Now showing items 1-20 of 82

  • Axiom-Based Transformations: Optimisation and Testing 

    Bagge, Anya Helene; Haveraaen, Magne (Elsevier, 2009-10-10)
    Programmers typically have knowledge about properties of their programs that aren't explicitly expressed in the code ­ properties that may be very useful for, e.g., compiler optimisation and automated testing. Although ...
  • Binding Leverage as a Molecular Basis for Allosteric Regulation 

    Mitternacht, Simon; Berezovsky, Igor N. (Public Library of Science, 2011-09-15)
    Allosteric regulation involves conformational transitions or fluctuations between a few closely related states, caused by the binding of effector molecules. We introduce a quantity called binding leverage that measures ...
  • BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains 

    Katayama, Toshiaki; Wilkinson, Mark D.; Aoki-Kinoshita, Kiyoko F.; Kawashima, Shuichi; Yamamoto, Yasunori; Yamaguchi, Atsuko; Okamoto, Shinobu; Kawano, Shin; Kim, Jin-Dong; Wang, Yue; Wu, Hongyan; Kano, Yoshinobu; Ono, Hiromasa; Bono, Hidemasa; Kocbek, Simon; Aerts, Jan; Akune, Yukie; Antezana, Erick; Arakawa, Kazuharu; Aranda, Bruno; Baran, Joachim; Bolleman, Jerven; Bonnal, Raoul J. P.; Buttigieg, Pier Luigi; Campbell, Matthew P.; Chen, Yi-an; Chiba, Hirokazu; Cock, Peter J. A.; Cohen, K. Bretonnel; Constantin, Alexandru; Duck, Geraint; Dumontier, Michel; Fujisawa, Takatomo; Fujiwara, Toyofumi; Goto, Naohisa; Hoehndorf, Robert; Igarashi, Yoshinobu; Itaya, Hidetoshi; Ito, Maori; Iwasaki, Wataru; Kalaš, Matúš; Katoda, Takeo; Kim, Taehong; Kokubu, Anna; Komiyama, Yusuke; Kotera, Masaaki; Laibe, Camille; Lapp, Hilmar; Lütteke, Thomas; Marshall, M. Scott; Mori, Takaaki; Mori, Hiroshi; Morita, Mizuki; Murakami, Katsuhiko; Nakao, Mitsuteru; Narimatsu, Hisashi; Nishide, Hiroyo; Nishimura, Yosuke; Nyström-Persson, Johan; Ogishima, Soichi; Okamura, Yasunobu; Okuda, Shujiro; Oshita, Kazuki; Packer, Nicki H; Prins, Pjotr; Ranzinger, Rene; Rocca-Serra, Philippe; Sansone, Susanna; Sawaki, Hiromichi; Shin, Sung-Ho; Splendiani, Andrea; Strozzi, Francesco; Tadaka, Shu; Toukach, Philip; Uchiyama, Ikuo; Umezaki, Masahito; Vos, Rutger; Whetzel, Patricia L.; Yamada, Issaku; Yamasaki, Chisato; Yamashita, Riu; York, William S.; Zmasek, Christian M.; Kawamoto, Shoko; Takagi, Toshihisa (BioMed Central, 2014-02-05)
    Abstract The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual ...
  • Blind search for post-translational modifications and amino acid substitutions using peptide mass fingerprints from two proteases 

    Barsnes, Harald; Mikalsen, Svein-Ole; Eidhammer, Ingvar (BioMed Central, 2008-12-19)
    Background: Mass spectrometric analysis of peptides is an essential part of protein identification and characterization, the latter meaning the identification of modifications and amino acid substitutions. There are two ...
  • CCZ-equivalence of bent vectorial functions and related constructions 

    Budaghyan, Lilya; Carlet, Claude (Springer, 2011-01-06)
    We observe that the CCZ-equivalence of bent vectorial functions over F2nFn2 (n even) reduces to their EA-equivalence. Then we show that in spite of this fact, CCZ-equivalence can be used for constructing bent functions ...
  • Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim 

    Balzer, Susanne Mignon; Malde, Ketil; Lanzén, Anders; Sharma, Animesh; Jonassen, Inge (Oxford University Press, 2010)
    Motivation: The commercial launch of 454 pyrosequencing in 2005was a milestone in genome sequencing in terms of performance and cost. Throughout the three available releases, average read lengths have increased to ∼500 ...
  • Coherent Conformational Degrees of Freedom as a Structural Basis for Allosteric Communication 

    Mitternacht, Simon; Berezovsky, Igor N. (Public Library of Science, 2011-12-08)
    Conformational changes in allosteric regulation can to a large extent be described as motion along one or a few coherent degrees of freedom. The states involved are inherent to the protein, in the sense that they are ...
  • Combining Aspect-Oriented and Strategic Programming 

    Kalleberg, Karl Trygve; Visser, Eelco (Elsevier, 2006-01)
    Properties such as logging, persistence, debugging, tracing, distribution, performance monitoring and exception handling occur in most programming paradigms and are normally very difficult or even impossible to modularizewith ...
  • Community-driven development for computational biology at Sprints, Hackathons and Codefests 

    Möller, Steffen; Afgan, Enis; Banck, Michael; Bonnal, Raoul J. P.; Booth, Timothy; Chilton, John; Cock, Peter J. A.; Gumbel, Markus; Harris, Nomi; Holland, Richard; Kalaš, Matúš; Kaján, László; Kibukawa, Eri; Powel, David R.; Prins, Pjotr; Quinn, Jacqueline; Sallou, Olivier; Strozzi, Francesco; Seemann, Torsten; Sloggett, Clare; Soiland-Reyes, Stian; Spooner, William; Steinbiss, Sascha; Tille, Andreas; Travis, Anthony J.; Guimera, Roman V.; Katayama, Toshiaki; Chapman, Brad A. (BioMed Central, 2014-11-27)
    Background: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools ...
  • Computing minimal triangulation in Time o(n^2.376) 

    Heggernes, Pinar; Telle, Jan Arne; Villanger, Yngve (SIAM Journals, 2005)
  • Conserved BK Channel-Protein Interactions Reveal Signals Relevant to Cell Death and Survival 

    Sokolowski, Bernd; Orchard, Sandra; Harvey, Margaret; Sridhar, Settu; Sakai, Yoshihisa (Public Library of Science, 2011-12-09)
    The large-conductance Ca2+-activated K+ (BK) channel and its b-subunit underlie tuning in non-mammalian sensory or hair cells, whereas in mammals its function is less clear. To gain insights into species differences and ...
  • Continuous Levels-of-Detail and Visual Abstraction for Seamless Molecular Visualization 

    Parulek, Julius; Jönsson, Daniel; Ropinski, Timo; Bruckner, Stefan; Ynnerman, Anders; Viola, Ivan (Wiley, 2014-05-06)
    Molecular visualization is often challenged with rendering of large molecular structures in real time. We introduce a novel approach that enables us to show even large protein complexes. Our method is based on the ...
  • Current Trends for 4D Space-Time Topology for Semantic Flow Segmentation 

    Matković, Krešimir; Lež, Alan; Hauser, Helwig; Pobitzer, Armin; Theisel, Holger; Kuhn, Alexander; Otto, Mathias; Peikert, Ronald; Schindler, Benjamin; Fuchs, Raphael (Elsevier, 2011)
  • Curve Density Estimates 

    Lampe, Ove Daae; Hauser, Helwig (Blackwell Publishing Ltd., 2011-06-28)
    In this work, we present a technique based on kernel density estimation for rendering smooth curves. With this approach, we produce uncluttered and expressive pictures, revealing frequency information about one, or, ...
  • Curve-Centric Volume Reformation for Comparative Visualization 

    Lampe, Ove Daae; Correa, Carlos; Ma, Kwan-Liu; Hauser, Helwig (IEEE, 2009-10-11)
    We present two visualization techniques for curve-centric volume reformation with the aim to create compelling comparative visualizations. A curve-centric volume reformation deforms a volume, with regards to a curve in ...
  • Data partitioning enables the use of standard SOAP Web Services in genome-scale workflows 

    Sztromwasser, Paweł; Puntervoll, Pål; Petersen, Kjell (IMBio e.V., 2011)
    Biological databases and computational biology tools are provided by research groups around the world, and made accessible on the Web. Combining these resources is a com- mon practice in bioinformatics, but integration ...
  • A Diagrammatic Logic for Object-Oriented Visual Modeling 

    Diskin, Zinovy; Wolter, Uwe Egbert (Elsevier, 2008-11-21)
    Formal generalized sketches is a graph-based specification format that borrows its main ideas from categorical and ordinary first-order logic, and adapts them to software engineering needs. In the engineering jargon, it ...
  • Directed graph representation of half-rate additive codes over GF(4) 

    Danielsen, Lars Eirik; Parker, Matthew G. (Springer, 2010)
    We show that (n, 2n) additive codes over GF(4) can be represented as directed graphs. This generalizes earlier results on self-dual additive codes over GF(4), which correspond to undirected graphs. Graph representation ...
  • Domain-Specific Languages for Composable Editor Plugins 

    Kats, Lennart C. L.; Kalleberg, Karl Trygve; Visser, Eelco (Elsevier, 2010-09-17)
    Modern IDEs increase developer productivity by incorporating many different kinds of editor services. These can be purely syntactic, such as syntax highlighting, code folding, and an outline for navigation; or they can be ...
  • Energy-scale Aware Feature Extraction for Flow Visualization 

    Pobitzer, Armin; Tutkun, Murat; Anreassen, Øyvind; Fuchs, Raphael; Peikert, Ronald; Hauser, Helwig (Blackwell Publishing Ltd., 2011)
    In the visualization of flow simulation data, feature detectors often tend to result in overly rich response, making some sort of filtering or simplification necessary to convey meaningful images. In this paper we present ...