BACKGROUND: Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python.RESULTS: The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS.CONCLUSIONS: pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.
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An illustrative non-technical review was published on Towards Data Science regarding our recent Journal paper “Automatic crack classification and segmentation on masonry surfaces using convolutional neural networks and transfer learning”.While new technologies have changed almost every aspect of our lives, the construction field seems to be struggling to catch up. Currently, the structural condition of a building is still predominantly manually inspected. In simple terms, even nowadays when a structure needs to be inspected for any damage, an engineer will manually check all the surfaces and take a bunch of photos while keeping notes of the position of any cracks. Then a few more hours need to be spent at the office to sort all the photos and notes trying to make a meaningful report out of it. Apparently this a laborious, costly, and subjective process. On top of that, safety concerns arise since there are parts of structures with access restrictions and difficult to reach. To give you an example, the Golden Gate Bridge needs to be periodically inspected. In other words, up to very recently there would be specially trained people who would climb across this picturesque structure and check every inch of it.
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Machine learning models have proven to be reliable methods in classification tasks. However, little research has been done on classifying dwelling characteristics based on smart meter & weather data before. Gaining insights into dwelling characteristics can be helpful to create/improve the policies for creating new dwellings at NZEB standard. This paper compares the different machine learning algorithms and the methods used to correctly implement the models. These methods include the data pre-processing, model validation and evaluation. Smart meter data was provided by Groene Mient, which was used to train several machine learning algorithms. The models that were generated by the algorithms were compared on their performance. The results showed that Recurrent Neural Network (RNN) 2performed the best with 96% of accuracy. Cross Validation was used to validate the models, where 80% of the data was used for training purposes and 20% was used for testing purposes. Evaluation metrices were used to produce classification reports, which can indicate which of the models work the best for this specific problem. The models were programmed in Python.
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Electrohydrodynamic Atomization (EHDA), also known as Electrospray (ES), is a technology which uses strong electric fields to manipulate liquid atomization. Among many other areas, electrospray is used as an important tool for biomedical application (droplet encapsulation), water technology (thermal desalination and metal recovery) and material sciences (nanofibers and nano spheres fabrication, metal recovery, selective membranes and batteries). A complete review about the particularities of this tool and its application was recently published (2018), as an especial edition of the Journal of Aerosol Sciences. One of the main known bottlenecks of this technique, it is the fact that the necessary strong electric fields create a risk for electric discharges. Such discharges destabilize the process but can also be an explosion risk depending on the application. The goal of this project is to develop a reliable tool to prevent discharges in electrospray applications.
