Browsing by Subject "Computational tools"

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Open Access
The BioPAX community standard for pathway data sharing
(Nature Publishing Group, 2010-09) Demir, Emek; Cary, M. P.; Paley, S.; Fukuda, K.; Lemer, C.; Vastrik, I.; Wu, G.; D'Eustachio, P.; Schaefer, C.; Luciano, J.; Schacherer, F.; Martinez-Flores, I.; Hu, Z.; Jimenez-Jacinto, V.; Joshi-Tope, G.; Kandasamy, K.; Lopez-Fuentes, A. C.; Mi, H.; Pichler, E.; Rodchenkov, I.; Splendiani, A.; Tkachev, S.; Zucker, J.; Gopinath, G.; Rajasimha, H.; Ramakrishnan, R.; Shah, I.; Syed, M.; Anwar, N.; Babur, Özgün; Blinov, M.; Brauner, E.; Corwin, D.; Donaldson, S.; Gibbons, F.; Goldberg, R.; Hornbeck, P.; Luna, A.; Murray-Rust, P.; Neumann, E.; Reubenacker, O.; Samwald, M.; Iersel, Martijn van; Wimalaratne, S.; Allen, K.; Braun, B.; Whirl-Carrillo, M.; Cheung, Kei-Hoi; Dahlquist, K.; Finney, A.; Gillespie, M.; Glass, E.; Gong, L.; Haw, R.; Honig, M.; Hubaut, O.; Kane, D.; Krupa, S.; Kutmon, M.; Leonard, J.; Marks, D.; Merberg, D.; Petri, V.; Pico, A.; Ravenscroft, D.; Ren, L.; Shah, N.; Sunshine, M.; Tang R.; Whaley, R.; Letovksy, S.; Buetow, K. H.; Rzhetsky, A.; Schachter, V.; Sobral, B. S.; Doğrusöz, Uğur; McWeeney, S.; Aladjem, M.; Birney, E.; Collado-Vides, J.; Goto, S.; Hucka, M.; Novère, Nicolas Le; Maltsev, N.; Pandey, A.; Thomas, P.; Wingender, E.; Karp, P. D.; Sander, C.; Bader, G. D.
Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery. © 2010 Nature America, Inc. All rights reserved.
Open Access
Visibility-based assessment of urban form: an alternative perspective for the residential development in urban peripheries
(2021-07) Cengu, Suard
It is highly important for urban designers to understand how the configuration of urban fabric influences the living experience of the city dwellers. While cities change through time, their evolution may produce spaces that may not have a positive contribution or don’t reach their full potential. We call these spaces as ‘lost spaces’. The fragmentation that has occurred as a result of master planning implementations in western development corridor of Ankara, has produced lost spaces. This thesis aims to assess spatial configurations of such spaces near residential buildings in Çayyolu. The chosen case study, Cayyolou, is a ‘developed’ area in Ankara which has been an outcome of the city’s urban expansion. Urban and architectural spaces are defined by the spatial relations and social synergy stimulated by visual interaction. We have considered visibility as an indicator of ‘positive space’ and used isovists as a tool that measures visibility levels. A space that can be seen from any vantage point is defined as isovist by, and a set of such spaces defines a visual field. By utilizing computational tools and geometrical properties of isovist and isovist fields, we can identify and improve visibility of selected areas. In addition to visibility assessment of existing conditions of selected sites, this framework provides some design interventions which help improve visibility and propounds a relationship between urban spaces and visibility.