Deploying Web-based Visual Exploration Tools on the Grid

We discuss a web-based portal for the exploration, encapsulation, and dissemination of visualization results over the Grid. This portal integrates three components: an interface client for structured visualization exploration, a visualization web application to manage the generation and capture of the visualization results, and a centralized portal application server to access and manage grid resources. Our approach uses standard web technologies to make the system accessible with minimal user setup. We demonstrate the usefulness of the developed system using an example for Adaptive Mesh Refinement (AMR) data visualization

Analytic provenance for sensemaking: A research agenda

Sensemaking is a process of finding meaning from information that often involves activities such as information foraging and hypothesis generation. It can be valuable to maintain a history of the data and reasoning involved. This history, commonly known as provenance information, can be a resource for 'reflection-in-action'' during analysis, supporting collaboration between analysts, and can help trace data quality and uncertainty through the analysis process. Currently, there is limited work on utilizing analytic provenance, which captures the interactive data exploration and human reasoning process, to support sensemaking. This article presents and extends the research challenges discussed in a IEEE VIS 2014 workshop on this topic to provide an agenda for sensemaking analytic provenance

Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches

Aptamers are oligonucleotide ligands, either RNA or ssDNA, selected for high-affinity binding to molecular targets, such as small organic molecules, proteins or whole microorganisms. While reports of new aptamers are numerous, characterization of their specific interaction is often restricted to the affinity of binding (KD). Over the years, crystal structures of aptamer-protein complexes have only scarcely become available. Here we describe some relevant technical issues about the process of crystallizing aptamer-protein complexes and highlight some biochemical details on the molecular basis of selected aptamer-protein interactions. In addition, alternative experimental and computational approaches are discussed to study aptamer-protein interactions.

Bifunctional inhibitors of urokinase and metalloproteinase-9 for cancer treatment - in silico evaluation

Matrix metalloproteinase-9 (MMP-9), and urokinase plasminogen activator (uPA) overexpression or/and increased activity are considered causative elements for cancer invasion and metastasis. These enzymes are degrading the extracellular matrix (ECM) providing space for cancer progression and cancer cell mobility. Process of angiogenesis, in which microvascular endothelial cells form blood vessels, requires local degradation of the underlying basal lamina to invade into the stroma proximal to cancer, and it strongly depends on the activity of MMP-9 and uPA as well. Malignant tumor invasion, cancer metastasis and angiogenesis have been documented as a fundamental factors in the morbidity and mortality among cancer patients, thus their inhibition can be exploit therapeutically. Numerous in vivo and in vitro studies have demonstrated that inhibition of proteolytic activity can reduce caner invasion, tumor size and limit angiogenesis. Consequently human clinical studies were designed inhibiting urokinase or MMPs, but these target specific inhibitors produce mix results. One of the possible explanation could be that cancers are overexpressing more than one enzyme simultaneously – for instance urokinase and MMPs. Thus upregulated net proteolytic activity should be normalized rather than trying to inhibit single proteolytic enzyme. Therefore, starting from specific inhibitors we have created - in silico - several hybrid molecules that could inhibit both uPA and MMP-9. The best hybrid (UI1xAGB) had theoretical affinities of Ki = 1.61-9 mol for MMP-9 and Ki = 1.36-9 mol for uPA. In the future each individual hybrid would need to be successfully synthesized and checked in the in vitro and in vivo analyses

Visual parameter optimisation for biomedical image processing

Background: Biomedical image processing methods require users to optimise input parameters to ensure high quality output. This presents two challenges. First, it is difficult to optimise multiple input parameters for multiple input images. Second, it is difficult to achieve an understanding of underlying algorithms, in particular, relationships between input and output. Results: We present a visualisation method that transforms users’ ability to understand algorithm behaviour by integrating input and output, and by supporting exploration of their relationships. We discuss its application to a colour deconvolution technique for stained histology images and show how it enabled a domain expert to identify suitable parameter values for the deconvolution of two types of images, and metrics to quantify deconvolution performance. It also enabled a breakthrough in understanding by invalidating an underlying assumption about the algorithm. Conclusions: The visualisation method presented here provides analysis capability for multiple inputs and outputs in biomedical image processing that is not supported by previous analysis software. The analysis supported by our method is not feasible with conventional trial-and-error approaches

Provenance and logging for sense making

Sense making is one of the biggest challenges in data analysis faced by both the industry and the research community. It involves understanding the data and uncovering its model, generating a hypothesis, selecting analysis methods, creating novel solutions, designing evaluation, and also critical thinking and learning wherever needed. The research and development for such sense making tasks lags far behind the fast-changing user needs, such as those that emerged recently as the result of so-called “Big Data”. As a result, sense making is often performed manually and the limited human cognition capability becomes the bottleneck of sense making in data analysis and decision making. One of the recent advances in sense making research is the capture, visualization, and analysis of provenance information. Provenance is the history and context of sense making, including the data/analysis used and the users’ critical thinking process. It has been shown that provenance can effectively support many sense making tasks. For instance, provenance can provide an overview of what has been examined and reveal gaps like unexplored information or solution possibilities. Besides, provenance can support collaborative sense making and communication by sharing the rich context of the sense making process. Besides data analysis and decision making, provenance has been studied in many other fields, sometimes under different names, for different types of sense making. For example, the Human-Computer Interaction community relies on the analysis of logging to understand user behaviors and intentions; the WWW and database community has been working on data lineage to understand uncertainty and trustworthiness; and finally, reproducible science heavily relies on provenance to improve the reliability and efficiency of scientific research. This Dagstuhl Seminar brought together researchers from the diverse fields that relate to provenance and sense making to foster cross-community collaboration. Shared challenges were identified and progress has been made towards developing novel solutions

Provenance analysis for sensemaking. IEEE Computer Graphics and Applications, 39 (6) . pp. 27-29. ISSN 0272-1716

The articles in this special section examine the concept of "sensemaking", which refers to how we structure the unknown so as to be able to act in it. In the context of data analysis it involves understanding the data, generating hypotheses, selecting analysis methods, creating novel solutions, and critical thinking and learning wherever needed. Due to its explorative and creative nature, sensemaking is arguably the most challenging part of any data analysis

5.4 Wykorzystanie technologii informacyjno–komunikacyjnych w edukacji geograficznej

Nowoczesna technologia zajmuje wyjątkowe miejsce wśród pomocy dydaktycznych zewzględu na możliwości zastosowania w całym systemie edukacyjnym, trafiające idealnie w oczekiwania ucznia. Dzięki wykorzystaniu programów czy aplikacji pełni rolę organizującą proces uczenia się poprzez dostarczanie treści, ćwiczeń i sprawowanie kontroli nad postępami uczącego się. Programy multimedialne mogą być wykorzystywane również w ramach indywidualnej pracy uczniów. W nauczaniu geografii aplikacje, programy, platformy pozwalają przenieść uczniów w odległe miejsce, pokazać ukształtowanie terenu, tworzyć profil terenu, analizować zdjęcia satelitarne, tworzyć diagramy i kartodiagramy, tworzyć gry dydaktyczne oraz sprawdzać wiedzę uczniów za pomocą m.in. quizów. Dostarczają także określonych porcji informacji w postaci tekstów, obrazów animowanych z możliwością stosowania w celu korygowania przebiegu procesu uczenia się

Bliżej świata i ludzi. Program nauczania geografii IV etap edukacyjny - zakres rozszerzony

Program nauczania geografii w szkołach ponadgimnazjalnych, tj. w ramach IV etapu nauczania, z uwzględnieniem wymagań reformy programowe