Computing an Optimal Layout for Cone Trees

Many visual representations for trees have been developed in information and software visualization. One of them are cone trees, a well-known three-dimensional representation for trees. This paper is based on an approach for constructing cone trees bottom-up. For this approach, an optimal layout for these trees is given together with a proof that based on the assumptions, there can be no better layouts. This comprises special cases, an optimal constant for the general case, and a post-processing step improving the layout

Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering

Background: Histone modifications play an important role in gene regulation. Their genomic locations are of great interest. Usually, the location is measured by ChIP-seq and analyzed with a peak-caller. Replicated ChIP-seq experiments become more and more available. However, their analysis is based on single-experiment peak-calling or on tools like PePr which allows peak-calling of replicates but whose underlying model might not be suitable for the conditions under which the experiments are performed. Results: We propose a new peak-caller called \"Sierra Platinum\" that allows peak-calling of replicated ChIP-seq experiments. Moreover, it provides a variety of quality measures together with integrated visualizations supporting the assessment of the replicates and the resulting peaks, as well as steering the peak-calling process. Conclusion: We show that Sierra Platinum outperforms currently available methods using a newly generated benchmark data set and using real data from the NIH Roadmap Epigenomics Project. It is robust against noisy replicates

MRC - A System for Computing Gröbner Bases in Monoid and Group Rings

Gröbner bases and Buchberger's algorithm have been generalized to monoid and group rings. In this paper we summarize procedures from this field and present a description of their implementation in the system Mrc V 1.0

MrcLambda - A System for Computing Gröbner Bases in Monoid and Group Rings

Gröbner bases and Buchberger's algorithm have been generalized to monoid and group rings. This paper presents a discription of an implementation of prefix Gröbner basis procedures in this setting

MrcLambda - A System for Computing Gröbner Bases in Monoid and Group Rings

Gröbner bases and Buchberger's algorithm have been generalized to monoid and group rings. This paper presents a discription of an implementation of prefix Gröbner basis procedures in this setting

MRC -- A System for Computing Gröbner Bases in Monoid and Group Rings

Gröbner bases and Buchberger's algorithm have been generalized to monoid and group rings. This paper presents a discription of an implementation of prefix Gröbner basis procedures in this setting

SyCaT-Vis: Visualization-Based Support of Analyzing System Behavior based on System Call Traces

Detecting anomalies in the behavior of a computer system is crucial for determining its security. One way of detecting these anomalies is based on the assessment of the amount and sequence of system calls issued by processes. While the number of processes on a computer can become very large, the number of system calls issued during the lifespan of such a process and its subprocesses can be humongous. In order to decide whether these anomalies are due to the intended system usage or if they are caused by malicious actions, this humongous amount of data needs being analyzed. Thus, a careful analysis of the system calls’ types, their amount, and their temporal sequence requires sophisticated support. Visualization is frequently used for this type of tasks. Starting with a carefully aggregation of the data presented in an overview representation, the quest for information is supported by carefully crafted interactions. These allow filtering the tremendous amount of data, thus removing the standard behavior data and leaving the potentially suspicious one. The latter can then be investigated on increasingly finer levels. Supporting this goal-oriented analysis, we propose novel interactive visualizations implemented in the tool SyCaT-Vis. SyCaT-Vis fosters obtaining important insights into the behavior of computer systems, the processes executed, and the system call sequences issued

Analyzing histone modifications using tiled binned clustering and 3D scatter plots

A major goal in epigenetics is understanding how cells differentiate into different cell types. Besides the increase of individual data sets, the amount of replicated experiments generating a tremendous amount of data is ever increasing. While biologists primarily analyze their data on the highest level using statistical correlations or on the lowest level analyzing nucleotide sequences, determining the fate of histone modifications during cell specification necessitates improved analysis capabilities on one or more intermediate levels. For this type of analysis, it proved to be very useful to use tiled binned scatter plot matrices showing binary relationships or to use tiled binned 3D scatter plots showing ternary relationships. Quarternary or general n-ary relationships are not easily analyzable using visualization techniques like scatter plots, only. Therefore, we augmented existing clustering methods with the tiling and binning idea enabling the analysis of n-ary relationships. Analyzing the changes of histone modifications comparing two cell lines using tiled binned clustering, we found new, unknown relations in the data