Now showing items 1-13 of 13

    • 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 ...
      Journal article
    • BioXSD: the common data-exchange format for everyday bioinformatics web services 

      Kalaš, Matúš; Puntervoll, Pål; Joseph, Alexandre; Bartaševičiūtė, Edita; Töpfer, Armin; Venkataraman, Prabakar; Pettifer, Steve; Bryne, Jan Christian; Ison, Jon; Blanchet, Christophe; Rapacki, Kristoffer; Jonassen, Inge (Oxford University Press, 2010)
      Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of ...
      Journal article
    • 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 ...
      Journal article
    • EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats 

      Ison, Jon; Kalaš, Matúš; Jonassen, Inge; Bolser, Dan; Uludag, Mahmut; McWilliam, Hamish; Malone, James; Lopez, Rodrigo; Pettifer, Steve; Rice, Peter (Oxford University Press, 2013)
      Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore ...
      Journal article
    • Efforts towards accessible and reliable bioinformatics 

      Kalaš, Matúš (The University of Bergen, 2015-11-19)
      The aim of the presented work was contributing to making scientific computing more accessible, reliable, and thus more efficient for researchers, primarily computational biologists and molecular biologists. Many approaches ...
      Doctoral thesis
    • The EMBRACE web service collection 

      Pettifer, Steve; Ison, Jon; Kalaš, Matúš; Thorne, David; McDermott, Philip; Jonassen, Inge; Ali, Liaquat; Fernandez, Jose M; Rodriguez, Jose M; Pisano, David G; Blanchet, Christophe; Uludag, Mahmut; Rice, Peter; Bartaseviciute, Edita; Rapacki, Kristoffer; Hekkelman, Maarten; Sand, Olivier; Stockinger, Heinz; Clegg, Andrew B; Bongcam-Rudloff, Eric; Salzemann, Jean; Breton, Vincent; Attwood, Teresa K; Cameron, Graham; Vriend, Gert (Oxford University Press (OUP), 2010-05-10)
      The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web ...
      Journal article
    • FreeContact: fast and free software for protein contact prediction from residue co-evolution 

      Kaján, László; Hopf, Thomas A.; Kalaš, Matúš; Marks, Debora S.; Rost, Burkhard (BioMed Central, 2014-03-26)
      Background: 20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations accurate enough to drive de novo predictions of protein ...
      Journal article
    • FreeContact: Fast and free software for protein contact prediction from residue co-evolution 

      Kaján, László; Hopf, Thomas A.; Kalaš, Matúš; Marks, Debora S.; Rost, Burkhard (BioMed Central, 2014-03-26)
      Background: 20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations accurate enough to drive de novo predictions of protein ...
      Journal article
    • The Genomic HyperBrowser: an analysis web server for genome-scale data 

      Sandve, Geir Kjetil; Gundersen, Sveinung; Johansen, Morten; Glad, Ingrid Kristine; Gunathasan, Krishanthi; Holden, Lars; Holden, Marit; Liestøl, Knut; Nygård, Ståle; Nygaard, Vegard; Paulsen, Jonas; Rydbeck, Halfdan; Trengereid, Kai; Clancy, Trevor; Drabløs, Finn; Ferkingstad, Egil; Kalaš, Matúš; Lien, Tonje Gulbrandsen; Rye, Morten Beck; Frigessi, Arnoldo; Hovig, Johannes Eivind (Oxford University Press (OUP), 2013-04-30)
      The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable ...
      Journal article
    • Identifying elemental genomic track types and representing them uniformly 

      Gundersen, Sveinung; Kalaš, Matúš; Abul, Osman; Frigessi, Arnoldo; Hovig, Eivind; Sandve, Geir Kjetil (BioMed Central, 2011-12-30)
      Background: With the recent advances and availability of various high-throughput sequencing technologies, data on many molecular aspects, such as gene regulation, chromatin dynamics, and the three-dimensional organization ...
      Journal article
    • Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis 

      Möller, Steffen; Prescott, Stuart W.; Wirzenius, Lars; Reinholdtsen, Petter; Chapman, Brad; Prins, Pjotr; Soiland-Reyes, Stian; Klötzl, Fabian; Bagnacani, Andrea; Kalaš, Matúš; Tille, Andreas; Crusoe, Michael R. (Springer, 2017-09)
      Information integration and workflow technologies for data analysis have always been major fields of investigation in bioinformatics. A range of popular workflow suites are available to support analyses in computational ...
      Journal article
    • Tools and data services registry: a community effort to document bioinformatics resources 

      Ison, Jon; Rapacki, Kristoffer; Ménager, Hervé; Kalaš, Matúš; et al., 69 authors (Oxford University Press, 2015-11-03)
      Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases ...
      Journal article
    • Using registries to integrate bioinformatics tools and services into workbench environments 

      Ménager, Hervé; Kalaš, Matúš; Rapacki, Kristoffer; Ison, Jon (Springer, 2015)
      The diversity and complexity of bioinformatics resources presents significant challenges to their localisation, deployment and use, creating a need for reliable systems that address these issues. Meanwhile, users demand ...
      Journal article