Scalable Vector Graphics Format Research Articles

Focus on software, data acquisition, and instrumentation

Focus on software, data acquisition, and instrumentation

Auto-generating of 2D tessellated crease patterns of 3D biomimetic spring origami structure

Computational simulations can accelerate the design and modelling of origami robots and mechanisms. This paper presents a computational method using algorithms developed in Python to generate different tessellated origami crease patterns simultaneously. This paper aims to automate this process by introducing a system that automatically generates origami crease patterns in Scalable Vector Graphics format. By introducing different parameters, variations of the same underlying tessellated crease pattern can be obtained. The user interface consists of an input file where the user can input the desired parameters, which are then processed by an algorithm written in Python to generate the respective origami 2D crease patterns. These origami crease patterns can serve as inputs to current origami design software and algorithms to generate origami design models for faster and easier visual comparison. This paper utilizes a basic biomimetic inspiration origami pattern to demonstrate the functionality by varying underlying crease pattern parameters that give rise to symmetric and asymmetric spring origami 3D structures. Furthermore, this paper conducts a qualitative analysis of the origami design outputs of an origami simulator from the input crease patterns and the respective manual folding of the origami structure.

PORTABILITY OF CARTOGRAPHIC SYMBOLS LIBRARY FOR OPEN STANDARDS

Abstract. The Geological Survey of Brazil has a library of palaeontology symbols to use in geological mapping works, currently in bitmap format and adapted for ESRI platform. This type of representation has presented anti-aliasing problems when reduced, in addition to not being suitable for map presentation on the web, according to OGC (Open Geospatial Consortium) specifications. This work presents a reproducible method in any symbol library type. The method consists of converting the symbol library to open-source format, resulting an OpenType font file, which can be installed on any operating system and view each symbol font in any software that has this functionality, such as a GIS (Geographic Information Systems) software. The need to develop font construction technique is due to improving typographic quality of cartographic representations and making library compatible with main GIS softwares. Those 61 pictorial palaeontology symbols were converted, one by one, to SVG (Scalable Vector Graphics) format. We imported each symbol as a glyph in FontForge font editor. Major computer platforms use OpenType format due to its wide availability and typographic flexibility, including provisions to deal with diverse characteristics of internationally symbolic alphabet systems. There is even the possibility of symbols standardizing in the UTF-8 alphabet system, an issue for the scientific community to study. The advantage of using the SVG format is its size, a compact text file, and has an excellent compression factor. In addition, version-control repositories, like GitHub, can store SVG files, which would facilitate content management. The adopted method proved to be applicable to any cartographic symbols library with good results. Rendering tests on different platforms (web or desktop) showed no noticeable differences. One of the most important aspects of the method presented in this work was to make cartographic symbols library public and open-source for use by the geoscientific community, regardless whether an open-source or proprietary platform is used, and so, the Geological Survey of Brazil will be able to distribute geological symbology patterns, according to Open Data definition.

Library of graphic symbols for power equipment in the scalable vector graphics format

This paper describes the results of developing and using a library of graphic symbols for components of power equipment under the state standards GOST 21.403-80 “Power Equipment” and GOST 2.789-74 “Heat Exchangers”. The library is implemented in the SVG (Scalable Vector Graphics) format. The obtained solutions are in line with the well-known studies on creating libraries of parametrical fragments of symbols for elements of diagrams and drawings in design systems for various industrial applications. The SVG format is intended for use in web applications, so the creation of SVG codes for power equipment under GOST 21.403-80 and GOST 2.789-74 is an essential stage in the development of web programs for the thermodynamic optimization of power plants. One of the major arguments in favor of the SVG format is that it can be integrated with codes. So, in process control systems developed based on a web platform, scalable vector graphics provides for a dynamic user interface, functionality of mimic panels and changeability of their components depending on the availability and status of equipment. An important reason for the acquisition and use of the SVG format is also that it is becoming the basis (recommended for the time being, and mandatory in future) for electronic document management in the sphere of design documentation as part of international efforts to standardize and harmonize data exchange formats. In a specific context, the effectiveness of the SVG format for the power equipment arrangement has been shown. The library is intended for solution of specific production problems involving an analysis of the power plant thermal circuits and in training of power engineering students. The library and related materials are publicly available through the Internet. A number of proposals on the future evolution of the library have been formulated.

Библиотека условных графических обозначений энергетического оборудования в формате масштабируемой векторной графики

Библиотека условных графических обозначений энергетического оборудования в формате масштабируемой векторной графики

TcsBU: a tool to extend TCS network layout and visualization.

TCS is a widely used haplotype network reconstruction software, but lacks the capability of overlapping genetic with geographic structure, which is often a first step in phylogeographic analysis. tcsBU is a web-based program that extends the capabilities of TCS, by implementing haplotype classification into an arbitrary user-defined scheme, which is displayed as pie-chart like graphs embedded into the network. Taking advantage of modern graphic libraries, tcsBU also improves the speed at which the final network layout is reached. Networks can be saved as a Scalable Vector Graphics format. tcsBU is available on-line at http://cibio.up.pt/software/tcsBU/. The source code is freely available from https://github.com/sairum/tcsbu/ under a standard MIT license.

SVGenes: a library for rendering genomic features in scalable vector graphic format

Motivation: Drawing genomic features in attractive and informative ways is a key task in visualization of genomics data. Scalable Vector Graphics (SVG) format is a modern and flexible open standard that provides advanced features including modular graphic design, advanced web interactivity and animation within a suitable client. SVGs do not suffer from loss of image quality on re-scaling and provide the ability to edit individual elements of a graphic on the whole object level independent of the whole image. These features make SVG a potentially useful format for the preparation of publication quality figures including genomic objects such as genes or sequencing coverage and for web applications that require rich user-interaction with the graphical elements.Results: SVGenes is a Ruby-language library that uses SVG primitives to render typical genomic glyphs through a simple and flexible Ruby interface. The library implements a simple Page object that spaces and contains horizontal Track objects that in turn style, colour and positions features within them. Tracks are the level at which visual information is supplied providing the full styling capability of the SVG standard. Genomic entities like genes, transcripts and histograms are modelled in Glyph objects that are attached to a track and take advantage of SVG primitives to render the genomic features in a track as any of a selection of defined glyphs. The feature model within SVGenes is simple but flexible and not dependent on particular existing gene feature formats meaning graphics for any existing datasets can easily be created without need for conversion.Availability: The library is provided as a Ruby Gem from https://rubygems.org/gems/bio-svgenes under the MIT license, and open source code is available at https://github.com/danmaclean/bioruby-svgenes also under the MIT License.Contact: dan.maclean@tsl.ac.uk

XML DATA SCHEMAS AND SCALABLE VECTOR GRAPHICS FORMAT FOR THE SEA LEVEL OBSERVATIONS

XML (Extended Markup Language) Data Schemas as the format for information exchange in graphical SVG (Scalable Vector Graphics) format is presented. SVG format is a language for two‐dimensional graphics and is based on XML. It is the advanced version of previous data exchange format TGX (Tide Gauge Independent Exchange Format), which contains the plain ASCII data. SVG graphics are formatted from sea level observations data at ESEAS station KLPD. Comparing with similar CGM (Computer Graphics Metafile) format, SVG has its advantages of being based on XML. XML Data Schemas, in addition, add a header information about the marine measurements site, sensors and any additional necessary information. The correct header formation and the advantages of such data exchange format are analysed. Header is important for an exchange between different sites from different countries so as it would be information standardisation. Visual appearance of the SVG file, the source, headers and formation of the file in script are described too.

Role of the Synthase Domain of Ags1p in Cell Wall α-Glucan Biosynthesis in Fission Yeast

The cell wall is important for maintenance of the structural integrity and morphology of fungal cells. Besides beta-glucan and chitin, alpha-glucan is a major polysaccharide in the cell wall of many fungi. In the fission yeast Schizosaccharomyces pombe, cell wall alpha-glucan is an essential component, consisting mainly of (1,3)-alpha-glucan with approximately 10% (1,4)-linked alpha-glucose residues. The multidomain protein Ags1p is required for alpha-glucan biosynthesis and is conserved among cell wall alpha-glucan-containing fungi. One of its domains shares amino acid sequence motifs with (1,4)-alpha-glucan synthases such as bacterial glycogen synthases and plant starch synthases. Whether Ags1p is involved in the synthesis of the (1,4)-alpha-glucan constituent of cell wall alpha-glucan had remained unclear. Here, we show that overexpression of Ags1p in S. pombe cells results in accumulation of (1,4)-alpha-glucan. To determine whether the synthase domain of Ags1p is responsible for this activity, we overexpressed Ags1p-E1526A, which carries a mutation in a putative catalytic residue of the synthase domain, but observed no accumulation of (1,4)-alpha-glucan. Compared with wild-type Ags1p, this mutant Ags1p showed a markedly reduced ability to complement the cell lysis phenotype of the temperature-sensitive ags1-1 mutant. Therefore, we conclude that, in S. pombe, the production of (1,4)-alpha-glucan by the synthase domain of Ags1p is important for the biosynthesis of cell wall alpha-glucan.

IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model.

BackgroundAlthough protein-protein interaction (PPI) networks have been explored by various experimental methods, the maps so built are still limited in coverage and accuracy. To further expand the PPI network and to extract more accurate information from existing maps, studies have been carried out to integrate various types of functional relationship data. A frequently updated database of computationally analyzed potential PPIs to provide biological researchers with rapid and easy access to analyze original data as a biological network is still lacking.ResultsBy applying a probabilistic model, we integrated 27 heterogeneous genomic, proteomic and functional annotation datasets to predict PPI networks in human. In addition to previously studied data types, we show that phenotypic distances and genetic interactions can also be integrated to predict PPIs. We further built an easy-to-use, updatable integrated PPI database, the Integrated Network Database (IntNetDB) online, to provide automatic prediction and visualization of PPI network among genes of interest. The networks can be visualized in SVG (Scalable Vector Graphics) format for zooming in or out. IntNetDB also provides a tool to extract topologically highly connected network neighborhoods from a specific network for further exploration and research. Using the MCODE (Molecular Complex Detections) algorithm, 190 such neighborhoods were detected among all the predicted interactions. The predicted PPIs can also be mapped to worm, fly and mouse interologs.ConclusionIntNetDB includes 180,010 predicted protein-protein interactions among 9,901 human proteins and represents a useful resource for the research community. Our study has increased prediction coverage by five-fold. IntNetDB also provides easy-to-use network visualization and analysis tools that allow biological researchers unfamiliar with computational biology to access and analyze data over the internet. The web interface of IntNetDB is freely accessible at . Visualization requires Mozilla version 1.8 (or higher) or Internet Explorer with installation of SVGviewer.

KaPPA-View. A Web-Based Analysis Tool for Integration of Transcript and Metabolite Data on Plant Metabolic Pathway Maps

The application of DNA array technology and chromatographic separation techniques coupled with mass spectrometry to transcriptomic and metabolomic analyses in plants has resulted in the generation of considerable quantitative data related to transcription and metabolism. The integration of "omic" data is one of the major concerns associated with research into identifying gene function. Thus, we developed a Web-based tool, KaPPA-View, for representing quantitative data for individual transcripts and/or metabolites on plant metabolic pathway maps. We prepared a set of comprehensive metabolic pathway maps for Arabidopsis (Arabidopsis thaliana) and depicted these graphically in Scalable Vector Graphics format. Individual transcripts assigned to a reaction are represented symbolically together with the symbols of the reaction and metabolites on metabolic pathway maps. Using quantitative values for transcripts and/or metabolites submitted by the user as Comma Separated Value-formatted text through the Internet, the KaPPA-View server inserts colored symbols corresponding to a defined metabolic process at that site on the maps and returns them to the user's browser. The server also provides information on transcripts and metabolites in pop-up windows. To demonstrate the process, we describe the dataset obtained for transgenic plants that overexpress the PAP1 gene encoding a MYB transcription factor on metabolic pathway maps. The presentation of data in this manner is useful for viewing metabolic data in a way that facilitates the discussion of gene function.

Circular genome visualization and exploration using CGView.

CGView (Circular Genome Viewer) is a Java application and library for generating high-quality, zoomable maps of circular genomes. It converts XML or tab-delimited input into a graphical map (PNG, JPG or Scalable Vector Graphics format), complete with sequence features, labels, legends and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any Web browser, allowing rapid genome browsing and facilitating data sharing. CGView (the standalone application, library or applet), sample input, sample maps and documentation can be obtained from http://wishart.biology.ualberta.ca/cgview/ david.wishart@ualberta.ca.