

THORONDOR: a software for fast treatment and analysis of low-energy XAS data

THORONDOR is a data treatment software with a graphical user interface (GUI) accessible via the browser-based Jupyter notebook framework. It aims to provide an interactive and user-friendly tool for the analysis of NEXAFS spectra collected during in situ experiments. The program allows on-the-fly representation and quick correction of large datasets from single or multiple experiments. In particular, it provides the possibility to align in energy several spectral profiles on the basis of user-defined references. Various techniques to calculate background subtraction and signal normalization have been made available. In this context, an innovation of this GUI involves the usage of a slider-based approach that provides the ability to instantly manipulate and visualize processed data for the user. Finally, the program is characterized by an advanced fitting toolbox based on the lmfit package. It offers a large selection of fitting routines as well as different peak distributions and empirical ionization potential step edges, which can be used for the fit of the NEXAFS rising-edge peaks. Statistical parameters describing the goodness of a fit such as χ² or the R-factor together with the parameter uncertainty distributions and the related correlations can be extracted for each chosen model.

Simultispin: A versatile graphical user interface for the simulation of solid-state continuous wave EPR spectra

Solid-state continuous wave (cw) electronic paramagnetic resonance (EPR) spectroscopy is particularly suitable for metal complex analysis. Extracting magnetic parameters by simulation is often necessary to describe the electronic structure of the studied molecular compounds that can have various electronic spin states and characterized by different parameters like g-values, hyperfine coupling or zero field splitting values. Easyspin toolbox on MATLAB is a powerful tool, but for the user, it requires spending time with coding and could discourage nonexperts. Facing this context, we have developed a graphical user interface called Simultispin, dedicated to solid-state cw-EPR spectra simulation. Some examples of experimental spectra of metal complexes (mixture of low spin and high spin Fe^III complexes, dynamic disorder of a Cu^II complex, photogeneration of a Mn^III complex), highlighting specific solid-state functions, are described and analyzed based on simulations performed with Simultispin. We hope that its ergonomy and the ease to set up a complete set of parameters to get reliable simulations could help a large EPR community to improve the efficiency of their interpretations.

MVPANI: A Toolkit With Friendly Graphical User Interface for Multivariate Pattern Analysis of Neuroimaging Data

With the rapid development of machine learning techniques, multivariate pattern analysis (MVPA) is becoming increasingly popular in the field of neuroimaging data analysis. Several software packages have been developed to facilitate its application in neuroimaging studies. As most of these software packages are based on command lines, researchers are required to learn how to program, which has greatly limited the use of MVPA for researchers without programming skills. Moreover, lacking a graphical user interface (GUI) also hinders the standardization of the application of MVPA in neuroimaging studies and, consequently, the replication of previous studies or comparisons of results between different studies. Therefore, we developed a GUI-based toolkit for MVPA of neuroimaging data: MVPANI (MVPA for Neuroimaging). Compared with other existing software packages, MVPANI has several advantages. First, MVPANI has a GUI and is, thus, more friendly for non-programmers. Second, MVPANI offers a variety of machine learning algorithms with the flexibility of parameter modification so that researchers can test different algorithms and tune parameters to identify the most suitable algorithms and parameters for their own data. Third, MVPANI also offers the function of data fusion at two levels (feature level or decision level) to utilize complementary information contained in different measures obtained from multimodal neuroimaging techniques. In this paper, we introduce this toolkit and provide four examples to demonstrate its usage, including (1) classification between patients and controls, (2) identification of brain areas containing discriminating information, (3) prediction of clinical scores, and (4) multimodal data fusion.

NICA: A Novel Toolbox for Near-Infrared Spectroscopy Calculations and Analyses

Functional near-infrared spectroscopy (fNIRS) measures the functional activity of the cerebral cortex. The concentration changes of oxygenated (oxy-Hb) and deoxygenated hemoglobin (deoxy-Hb) can be detected and associated with activation of the cortex in the investigated area (neurovascular coupling). Recorded signals of hemodynamic responses may contain influences from physiological signals (systemic influences, physiological artifacts) which do not originate from the cerebral cortex activity. The physiological artifacts contain the blood pressure (BP), respiratory patterns, and the pulsation of the heart. In order to perform a comprehensive analysis of recorded fNIRS data, a proper correction of these physiological artifacts is necessary. This article introduces NICA – a novel toolbox for near-infrared spectroscopy calculations and analyses based on MATLAB. With NICA it is possible to process and visualize fNIRS data, including different signal processing methods for physiological artifact correction. The artifact correction methods used in this toolbox are common average reference (CAR), independent component analysis (ICA), and transfer function (TF) models. A practical example provides results from a study, where NICA was used for analyzing the measurement data, in order to demonstrate the signal processing steps and the physiological artifact correction. The toolbox was developed for fNIRS data recorded with the NIRScout 1624 measurement device and the corresponding recording software NIRStar.

Designing and evaluating dose-escalation studies made easy: The MoDEsT web app

BACKGROUND/AIMS

Dose-escalation studies are essential in the early stages of developing novel treatments, when the aim is to find a safe dose for administration in humans. Despite their great importance, many dose-escalation studies use study designs based on heuristic algorithms with well-documented drawbacks. Bayesian decision procedures provide a design alternative that is conceptually simple and methodologically sound, but very rarely used in practice, at least in part due to their perceived statistical complexity. There are currently very few easily accessible software implementations that would facilitate their application.

METHODS

We have created MoDEsT, a free and easy-to-use web application for designing and conducting single-agent dose-escalation studies with a binary toxicity endpoint, where the objective is to estimate the maximum tolerated dose. MoDEsT uses a well-established Bayesian decision procedure based on logistic regression. The software has a user-friendly point-and-click interface, makes changes visible in real time, and automatically generates a range of graphs, tables, and reports. It is aimed at clinicians as well as statisticians with limited expertise in model-based dose-escalation designs, and does not require any statistical programming skills to evaluate the operating characteristics of, or implement, the Bayesian dose-escalation design.

RESULTS

MoDEsT comes in two parts: a 'Design' module to explore design options and simulate their operating characteristics, and a 'Conduct' module to guide the dose-finding process throughout the study. We illustrate the practical use of both modules with data from a real phase I study in terminal cancer.

CONCLUSION

Enabling both methodologists and clinicians to understand and apply model-based study designs with ease is a key factor towards their routine use in early-phase studies. We hope that MoDEsT will enable incorporation of Bayesian decision procedures for dose escalation at the earliest stage of clinical trial design, thus increasing their use in early-phase trials.

SnappySonic: An Ultrasound Acquisition Replay Simulator

SnappySonic provides an ultrasound acquisition replay simulator designed for public engagement and training. It provides a simple interface to allow users to experience ultrasound acquisition without the need for specialist hardware or acoustically compatible phantoms. The software is implemented in Python, built on top of a set of open source Python modules targeted at surgical innovation. The library has high potential for reuse, most obviously for those who want to simulate ultrasound acquisition, but it could also be used as a user interface for displaying high dimensional images or video data.