Recently, new technologies have been developed that allow physical and virtual space to converge. We reviewed a range of innovative technologies that enable immersive and 3D interaction, which we believe are of particular interest to apply Universal Design for Learning (UDL) principles in teaching and learning practices, with a particular interest in higher education. We found limitations related to hardware and interactive systems that cannot be customised to meet the needs of all different students and some users may be marginalised. We draw attention to problems that lead to the risk of intentional exclusion while highlighting relevant inclusion opportunities. The main contribution of this paper is to present a selection of use cases to discuss how software applications can be designed to meet the guidelines for UDL, and improve the accessibility of 3D interaction for innovative Virtual Learning Environments (VLEs).

The amount of data needed for training machine learning methods is an open question. Here, we use a problem from chemistry for examining this question. The problem is a special case of a graph data analysis. It can be tackled inter alia by using graph convolutional networks. We show that newer methods can provide good results, but need large amounts of data, which are not always available. In some cases, older methods may be preferable for low amounts of data. In the longer term, open databases can help with this problem.

We have demonstrated in previous work that the Calculus of Covalent Bonding (CCB) can be used to simulate higher-level biochemical processes. This is significant since CCB was originally devised to model lower-level organic chemical reactions. In this paper we extend the use of the calculus to model an important gene repair pathway, namely DNA Mismatch Repair (MMR). This complex pathway involves four helper proteins and needs a distinction between the two chains in a DNA strand. In order to achieve this, we extend the calculus by allowing prefixing with collections of bonding sites.

Developments in artificial intelligence can be leveraged to support the diagnosis of degenerative disorders, such as epilepsy and Parkinson's disease. This study aims to provide a software solution, focused initially towards Parkinson's disease, which can positively impact medical practice surrounding degenerative diagnoses. Through the use of a dataset containing numerical data representing acoustic features extracted from an audio recording of an individual, it is determined if a neural approach can provide an improvement over previous results in the area. This is achieved through the implementation of a feedforward neural network and a layer recurrent neural network. By comparison with the state-of-the-art, a Bayesian approach providing a classification accuracy benchmark of 87.1%, it is found that the implemented neural networks are capable of average accuracy of 96%, highlighting improved accuracy for the classification process. The solution is capable of supporting the diagnosis of Parkinson's disease in an advisory capacity and is envisioned to inform the process of referral through general practice.

This study combines two novel deterministic methods with a Convolutional Neural Network to develop a machine learning method that is aware of directionality of light in images. The first method detects shadows in terrestrial images by using a sliding-window algorithm that extracts specific hue and value features in an image. The second method interpolates light-sources by utilising a line-algorithm, which detects the direction of light sources in the image. Both of these methods are single-image solutions and employ deterministic methods to calculate the values from the image alone, without the need for illumination-models. They extract real-time geometry from the light source in an image, rather than mapping an illuminationmodel onto the image, which are the only models used today. Finally, those outputs are used to train a Convolutional Neural Network. This displays greater accuracy than previous methods for shadow detection and can predict light source-direction and thus orientation accurately, which is a considerable innovation for an unsupervised CNN. It is significantly faster than the deterministic methods. We also present a reference dataset for the problem of shadow and light direction detection.

BACKGROUND: Contemporary biological research integrates neighboring scientific domains to answer complex questions in fields such as systems biology and drug discovery. This calls for tools that are intuitive to use, yet flexible to adapt to new tasks. RESULTS: Bioclipse is a free, open source workbench with advanced features for the life sciences. Version 2.0 constitutes a complete rewrite of Bioclipse, and delivers a stable, scalable integration platform for developers and an intuitive workbench for end users. All functionality is available both from the graphical user interface and from a built-in novel domain-specific language, supporting the scientist in interdisciplinary research and reproducible analyses through advanced visualization of the inputs and the results. New components for Bioclipse 2 include a rewritten editor for chemical structures, a table for multiple molecules that supports gigabyte-sized files, as well as a graphical editor for sequences and alignments. CONCLUSION: Bioclipse 2 is equipped with advanced tools required to carry out complex analysis in the fields of bio- and cheminformatics. Developed as a Rich Client based on Eclipse, Bioclipse 2 leverages on today's powerful desktop computers for providing a responsive user interface, but also takes full advantage of the Web and networked (Web/Cloud) services for more demanding calculations or retrieval of data. The fact that Bioclipse 2 is based on an advanced and widely used service platform ensures wide extensibility, making it easy to add new algorithms, visualizations, as well as scripting commands. The intuitive tools for end users and the extensible architecture make Bioclipse 2 ideal for interdisciplinary and integrative research.Bioclipse 2 is released under the Eclipse Public License (EPL), a flexible open source license that allows additional plugins to be of any license. Bioclipse 2 is implemented in Java and supported on all major platforms; Source code and binaries are freely available at http://www.bioclipse.net.

BACKGROUND: Current efforts in Metabolomics, such as the Human Metabolome Project, collect structures of biological metabolites as well as data for their characterisation, such as spectra for identification of substances and measurements of their concentration. Still, only a fraction of existing metabolites and their spectral fingerprints are known. Computer-Assisted Structure Elucidation (CASE) of biological metabolites will be an important tool to leverage this lack of knowledge. Indispensable for CASE are modules to predict spectra for hypothetical structures. This paper evaluates different statistical and machine learning methods to perform predictions of proton NMR spectra based on data from our open database NMRShiftDB. RESULTS: A mean absolute error of 0.18 ppm was achieved for the prediction of proton NMR shifts ranging from 0 to 11 ppm. Random forest, J48 decision tree and support vector machines achieved similar overall errors. HOSE codes being a notably simple method achieved a comparatively good result of 0.17 ppm mean absolute error. CONCLUSION: NMR prediction methods applied in the course of this work delivered precise predictions which can serve as a building block for Computer-Assisted Structure Elucidation for biological metabolites.

BACKGROUND: There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no successful attempts have been made to integrate chemo- and bioinformatics into a single framework. RESULTS: Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. CONCLUSION: Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.