Epiviz: Integrative Visual Analysis Software for Genomics

Computational and visual data analysis for genomics has traditionally involved a combination of tools and resources, of which the most ubiquitous consist of genome browsers, focused mainly on integrative visualization of large numbers of big datasets, and computational environments, focused on data modeling of a small number of moderately sized datasets. Workflows that involve the integration and exploration of multiple heterogeneous data sources, small and large, public and user specific have been poorly addressed by these tools. Commonly, the data visualized in these tools is the output of analyses performed in powerful computing environments like R/Bioconductor or Python. Two essential aspects of data analysis are usually treated as distinct, in spite of being part of the same exploratory process: algorithmic analysis and interactive visualization. In current technologies these are not integrated within one tool, but rather, one precedes the other. Recent technological advances in web-based data visualization have made it possible for interactive visualization tools to tightly integrate with powerful algorithmic tools, without being restricted to one such tool in particular. We introduce Epiviz (http://epiviz.cbcb.umd.edu), an integrative visualization tool that bridges the gap between the two types of tools, simplifying genomic data analysis workflows. Epiviz is the first genomics interactive visualization tool to provide tight-knit integration with computational and statistical modeling and data analysis. We discuss three ways in which Epiviz advances the field of genomic data analysis: 1) it brings code to interactive visualizations at various different levels; 2) takes the first steps in the direction of collaborative data analysis by incorporating user plugins from source control providers, as well as by allowing analysis states to be shared among the scientific community; 3) combines established analysis features that have never before been available simultaneously in a visualization tool for genomics. Epiviz can be used in multiple branches of genomics data analysis for various types of datasets, of which we detail two: functional genomics data, aligned to a continuous coordinate such as the genome, and metagenomics, organized according to volatile hierarchical coordinate spaces. We also present security implications of the current design, performance benchmarks, a series of limitations and future research steps

The analysis of agricultural landscape change using GIS techniques: case study: Podoleni, Romania

The increasingly tensions rising between society’s need for resources and space on the one hand, and the capacity of the land to support these needs on the other hand lead to unprecedented changes in landscape configuration, and hence, to the environment. This paper analyzes changes in the agricultural landscape of Podoleni, Neamt County, Romania, in spatio - temporal terms, as a result of the modernization of the ground processing techniques, types of crops, and the degree of fragmentation of land parcels. The study was conducted using Geographical Information Systems techniques, the main materials used in the analysis are topographic maps from different representative periods, and the 2006 orthophotomaps. Application of GIS techniques at a detailed scale (1:5000) allows an efficient management of land use for local authorities. The results highlight the optimal management of agricultural land so as to maintain a balance between their basic function (food needs) and preservation of nature (landscape, environment)

Epiviz: a view inside the design of an integrated visual analysis software for genomics

Computational and visual data analysis for genomics has traditionally involved a combination of tools and resources, of which the most ubiquitous consist of genome browsers, focused mainly on integrative visualization of large numbers of big datasets, and computational environments, focused on data modeling of a small number of moderately sized datasets. Workflows that involve the integration and exploration of multiple heterogeneous data sources, small and large, public and user specific have been poorly addressed by these tools. In our previous work, we introduced Epiviz, which bridges the gap between the two types of tools, simplifying these workflows. In this paper we expand on the design decisions behind Epiviz, and introduce a series of new advanced features that further support the type of interactive exploratory workflow we have targeted. We discuss three ways in which Epiviz advances the field of genomic data analysis: 1) it brings code to interactive visualizations at various different levels; 2) takes the first steps in the direction of collaborative data analysis by incorporating user plugins from source control providers, as well as by allowing analysis states to be shared among the scientific community; 3) combines established analysis features that have never before been available simultaneously in a genome browser. In our discussion section, we present security implications of the current design, as well as a series of limitations and future research steps. Since many of the design choices of Epiviz are novel in genomics data analysis, this paper serves both as a document of our own approaches with lessons learned, as well as a start point for future efforts in the same direction for the genomics community.https://doi.org/10.1186/1471-2105-16-S11-S

Soundscape in North-Eastern Part of Iasi City (Sararie – Ticau District)

This paper presents a complex study of noise levels from road traffic source and the variation during the seasons in an old residential area located in the north-eastern part of Iasi city, an important educational and cultural centre of the country. The study reveal the correlation between noise levels and social activities developed in the area: low number of inhabitants because of the holidays time in August and the resumption of the educational activity in autumn, including school start in September and of the university activity in October. After direct observations, the measurements were made with digital sound –level meter Quest Technologies, 1400 model in five hour intervals 7:00 - 8:00; 10:00 - 11:00; 13:30 - 14:30; 18:00 - 19:00; 19:00 - 20:00. The monitoring of Equivalent Continuous Noise Level (Leq) were made in 30 points located along the different type of roads in the second part of August – October 2009, with different admissible levels, showing the exceeding of the limit in 5 points in September and 8 points in October. It can be observed an important difference during the week in the monitoring period, between Monday to Friday and the week-end with lower values 59.64 - 6.5 dB (A) in August, 61.98 - 5.14 dB (A) in September, 63.9 - 5.3 dB (A) in October and among the four street categories with major differences between first category: 66.89 dB (A) and fourth category 47.69 dB (A), so that urban noise can be stratified according to a prior classification of a town’s streets due to their use and functional characteristics. Sound levels monitoring and statistical data processing (Pearson correlation coefficient, Tukey range test) sustain the fact that road traffic is main source of noise in the area, differentiated in correlation with street category, a decrease in noise with increasing street category, with insignificant differences between first and second street category thank to the best management and traffic control

The analysis of agricultural landscape change using GIS techniques. Case study: Podoleni, Romania

The increasingly tensions rising between society’s need for resources and space on the one hand, and the capacity of the land to support these needs on the other hand lead to unprecedented changes in landscape configuration, and hence, to the environment. This paper analyzes changes in the agricultural landscape of Podoleni, Neamt County, Romania, in spatio -temporal terms, as a result of the modernization of the ground processing techniques, types of crops, and the degree of fragmentation of land parcels. The study was conducted using Geographical Information Systems techniques, the main materials used in the analysis are topographic maps from different representative periods, and the 2006 ortho-photomaps. Application of GIS techniques at a detailed scale (1:5000) allows an efficient management of land use for local authorities. The results highlight the optimal management of agricultural land so as to maintain a balance between their basic function (food needs) and preservation of nature (landscape, environment)

Quantifying the changes in landscape configuration using open source GIS. Case study: Bistrita subcarpathian valley

Gradually, the study of the landscape became a core topic of environmental studies, due to its interdisciplinary research methods, integrating both natural and socio-economic data. The goal of the study is to quantify the structural evolution of Bistrita subcarpathian valley landscape, by using several GIS applications, having an important role in highlighting its functionality. The applications were realized for the extended area limit of Bistrita subcarpathian valley, which presents a complex landscape morphology, with features ranging from forested mountains to densely populated lowlands. The analysis was based on the two land cover maps resulted from the extraction of the spatial layers from the 1986 cadastral plans, 1:10.000 scale, respectively the 2005/2006 ortophotomaps, 1:5.000 scale. For completing the study, were calculated for the two periods a series of specific indicators, called landscape metrics, which contain quantitative information about the structure and features of the landscape. The results of the analysis proved the utility of these indicators in quantifying the structural evolution of the landscape, and also highlighted the capabilities of using Open Source software for complex spatial analysis. This type of analysis has a great importance for the authorities and other decision making factors regarding the territorial planning processes

Rural waste generation : a geographical survey at local scale

The paper examines the per capita waste generation rates from from rural areas of Neamț County (Romania) using thematic cartography. Geographical approach of this issue is difficult because the lack of a geostatistic database at commune scale. Spatial analysis of waste indicators reveals several disparities between localities. Comparability of data between communes located in various geographical conditions must be carrefully made according to local waste management systems. Several dysfunctionalities are outlined in order to compare these results, on the one hand, between localities and on the one hand, between recent years. Geographical analysis of waste generation rates is imperative for a proper monitoring of this sector. Data from 2009, 2010 and 2012 shows that rural waste management is in a full process of change towards a more organized, stable and efficient system

Soundscape in North-Eastern Part of Iasi City (Sararie – Ticau District)

This paper presents a complex study of noise levels from road traffic source and the variation during the seasons in an old residential area located in the north-eastern part of Iasi city, an important educational and cultural centre of the country. The study reveal the correlation between noise levels and social activities developed in the area: low number of inhabitants because of the holidays time in August and the resumption of the educational activity in autumn, including school start in September and of the university activity in October. After direct observations, the measurements were made with digital sound –level meter Quest Technologies, 1400 model in five hour intervals 7:00 - 8:00; 10:00 - 11:00; 13:30 - 14:30; 18:00 - 19:00; 19:00 - 20:00. The monitoring of Equivalent Continuous Noise Level (Leq) were made in 30 points located along the different type of roads in the second part of August – October 2009, with different admissible levels, showing the exceeding of the limit in 5 points in September and 8 points in October. It can be observed an important difference during the week in the monitoring period, between Monday to Friday and the week-end with lower values 59.64 - 6.5 dB (A) in August, 61.98 - 5.14 dB (A) in September, 63.9 - 5.3 dB (A) in October and among the four street categories with major differences between first category: 66.89 dB (A) and fourth category 47.69 dB (A), so that urban noise can be stratified according to a prior classification of a town’s streets due to their use and functional characteristics. Sound levels monitoring and statistical data processing (Pearson correlation coefficient, Tukey range test) sustain the fact that road traffic is main source of noise in the area, differentiated in correlation with street category, a decrease in noise with increasing street category, with insignificant differences between first and second street category thank to the best management and traffic control