16 results on '"Oshita, Kazuki"'
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2. Functional equations and gamma factors of local zeta functions for the metaplectic cover of SL2
- Author
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Oshita, Kazuki and Tsuzuki, Masao
- Published
- 2024
- Full Text
- View/download PDF
3. The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
- Author
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Katayama, Toshiaki, Wilkinson, Mark D, Micklem, Gos, Kawashima, Shuichi, Yamaguchi, Atsuko, Nakao, Mitsuteru, Yamamoto, Yasunori, Okamoto, Shinobu, Oouchida, Kenta, Chun, Hong-Woo, Aerts, Jan, Afzal, Hammad, Antezana, Erick, Arakawa, Kazuharu, Aranda, Bruno, Belleau, Francois, Bolleman, Jerven, Bonnal, Raoul JP, Chapman, Brad, Cock, Peter JA, Eriksson, Tore, Gordon, Paul MK, Goto, Naohisa, Hayashi, Kazuhiro, Horn, Heiko, Ishiwata, Ryosuke, Kaminuma, Eli, Kasprzyk, Arek, Kawaji, Hideya, Kido, Nobuhiro, Kim, Young Joo, Kinjo, Akira R, Konishi, Fumikazu, Kwon, Kyung-Hoon, Labarga, Alberto, Lamprecht, Anna-Lena, Lin, Yu, Lindenbaum, Pierre, McCarthy, Luke, Morita, Hideyuki, Murakami, Katsuhiko, Nagao, Koji, Nishida, Kozo, Nishimura, Kunihiro, Nishizawa, Tatsuya, Ogishima, Soichi, Ono, Keiichiro, Oshita, Kazuki, Park, Keun-Joon, Prins, Pjotr, Saito, Taro L, Samwald, Matthias, Satagopam, Venkata P, Shigemoto, Yasumasa, Smith, Richard, Splendiani, Andrea, Sugawara, Hideaki, Taylor, James, Vos, Rutger A, Withers, David, Yamasaki, Chisato, Zmasek, Christian M, Kawamoto, Shoko, Okubo, Kosaku, Asai, Kiyoshi, and Takagi, Toshihisa
- Abstract
Abstract Background BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. Results The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. Conclusion We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.
- Published
- 2013
4. The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications
- Author
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Katayama, Toshiaki, Wilkinson, Mark D, Vos, Rutger, Kawashima, Takeshi, Kawashima, Shuichi, Nakao, Mitsuteru, Yamamoto, Yasunori, Chun, Hong-Woo, Yamaguchi, Atsuko, Kawano, Shin, Aerts, Jan, Aoki-Kinoshita, Kiyoko F, Arakawa, Kazuharu, Aranda, Bruno, Bonnal, Raoul JP, Fernández, José M, Fujisawa, Takatomo, Gordon, Paul MK, Goto, Naohisa, Haider, Syed, Harris, Todd, Hatakeyama, Takashi, Ho, Isaac, Itoh, Masumi, Kasprzyk, Arek, Kido, Nobuhiro, Kim, Young-Joo, Kinjo, Akira R, Konishi, Fumikazu, Kovarskaya, Yulia, von Kuster, Greg, Labarga, Alberto, Limviphuvadh, Vachiranee, McCarthy, Luke, Nakamura, Yasukazu, Nam, Yunsun, Nishida, Kozo, Nishimura, Kunihiro, Nishizawa, Tatsuya, Ogishima, Soichi, Oinn, Tom, Okamoto, Shinobu, Okuda, Shujiro, Ono, Keiichiro, Oshita, Kazuki, Park, Keun-Joon, Putnam, Nicholas, Senger, Martin, Severin, Jessica, Shigemoto, Yasumasa, Sugawara, Hideaki, Taylor, James, Trelles, Oswaldo, Yamasaki, Chisato, Yamashita, Riu, Satoh, Noriyuki, and Takagi, Toshihisa
- Abstract
Abstract Background The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Results Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Conclusions Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.
- Published
- 2011
5. G-language genome analysis environment with REST and SOAP web service interfaces
- Author
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Arakawa, Kazuharu, Kido, Nobuhiro, Oshita, Kazuki, and Tomita, Masaru
- Published
- 2010
- Full Text
- View/download PDF
6. G-Links: a gene-centric link acquisition service
- Author
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Oshita, Kazuki, primary, Tomita, Masaru, additional, and Arakawa, Kazuharu, additional
- Published
- 2015
- Full Text
- View/download PDF
7. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
- Author
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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 JP, Buttigieg, Pier, Campbell, Matthew P, Chen, Yi-an, Chiba, Hirokazu, Cock, Peter JA, Cohen, K, 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, Mori, Takaaki, Mori, Hiroshi, Morita, Mizuki, Murakami, Katsuhiko, Nakao, Mitsuteru, Narimatsu, Hisashi, Nishide, Hiroyo, Nishimura, Yosuke, Nystrom-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, 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 JP, Buttigieg, Pier, Campbell, Matthew P, Chen, Yi-an, Chiba, Hirokazu, Cock, Peter JA, Cohen, K, 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, Mori, Takaaki, Mori, Hiroshi, Morita, Mizuki, Murakami, Katsuhiko, Nakao, Mitsuteru, Narimatsu, Hisashi, Nishide, Hiroyo, Nishimura, Yosuke, Nystrom-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, and Takagi, Toshihisa
- 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 BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.
- Published
- 2014
8. G-Links: a gene-centric link acquisition service
- Author
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Oshita, Kazuki, primary, Tomita, Masaru, additional, and Arakawa, Kazuharu, additional
- Published
- 2014
- Full Text
- View/download PDF
9. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
- Author
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Katayama, Toshiaki, primary, Wilkinson, Mark D, additional, Aoki-Kinoshita, Kiyoko F, additional, Kawashima, Shuichi, additional, Yamamoto, Yasunori, additional, Yamaguchi, Atsuko, additional, Okamoto, Shinobu, additional, Kawano, Shin, additional, Kim, Jin-Dong, additional, Wang, Yue, additional, Wu, Hongyan, additional, Kano, Yoshinobu, additional, Ono, Hiromasa, additional, Bono, Hidemasa, additional, Kocbek, Simon, additional, Aerts, Jan, additional, Akune, Yukie, additional, Antezana, Erick, additional, Arakawa, Kazuharu, additional, Aranda, Bruno, additional, Baran, Joachim, additional, Bolleman, Jerven, additional, Bonnal, Raoul JP, additional, Buttigieg, Pier, additional, Campbell, Matthew P, additional, Chen, Yi-an, additional, Chiba, Hirokazu, additional, Cock, Peter JA, additional, Cohen, K, additional, Constantin, Alexandru, additional, Duck, Geraint, additional, Dumontier, Michel, additional, Fujisawa, Takatomo, additional, Fujiwara, Toyofumi, additional, Goto, Naohisa, additional, Hoehndorf, Robert, additional, Igarashi, Yoshinobu, additional, Itaya, Hidetoshi, additional, Ito, Maori, additional, Iwasaki, Wataru, additional, Kalaš, Matúš, additional, Katoda, Takeo, additional, Kim, Taehong, additional, Kokubu, Anna, additional, Komiyama, Yusuke, additional, Kotera, Masaaki, additional, Laibe, Camille, additional, Lapp, Hilmar, additional, Lütteke, Thomas, additional, Marshall, M, additional, Mori, Takaaki, additional, Mori, Hiroshi, additional, Morita, Mizuki, additional, Murakami, Katsuhiko, additional, Nakao, Mitsuteru, additional, Narimatsu, Hisashi, additional, Nishide, Hiroyo, additional, Nishimura, Yosuke, additional, Nystrom-Persson, Johan, additional, Ogishima, Soichi, additional, Okamura, Yasunobu, additional, Okuda, Shujiro, additional, Oshita, Kazuki, additional, Packer, Nicki H, additional, Prins, Pjotr, additional, Ranzinger, Rene, additional, Rocca-Serra, Philippe, additional, Sansone, Susanna, additional, Sawaki, Hiromichi, additional, Shin, Sung-Ho, additional, Splendiani, Andrea, additional, Strozzi, Francesco, additional, Tadaka, Shu, additional, Toukach, Philip, additional, Uchiyama, Ikuo, additional, Umezaki, Masahito, additional, Vos, Rutger, additional, Whetzel, Patricia L, additional, Yamada, Issaku, additional, Yamasaki, Chisato, additional, Yamashita, Riu, additional, York, William S, additional, Zmasek, Christian M, additional, Kawamoto, Shoko, additional, and Takagi, Toshihisa, additional
- Published
- 2014
- Full Text
- View/download PDF
10. The 3rd DBCLS BioHackathon:improving life science data integration with semantic Web technologies
- Author
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Katayama, Toshiaki, Wilkinson, Mark D, Micklem, Gos, Kawashima, Shuichi, Yamaguchi, Atsuko, Nakao, Mitsuteru, Yamamoto, Yasunori, Okamoto, Shinobu, Oouchida, Kenta, Chun, Hong-Woo, Aerts, Jan, Afzal, Hammad, Antezana, Erick, Arakawa, Kazuharu, Aranda, Bruno, Belleau, Francois, Bolleman, Jerven, Bonnal, Raoul Jean, Chapman, Brad, Cock, Peter, Eriksson, Tore, Gordon, Paul, Goto, Naohisa, Hayashi, Kazuhiro, Horn, Heiko, Ishiwata, Ryosuke, Kaminuma, Eli, Kasprzyk, Arek, Kawaji, Hideya, Kido, Nobuhiro, Kim, Young Joo, Kinjo, Akira R, Konishi, Fumikazu, Kwon, Kyung-Hoon, Labarga, Alberto, Lamprecht, Anna-Lena, Lin, Yu, Lindenbaum, Pierre, McCarthy, Luke, Morita, Hideyuki, Murakami, Katsuhiko, Nagao, Koji, Nishida, Kozo, Nishimura, Kunihiro, Nishizawa, Tatsuya, Ogishima, Soichi, Ono, Keiichiro, Oshita, Kazuki, Park, Keun-Joon, Prins, Pjotr, Saito, Taro L, Samwald, Matthias, Satagopam, Venkata P, Shigemoto, Yasumasa, Smith, Richard, Splendiani, Andrea, Sugawara, Hideaki, Taylor, James, Vos, Rutger, Withers, David, Yamasaki, Chisato, Zmasek, Christian M, Kawamoto, Shoko, Okubo, Kosaku, Asai, Kiyoshi, Takagi, Toshihisa, Katayama, Toshiaki, Wilkinson, Mark D, Micklem, Gos, Kawashima, Shuichi, Yamaguchi, Atsuko, Nakao, Mitsuteru, Yamamoto, Yasunori, Okamoto, Shinobu, Oouchida, Kenta, Chun, Hong-Woo, Aerts, Jan, Afzal, Hammad, Antezana, Erick, Arakawa, Kazuharu, Aranda, Bruno, Belleau, Francois, Bolleman, Jerven, Bonnal, Raoul Jean, Chapman, Brad, Cock, Peter, Eriksson, Tore, Gordon, Paul, Goto, Naohisa, Hayashi, Kazuhiro, Horn, Heiko, Ishiwata, Ryosuke, Kaminuma, Eli, Kasprzyk, Arek, Kawaji, Hideya, Kido, Nobuhiro, Kim, Young Joo, Kinjo, Akira R, Konishi, Fumikazu, Kwon, Kyung-Hoon, Labarga, Alberto, Lamprecht, Anna-Lena, Lin, Yu, Lindenbaum, Pierre, McCarthy, Luke, Morita, Hideyuki, Murakami, Katsuhiko, Nagao, Koji, Nishida, Kozo, Nishimura, Kunihiro, Nishizawa, Tatsuya, Ogishima, Soichi, Ono, Keiichiro, Oshita, Kazuki, Park, Keun-Joon, Prins, Pjotr, Saito, Taro L, Samwald, Matthias, Satagopam, Venkata P, Shigemoto, Yasumasa, Smith, Richard, Splendiani, Andrea, Sugawara, Hideaki, Taylor, James, Vos, Rutger, Withers, David, Yamasaki, Chisato, Zmasek, Christian M, Kawamoto, Shoko, Okubo, Kosaku, Asai, Kiyoshi, and Takagi, Toshihisa
- Abstract
BACKGROUND: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. RESULTS: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. CONCLUSION: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.
- Published
- 2013
11. GEMBASSY: an EMBOSS associated software package for comprehensive genome analyses
- Author
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Itaya, Hidetoshi, primary, Oshita, Kazuki, additional, Arakawa, Kazuharu, additional, and Tomita, Masaru, additional
- Published
- 2013
- Full Text
- View/download PDF
12. Quantitative assay for TALEN activity at endogenous genomic loci
- Author
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Hisano, Yu, primary, Ota, Satoshi, additional, Arakawa, Kazuharu, additional, Muraki, Michiko, additional, Kono, Nobuaki, additional, Oshita, Kazuki, additional, Sakuma, Tetsushi, additional, Tomita, Masaru, additional, Yamamoto, Takashi, additional, Okada, Yasushi, additional, and Kawahara, Atsuo, additional
- Published
- 2013
- Full Text
- View/download PDF
13. KBWS: an EMBOSS associated package for accessing bioinformatics web services
- Author
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Oshita, Kazuki, primary, Arakawa, Kazuharu, additional, and Tomita, Masaru, additional
- Published
- 2011
- Full Text
- View/download PDF
14. Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API
- Author
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Kono, Nobuaki, primary, Arakawa, Kazuharu, additional, Ogawa, Ryu, additional, Kido, Nobuhiro, additional, Oshita, Kazuki, additional, Ikegami, Keita, additional, Tamaki, Satoshi, additional, and Tomita, Masaru, additional
- Published
- 2009
- Full Text
- View/download PDF
15. A web server for interactive and zoomable Chaos Game Representation images
- Author
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Arakawa, Kazuharu, primary, Oshita, Kazuki, additional, and Tomita, Masaru, additional
- Published
- 2009
- Full Text
- View/download PDF
16. Volume Measurement of Municipal Solid Waste in a Hopper Using the Stereo Image Processing Technique
- Author
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Itoh, Daisuke, primary, Takaoka, Masaki, additional, Nakatsuka, Daisuke, additional, Kakuta, Yoshitada, additional, Takeda, Nobuo, additional, Fujiwara, Takeshi, additional, and Oshita, Kazuki, additional
- Published
- 2005
- Full Text
- View/download PDF
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