PoMaMo—a comprehensive database for potato genome data

A database for potato genome data (PoMaMo, Potato Maps and More) was established. The database contains molecular maps of all twelve potato chromosomes with about 1000 mapped elements, sequence data, putative gene functions, results from BLAST analysis, SNP and InDel information from different diploid and tetraploid potato genotypes, publication references, links to other public databases like GenBank (http://www.ncbi.nlm.nih.gov/) or SGN (Solanaceae Genomics Network, http://www.sgn.cornell.edu/), etc. Flexible search and data visualization interfaces enable easy access to the data via internet (https://gabi.rzpd.de/PoMaMo.html). The Java servlet tool YAMB (Yet Another Map Browser) was designed to interactively display chromosomal maps. Maps can be zoomed in and out, and detailed information about mapped elements can be obtained by clicking on an element of interest. The GreenCards interface allows a text-based data search by marker-, sequence- or genotype name, by sequence accession number, gene function, BLAST Hit or publication reference. The PoMaMo database is a comprehensive database for different potato genome data, and to date the only database containing SNP and InDel data from diploid and tetraploid potato genotypes

Multi-hazard risk assessment using GIS in urban areas: a case study for the city of Turrialba, Costa Rica

In the framework of the UNESCO sponsored project on “Capacity Building for Natural Disaster Reduction” a case study was carried out on multi-hazard risk assessment of the city of Turrialba, located in the central part of Costa Rica. The city with a population of 33,000 people is located in an area, which is regularly affected by flooding, landslides and earthquakes. In order to assist the local emergency commission and the municipality, a pilot study was carried out in the development of a GIS –based system for risk assessment and management. The work was made using an orthophoto as basis, on which all buildings, land parcels and roads, within the city and its direct surroundings were digitized, resulting in a digital parcel map, for which a number of hazard and vulnerability attributes were collected in the field. Based on historical information a GIS database was generated, which was used to generate flood depth maps for different return periods. For determining the seismic hazard a modified version of the Radius approach was used and the landslide hazard was determined based on the historical landslide inventory and a number of factor maps, using a statistical approach. The cadastral database of the city was used, in combination with the various hazard maps for different return periods to generate vulnerability maps for the city. In order to determine cost of the elements at risk, differentiation was made between the costs of the constructions and the costs of the contents of the buildings. The cost maps were combined with the vulnerability maps and the hazard maps per hazard type for the different return periods, in order to obtain graphs of probability versus potential damage. The resulting database can be a tool for local authorities to determine the effect of certain mitigation measures, for which a cost-benefit analysis can be carried out. The database also serves as an important tool in the disaster preparedness phase of disaster management at the municipal level

Soft topographic map for clustering and classification of bacteria

In this work a new method for clustering and building a topographic representation of a bacteria taxonomy is presented. The method is based on the analysis of stable parts of the genome, the so-called “housekeeping genes”. The proposed method generates topographic maps of the bacteria taxonomy, where relations among different type strains can be visually inspected and verified. Two well known DNA alignement algorithms are applied to the genomic sequences. Topographic maps are optimized to represent the similarity among the sequences according to their evolutionary distances. The experimental analysis is carried out on 147 type strains of the Gammaprotebacteria class by means of the 16S rRNA housekeeping gene. Complete sequences of the gene have been retrieved from the NCBI public database. In the experimental tests the maps show clusters of homologous type strains and present some singular cases potentially due to incorrect classification or erroneous annotations in the database

Novel developments in SBGN-ED and applications

Systems Biology Graphical Notation (SBGN, http://sbgn.org) [1] is an emerging standard for graphical representations of biochemical and cellular processes studied in systems biology. Three different views (Process Description, Entity Relationship, and Activity Flow) cover several aspects of the represented processes in different levels of detail. SBGN helps to communicate biological knowledge more efficient and accurate between different research communities in the life sciences. However, to support SBGN, methods and tools for editing, validating, and translating of SBGN maps are necessary.
We present methods for these tasks and novel developments in SBGN-ED (www.sbgn-ed.org) [2], a tool which allows to create all three types of SBGN maps from scratch, to validate these maps for syntactical and semantical correctness, to translate maps from the KEGG database into SBGN, and to export SBGN maps into several file and image formats. SBGN-ED is based on VANTED (Visualization and Analysis of NeTworks containing Experimental Data, http://www.vanted.org) [3].
As applications of SBGN and SBGN-ED we present furthermore MetaCrop (http://metacrop.ipk-gatersleben.de) [4], a database that summarizes diverse information about metabolic pathways in crop plants, and RIMAS (Regulatory Interaction Maps of Arabidopsis Seed Development, http://rimas.ipk-gatersleben.de) [5], an information portal that provides a comprehensive overview of regulatory pathways and genetic interactions during Arabidopsis embryo and seed development. 

[1] Le Novère, N. et al. (2009) The Systems Biology Graphical Notation. Nature Biotechnology, 27, 735-741.
[2] Czauderna, T., Klukas, C., Schreiber, F. (2010) Editing, validating, and translating of SBGN maps. Bioinformatics, 26 (18), 2340-2341.
[3] Junker, B.H., Klukas, C., Schreiber, F. (2006) VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics, 7, 109+.
[4] Grafahrend-Belau, E., Weise, S., Koschützki, D., Scholz, U., Junker, B.H., Schreiber, F. (2008) MetaCrop - A detailed database of crop plant metabolism. Nucleic Acids Research, 36, D954-D958.
[5] Junker, A., Hartmann, A., Schreiber, F., Bäumlein, H. (2010) An engineer's view on regulation of seed development. Trends in Plant Science, 15(6), 303-307.
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Glasgow's Stereo Image Database of Garments

To provide insight into cloth perception and manipulation with an active binocular robotic vision system, we compiled a database of 80 stereo-pair colour images with corresponding horizontal and vertical disparity maps and mask annotations, for 3D garment point cloud rendering has been created and released. The stereo-image garment database is part of research conducted under the EU-FP7 Clothes Perception and Manipulation (CloPeMa) project and belongs to a wider database collection released through CloPeMa (www.clopema.eu). This database is based on 16 different off-the-shelve garments. Each garment has been imaged in five different pose configurations on the project's binocular robot head. A full copy of the database is made available for scientific research only at https://sites.google.com/site/ugstereodatabase/.Comment: 7 pages, 6 figure, image databas