Biological sequence motif discovery using motif-x.

Machine learning for Big Data analytics in plants.

When preparing large databases, obtaining quality data for analysis without any missing values is almost impossible in many cases. Integration of raw data from multiple heterogeneous sources often results in some values missing leading to loss of valuable information. Even though many methods have been introduced by researchers, only less effort has been spent on handling missing values in heterogeneous attributes (both discrete and continuous) under Missing At Random pattern, the common scenario where missing values have dependency on covariates in the dataset. Also, only few techniques are capable of dealing with missing values in large databases and this demands immediate attention of researchers. This paper addresses both these problems by introducing a single technique called Bayesian Ant colony Optimization (BACO) which combines the searching capability of Ant Colony Optimization with probabilistic nature of Bayesian principles. The algorithm is designed in such a way that missing values in both discrete and continuous attributes in large datasets are efficiently imputed. BACO is implemented in six large real datasets, and it is observed that its imputation accuracy outperforms than that of existing standard techniques. The statistical tests conducted also prove the superior results of BACO in the imputation process.

Online teaching files are an important source of educational and referential materials in the radiology community. The commonly used Digital Imaging and Communications in Medicine (DICOM) file format of the radiology community is not natively supported by common Web browsers. The ability of the Web server to convert and parse DICOM is important when the DICOM-converting tools are not available. In this paper, we describe our approach to develop a Web-based teaching file authoring tool. Our server is built using Apache Web server running on FreeBSD operating system. The dynamic page content is produced by Hypertext Preprocessor (PHP). Digital Imaging and Communications in Medicine images are converted by ImageMagick into Joint Photographic Experts Group (JPEG) format. Digital Imaging and Communications in Medicine attributes are parsed by dicom3tools and stored in PostgreSQL database. Using free software available from the Internet, we build a Web service that allows radiologists to create their own online teaching file cases with a common Web browser.

Unlocking massively parallel spectral proper orthogonal decompositions in the PySPOD package

Location‐only and use‐availability data: analysis methods converge

Video quality assessment with subjective testing is both time consuming and expensive. An interesting new approach to traditional testing is the so-called crowdsourcing, moving the testing effort into the internet. We therefore propose in this contribution the QualityCrowd framework to effortlessly perform subjective quality assessment with crowdsourcing. QualityCrowd allows codec independent quality assessment with a simple web interface, usable with common web browsers. We compared the results from an online subjective test using this framework with the results from a test in a standardized environment. This comparison shows that QualityCrowd delivers equivalent results within the acceptable inter-lab correlation. While we only consider video quality in this contribution, QualityCrowd can also be used for multimodal quality assessment.

Abstract. Recent advances in open-source geospatial technologies in WebGIS allowed the visualization of a 3D complex environment on the web, exploiting realistic Globe reproduction of the real territorial asset. At the same time, in the field of gaming technologies, the new possibilities offered by open-source WebGL JavaScript libraries allowed the creation of Virtual Reality navigation models on the web. The integration between 3D GIS globe navigation models and VR environment navigation is a solution that offers a further level of detail in web navigation, exploiting the capabilities of web browsers in the best way. This research further contributes to this field, showing a workflow to integrate different 3D data in a VR and 3D WebGIS navigation model. The case study for this research is the new building of the University of Twente, Faculty of Geo-Information Science and Earth Observation (ITC) of Enschede (The Netherlands). This work tests the online integration of variety of 3D input data that can lead to different Levels of Details (LoD) of the buildings inside the Globe-based WebGIS platform. The developed solution works on desktop and mobile devices using the capabilities of the most common web browsers, avoiding any software installation. The result of this work is based on completely open-source solutions that offers the possibility to navigate within a 3D model, which is useful for citizens, governmental or private institutions in decision-making processes. This work represents a first step towards the ambition to generate a web Digital Twin platform to combine datasets from different sources in a unique open-source solution.

Recording large amounts of users’ sessions performed through 3D applications may provide crucial insights into interaction patterns. Such data can be captured from interactive experiences in public exhibits, remote motion tracking equipment, immersive XR devices, lab installations or online web applications. Immersive analytics (IA) deals with the benefits and challenges of using immersive environments for data analysis and related design solutions to improve the quality and efficiency of the analysis process. Today, web technologies allow us to craft complex applications accessible through common browsers, and APIs like WebXR allow us to interact with and explore virtual 3D environments using immersive devices. These technologies can be used to access rich, immersive spaces but present new challenges related to performance, network bottlenecks and interface design. WebXR IA tools are still quite new in the literature: they present several challenges and leave quite unexplored the possibility of synchronous collaborative inspection. The opportunity to share the virtual space with remote analysts in fact improves sense-making tasks and offers new ways to discuss interaction patterns together, while inspecting captured records or data aggregates. Furthermore, with proper collaborative approaches, analysts are able to share machine learning (ML) pipelines and constructively discuss the outcomes and insights through tailored data visualization, directly inside immersive 3D spaces, using a web browser. Under the H2IOSC project, we present the first results of an open-source pipeline involving tools and services aimed at capturing, processing and inspecting interactive sessions collaboratively in WebXR with other analysts. The modular pipeline can be easily deployed in research infrastructures (RIs), remote dedicated hubs or local scenarios. The developed WebXR immersive analytics tool specifically offers advanced features for volumetric data inspection, query, annotation and discovery, alongside spatial interfaces. We assess the pipeline through users’ sessions captured during two remote public exhibits, by a WebXR application presenting generative AI content to visitors. We deployed the pipeline to assess the different services and to better understand how people interact with generative AI environments. The obtained results can be easily adopted for a multitude of case studies, interactive applications, remote equipment or online applications, to support or accelerate the detection of interaction patterns among remote analysts collaborating in the same 3D space.

Geochemical data are frequently collected from mineral exploration drill-hole samples to more accurately define and characterise the geological units intersected by the drill hole. However, large multi-element data sets are slow and challenging to interpret without using some form of automated analysis, such as mathematical, statistical or machine learning techniques. Automated analysis techniques also have the advantage in that they are repeatable and can provide consistent results, even for very large data sets. In this paper, an automated litho-geochemical interpretation workflow is demonstrated, which includes data exploration and data preparation using appropriate compositional data-analysis techniques. Multiscale analysis using a modified wavelet tessellation has been applied to the data to provide coherent geological domains. Unsupervised machine learning (clustering) has been used to provide a first-pass classification. The results are compared with the detailed geologist’s logs. The comparison shows how the integration of automated analysis of geochemical data can be used to enhance traditional geological logging and demonstrates the identification of new geological units from the automated litho-geochemical logging that were not apparent from visual logging but are geochemically distinct. KEY POINTS To reduce computational complexity and facilitate interpretation, a subset of geochemical elements is selected, and then a centred log-ratio transform is applied. The wavelet tessellation method is used to domain the drill holes into rock units at a range of scales. Several clustering methods were tested to identify distinct rock units in the samples and multiscale domains for classification. Results are compared with geologist’s logs to assess how geochemical data analysis can inform and improve traditional geology logs.

Introduction: Colon cancer is the fourth most common cancer in the United States and the third leading cause of cancer-related death. High throughput genomic sequencing has led to a number of significant advances in tumor biology and in identifying novel signaling molecules such as long non-coding RNA (lncRNA). The aim of this study was to identify differentially expressed lncRNA in colon cancer from a large RNA-sequencing (RNA-seq) data set. Methods: The raw RNA-seq files of 398 patients with colon cancer were downloaded from The Cancer Genome Atlas (TCGA). Sequencing files were aligned using STAR (Spliced Transcripts Alignment to a Reference) to the most recent genome annotation. Using a subset of patients with paired colon cancer and normal colon epithelium RNA-seq data (n=40), an exploratory binomial regression model was used to calculate differential RNA expression. The most differentially expressed lncRNA were identified from the exploratory analysis and verified by comparing the larger colon cancer RNA-seq data set (n=358) with the normal colon epithelium RNA-seq data set (n=40). Results: 33,514 genes were identified from the comparative analysis, and using differential expression cut off values of > +1.5 or < -1.5 log fold change and a false discovery rate of <0.05; 543 were upregulated and 1822 were downregulated. Within this dysregulated group, 60 lncRNAs were identified. Using the larger data set (n=358 vs n=40), 41/60 lncRNA remained differentially expressed, of which 15 were downregulated and 26 were upregulated. Twenty-four of these lncRNAs have not previously been described in colon cancer, 12 of which are upregulated and 12 of which are downregulated (Table 1). Conclusions: This analysis of RNA-seq data from TCGA has identified dysregulated lncRNAs which have not previously been described in human colon cancer. These lncRNAs may have significant roles in colon cancer tumor signaling. Table 1.Differential expression of lncRNA not described in colon cancerlncRNALog Fold ChangeP-valueDescription in other cancersKRT16P14.1041.36E-21Increased in lung squamous cell carcinomaBOK-AS13.7784.98E-09Increased in oral squamous cell carcinomaCELP3.1151.30E-09Not availableCLDN10-AS12.3944.61E-12Not availablePOU6F2-AS12.2678.25E-09Not availableSLC7A11-AS12.1931.60E-13Decreased in gastric adenocarcinomaCSAG42.1083.59E-10Not availableLUCAT12.0224.21E-11Increased in Ovarian cancer, renal clear cell carcinoma, head and neck squamous cell carcinoma, Non-small cell cancer, glioma, osteosarcoma, esophageal squamous cell carcinomaVPS9D1-AS11.9795.27E-21Decreased in gastric adenocarcinoma, Increased in non-small cell lung cancerLEF1-AS11.8464.48E-13Increased in glioblastomaCASC81.6485.64E-06Single nucleotide polymorphisms in colorectal adenocarcinomaLINC004911.5903.11E-04Not availableLINC00648-1.5021.02E-15Not availableLINC00163-1.6751.03E-22Not availableSATB2-AS1-1.8074.18E-09Increased in osteosarcomaLINC00702-2.1424.81E-18Not availableTRHDE-AS1-2.2623.44E-24Not availableLINC00908-2.3082.76E-103Not availableLINC00483-2.4012.87E-39Increased in gastric adenocarcinomaLINC00461-2.4401.42E-41Increased in glioma, multiple myelomaFENDRR-2.6872.12E-58Decreased in breast cancer, prostate cancer, osteosarcoma, gastric adenocarcinoma,ARHGEF26-AS1-2.7148.55E-32Not availableADAMTS9-AS2-2.9041.78E-74Increased in lung cancer salivary adenoid cystic carcinoma, Decreased in glioma, gastric adenocarcinomaMT1JP-4.4601.08E-114Decreased in retinoblastoma, Decreased in gastric adenocarcinoma Citation Format: Stephen J. O'Brien, Theodore Kalbfleisch, Sudhir Srivastava, Shesh Rai, Susan Galandiuk. Differential expression of long non-coding RNA in colon adenocarcinoma RNA-sequence data set [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1817.

Sutirtha Chatterjee) join the editor-in-chief (Robert Davison) to craft a position statement regarding the ISJ's view on theory. It is applicable, with sensitivity, to the empirical research articles that we consider for publication.

Background . Networks and models in systems biology today have been scaled up to the sizes of full genomes. They comprise thousands of reactions, metabolites, regulatory events, and many further biochemical components. In order to build, analyze, and explore networks and models on this scale, highly specific software solutions are required. Results . In this talk, we introduce the systems biology software collection that has been developed and continuously maintained at the Center for Bioinformatics Tuebingen (ZBIT) over more than one decade now. All tools have been created to solve research questions in ongoing large-scale systems biology projects with numerous national and international collaborators. These tools cover all aspects of the model life cycle. KEGGtranslator and BioPAX2SBML can be used to gather data for building draft networks based on the KEGG PATHWAY database and files in BioPAX format. SBMLsqueezer generates kinetic equations and derives the units for the parameters therein. SBMLsimulator unifies the Simulation Core Library and the heuristic optimization toolbox EvA2 for model simulation and calibration. ModelPolisher accesses the BiGG Models knowledge-base for model annotation. SBML2LaTeX documents models by creating human-readable reports. Conclusion . All tools presented are freely available and can either be used as online programs at http://webservices.cs.uni-tuebingen.de using any common web browser, or for download as desktop programs from http://www.cogsys.cs.uni-tuebingen.de/software . These tools have been used in several research projects, including community efforts, such as the path2models project. Their development has often been a driving force for further community efforts, such as the JSBML project.

An important feature of X‐ray Piezoelectric Bimorph Mirror (PBM) is the possibility to continuously vary its curvature (dynamical bending); this ability allows the precise adjustment of their optical properties to different beamline geometries and permits the variation of the grazing angle of incidence or to optimize the focal spot dimensions in the experimental chamber. When a driving voltage is applied at a particular position of the mirror, one of the piezo plates shrinks while the other one expands and, as an example, it can result in a purely spherical bending of the device if the same voltage is applied to all electrodes. The applied voltages have to be kept extremely stable on a very long time scale (weeks or even months). This means that the performance and the general behavior of the mirror are strongly dependent on the power supply used to drive it. For this challenging application, Sincrotrone Trieste developed a particularly stable high voltage bipolar power supply system (ranging from −2kV to + 2kV, zero crossing). This system is controlled by an Intel SBC board and accessible via Ethernet through any common web browser, Lab VIEW client or some of the most popular synchrotron facility control systems (Epics and Tango for instance). The maximum drain and source capabilities are 500uA per channel. Voltage monitoring is achieved by sensing the real output and feeding it to a true 16bit ADC. The voltage resolution achieved is about 60mV while the current resolution is about 60nA. Noise and residual ripple (rms) are better than 15ppm/FS and, most important, the long term stability (1 week observation) is better than 100ppm/FS. Some metrological measurements, on different bimorph mirrors, was carried out at the optical laboratory of Elettra. These measures demonstrate the high level of resolution and stability of the power supplies, able to change considerably the radius of curvature of the mirror and, in the meantime, correct even very small shape error.

This paper demonstrates a way to let companies offer web-based applications or services over the Internet where the data is transmitted over a highly secured SSL connection, even for exportable browsers providing only a weak SSL implementation. The solution is based on a Java Applet which itself implements the SSL protocol and therefore is independent of the browsers implementation. After the Applet has been started it reopens a strong SSL connection back to the server where it was loaded from. Further this paper discusses problems related to firewalls which don't allow an Applet to connect directly to another host outside the LAN. Using a demo Applet, some restrictions of SSL connections opened in that way are shown. In addition, problems concerning the different JDK implementations found in common web browsers and a technology called Java Activator are analyzed with respect to our example.

Information Visualizations are well established to represent high density information in an intuitive and interactive way. There are no popular general retrieval systems, however, which utilize the power of information visualizations for search result representation. This paper describes Knowde, a search interface with purely visual result representation. It employs a powerful information retrieval system and works in a common web browser in real-time. This working prototype, with three different variations of network graphs will assist us in exploring current issues in visualization research, such as the challenge of system evaluation.