ETDB-Caltech: a blockchain-based distributed public database for electron tomography

Three-dimensional electron microscopy techniques like electron tomography provide valuable insights into cellular structures, and present significant challenges for data storage and dissemination. Here we explored a novel method to publicly release more than 11,000 such datasets, more than 30 TB in total, collected by our group. Our method, based on a peer-to-peer file sharing network built around a blockchain ledger, offers a distributed solution to data storage. In addition, we offer a user-friendly browser-based interface, https://etdb.caltech.edu, for anyone interested to explore and download our data. We discuss the relative advantages and disadvantages of this system and provide tools for other groups to mine our data and/or use the same approach to share their own imaging datasets

Visual communication in urban planning and urban design

This report documents the current status of visual communication in urban design and planning. Visual communication is examined through discussion of standalone and network media, specifically concentrating on visualisation on the World Wide Web(WWW).Firstly, we examine the use of Solid and Geometric Modelling for visualising urban planning and urban design. This report documents and compares examples of the use of Virtual Reality Modelling Language (VRML) and proprietary WWW based Virtual Reality modelling software. Examples include the modelling of Bath and Glasgow using both VRML 1.0 and 2.0. A review is carried out on the use of Virtual Worldsand their role in visualising urban form within multi-user environments. The use of Virtual Worlds is developed into a case study of the possibilities and limitations of Virtual Internet Design Arenas (ViDAs), an initiative undertaken at the Centre for Advanced Spatial Analysis, University College London. The use of Virtual Worlds and their development towards ViDAs is seen as one of the most important developments in visual communication for urban planning and urban design since the development plan.Secondly, photorealistic media in the process of communicating plans is examined.The process of creating photorealistic media is documented, examples of the Virtual Streetscape and Wired Whitehall Virtual Urban Interface System are provided. The conclusion is drawn that although the use of photo-realistic media on the WWW provides a way to visually communicate planning information, its use is limited. The merging of photorealistic media and solid geometric modelling is reviewed in the creation of Augmented Reality. Augmented Reality is seen to provide an important step forward in the ability to quickly and easily visualise urban planning and urban design information.Thirdly, the role of visual communication of planning data through GIS is examined interms of desktop, three dimensional and Internet based GIS systems. The evolution to Internet GIS is seen as a critical component in the development of virtual cities which will allow urban planners and urban designers to visualise and model the complexity of the built environment in networked virtual reality.Finally a viewpoint is put forward of the Virtual City, linking Internet GIS with photorealistic multi-user Virtual Worlds. At present there are constraints on how far virtual cities can be developed, but a view is provided on how these networked virtual worlds are developing to aid visual communication in urban planning and urban design

Revisiting revisitation in computer interaction: organic bookmark management.

According to Milic-Frayling et al. (2004), there are two general ways of user browsing i.e. search (finding a website where the user has never visited before) and revisitation (returning to a website where the user has visited in the past). The issue of search is relevant to search engine technology, whilst revisitation concerns web usage and browser history mechanisms. The support for revisitation is normally through a set of functional built-in icons e.g. History, Back, Forward and Bookmarks. Nevertheless, for returning web users, they normally find it is easier and faster to re-launch an online search again, rather than spending time to find a particular web site from their personal bookmark and history records. Tauscher and Greenberg (1997) showed that revisiting web pages forms up to 58% of the recurrence rate of web browsing. Cockburn and McKenzie (2001) also stated that 81% of web pages have been previously visited by the user. According to Obendorf et al. (2007), revisitation can be divided into four classifications based on time: short-term (72.6% revisits within an hour), medium-term (12% revisits within a day and 7.8% revisits within a week), and long-term (7.6% revisits longer than a week)

Material Thermal Inputs of Iowa Materials for MEPDG, 2011

The thermal properties of concrete materials, such as coeffi cient of thermal expansion (CTE), thermal conductivity, and heat capacity, are required by the MEPDG program as the material inputs for pavement design. However, a limited amount of test data is available on the thermal properties of concrete in Iowa. The default values provided by the MEPDG program may not be suitable for Iowa concrete, since aggregate characteristics have signifi cant infl uence on concrete thermal properties

WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets.

BackgroundSharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientific communication. There is a need for a simple, free, open-source program that can automatically export aggregated reports of entire chemical data sets to files viewable on any computer, regardless of the operating system and without requiring the installation of additional software.ResultsWe here present a program called WebChem Viewer that automatically generates these types of highly portable reports. Furthermore, in designing WebChem Viewer we have also created a useful online web application for remotely generating molecular structures from SMILES strings. We encourage the direct use of this online application as well as its incorporation into other software packages.ConclusionsWith these features, WebChem Viewer enables interdisciplinary collaborations that require the sharing and visualization of small molecule structures and associated sets of heterogeneous chemical data. The program is released under the FreeBSD license and can be downloaded from http://nbcr.ucsd.edu/WebChemViewer. The associated web application (called "Smiley2png 1.0") can be accessed through freely available web services provided by the National Biomedical Computation Resource at http://nbcr.ucsd.edu

The Genomic HyperBrowser: inferential genomics at the sequence level

The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical analysis of sequence-level genomic information. We provide a growing collection of generic biological investigations that query pairwise relations between tracks, represented as mathematical objects, along the genome. The Genomic HyperBrowser implements the approach and is available at http://hyperbrowser.uio.no

TICAL - a web-tool for multivariate image clustering and data topology preserving visualization

In life science research bioimaging is often used to study two kinds of features in a sample simultaneously: morphology and co-location of molecular components. While bioimaging technology is rapidly proposing and improving new multidimensional imaging platforms, bioimage informatics has to keep pace in order to develop algorithmic approaches to support biology experts in the complex task of data analysis. One particular problem is the availability and applicability of sophisticated image analysis algorithms via the web so different users can apply the same algorithms to their data (sometimes even to the same data to get the same results) and independently from her/his whereabouts and from the technical features of her/his computer. In this paper we describe TICAL, a visual data mining approach to multivariate microscopy analysis which can be applied fully through the web.We describe the algorithmic approach, the software concept and present results obtained for different example images

The 3D Genome Browser: A web-based browser for visualizing 3D genome organization and long-range chromatin interactions

Abstract Here, we introduce the 3D Genome Browser, http://3dgenome.org, which allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different types. We design a new binary data format for Hi-C data that reduces the file size by at least a magnitude and allows users to visualize chromatin interactions over millions of base pairs within seconds. Our browser provides multiple methods linking distal cis-regulatory elements with their potential target genes. Users can seamlessly integrate thousands of other omics data to gain a comprehensive view of both regulatory landscape and 3D genome structure