A Web Map Service implementation for the visualization of multidimensional gridded environmental data

We describe ncWMS, an implementation of the Open Geospatial Consortium’s Web Map Service (WMS) specification for multidimensional gridded environmental data. ncWMS can read data in a large number of common scientific data formats – notably the NetCDF format with the Climate and Forecast conventions – then efficiently generate map imagery in thousands of different coordinate reference systems. It is designed to require minimal configuration from the system administrator and, when used in conjunction with a suitable client tool, provides end users with an interactive means for visualizing data without the need to download large files or interpret complex metadata. It is also used as a “bridging” tool providing interoperability between the environmental science community and users of geographic information systems. ncWMS implements a number of extensions to the WMS standard in order to fulfil some common scientific requirements, including the ability to generate plots representing timeseries and vertical sections. We discuss these extensions and their impact upon present and future interoperability. We discuss the conceptual mapping between the WMS data model and the data models used by gridded data formats, highlighting areas in which the mapping is incomplete or ambiguous. We discuss the architecture of the system and particular technical innovations of note, including the algorithms used for fast data reading and image generation. ncWMS has been widely adopted within the environmental data community and we discuss some of the ways in which the software is integrated within data infrastructures and portals

BlogMyData: a Virtual Research Environment for collaborative visualization of environmental data

Understanding and predicting the Earth system requires the collaborative effort of scientists from many different disciplines and institutions. The National Centre for Earth Observation (NCEO) and the National Centre for Atmospheric Science Climate Group (NCAS-Climate) are both high-profile interdisciplinary research centres involving numerous universities and institutes around the UK and many international collaborators. Both groups make use of the latest numerical models of the climate and earth system, validated by observations, to simulate the environment and its response to forcings such as an increase in greenhouse gas emissions. Their scientists must work together closely to understand the various aspects of these models and assess their strengths and weaknesses.At the present time, collaborations take place chiefly through face-to-face meetings, the scholarly literature and informal electronic exchanges of emails and documents. All of these methods suffer from serious deficiencies that hamper effective collaboration. For practical reasons, face-to-face meetings can be held only infrequently. The scholarly literature does not yet adequately link scientific results to the source data and thought processes that yielded them, and additionally suffers from a very slow turnaround time. Informal exchanges of electronic information commonly lose vital context; for example, scientists typically exchange static visualizations of data (as GIFs or PostScript plots for example), but the recipient cannot easily access the data behind the visualization, or customize the visualization in any way. Emails are rarely published or preserved adequately for future use. The recent adoption of “off the shelf” Wikis and basic blogs has addressed some of these issues, but does not usually address specific scientific needs or enable the interactive visualization of data

The evaluation of retinal nerve fiber thickness in chonic obtructive lung disease with optical cohorence tomograpy.

Kronik obstrüktif akciğer hastalığının (KOAH) retina sinir lifi tabakası (RSLT) üzerindeki etkisini optik koherens tomografi (OCT), (Stratus OCT-3) ile değerlendirmek ve yaşı uygun sağlıklı bireylerle karşılaştırmaktır.KOAH tanısı konulan veya KOAH tanısıyla takibi yapılan 30 olgu ile 30 sağlıklı gönüllü çalışmaya dahil edilmiştir. Tüm olguların tam bir oftalmolojik muayeneyi takiben OCT fast RNFL protokolü ile ölçümleri yapıldı.Değerlendirilen OCT parametrelerinde, ortalama RSLT değerleri KOAH grubunda sağlıklı kontrol grubuna göre anlamlı derecede kalın bulundu (p<0.001). KOAH grubunda üst kadran ve temporal kadran değerleri (141.07±18.18, 88.37±23.12, sırasıyla), kontrol grubuna (130.17±14.78, 78.30±13.62, sırasıyla) göre istatistiksel olarak anlamlı yüksek bulundu (p=0.013, 0.044, sırasıyla), fakat nazal ve alt kadran RSLT değerleri açısından iki grup arasında anlamlı fark bulunmadı. Olguların RSLT değerleri ile hastalık süresi karşılaştırıldığında, üst kadrana ait RSLT kalınlığı hastalık süresi ile azalmaktaydı (Pearson=-0.375, p<0.05). Tedavi süresi ile karşılaştırıldığında ortalama RSLT kalınlığının da süreyle parelel olarak azaldığı gösterildi (Pearson=-0.537, p<0.05). Olgular hastalığın evresine göre gruplandırıldığında, evre IV KOAH grubunda ortalama RSLT evre III'e göre daha kalın bulundu, ancak fark anlamlı değildi (p=0.39). Diabetes mellitus, hiperkolesterolemi, yaş, sigara kullanımının RSLT üzerine etkisi anlamlı bulunmadı. Kalp hastalığının RSLT kalınlığını arttırdığını, hipertansiyonun ise RSLT kalınlığını azalttığı görüldü.he purpose of this study was to measure the retinal nerve fiber layer (RNFL) thickness of patients with chronic obstructive lung disease (COPD) by using optical coherence tomography (OCT), (Stratus OCT-3) and to compare the measurements with those obtained from the healthy subjects.Thirty patients with COPD and 30 healthy volunteers were included into this study. After ocular examination, all subjects underwent fast RNFL analysis measured by OCT.The mean RNFL thickness value of the COPD group was statistically higher compared to the control group (p<0.001). RNFL thickness in superior and temporal quadrants of the COPD group (141.07±18.18, 88.37±23.12, respectively) were thicker than the control group (130.17±14.78, 78.30±13.62, respectively) which was statistically significant (p=0.013, 0.044, respectively), however there was no difference in RNFL thickness values of the nasal and inferior quadrants. The RNFL thickness of the superior quadrant showed a decrease with the duration of the disease (Pearson=-0.375, p<0.05) and the mean RNFL thickness was decreased with the duration of treatment (Pearson=-0.537, p<0.05). When the COPD subjects classified according to the stage of the disease, the mean RNFL was more thicker in stage IV COPD group compared with stage III COPD group, but the difference was not significant (p=0.39). Diabetes mellitus, hypercholesterolemia, and smoking had no statistically significant effects on the RNFL, whereas the RNFL thickness increased in cardiac disease and decreased in hypertension

Data streaming, workflow and firewall-friendly Grid Services with Styx

We present the Styx Grid Service (SGS), a remote service type that allows data to be streamed\ud directly between service instances. The Styx Grid Service is built upon the Styx protocol, an\ud established protocol for building distributed systems. Through the use of persistent connections,\ud clients can monitor progress, status and other service data without requiring inbound ports to\ud be open through the firewall. Security is assured through the use of SSL to authenticate and\ud encrypt communications between systems. SGSs can interoperate with other service types such\ud as Web Services in a workflow through the use of suitable wrappers. We present two case studies\ud of the use of the SGS. In the first, Styx Grid Services are used in the streaming of large amounts\ud of data between Web Services in a workflow. In the second case study we show how the Styx\ud Grid Service architecture can be used in collaborative visualization and computational steering