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60 Publications visible to you, out of a total of 60
Taverna: a tool for building and running workflows of services

Abstract (Expand)

Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services. It allows bioinformaticians … to construct workflows or pipelines of services to perform a range of different analyses, such as sequence analysis and genome annotation. These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from http://taverna.sourceforge.net/.

Authors: Duncan Hull, Firstname Lastname, Robert Stevens, Firstname Lastname, Mathew R Pocock, Peter Li, Tom Oinn

Date Published: 18th Jul 2006

Publication Type: Not specified

The dynamic architecture of the metabolic switch in Streptomyces coelicolor

Abstract (Expand)

BACKGROUND: During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene … expression patterns during this switch, using a specifically designed Affymetrix genechip and a high-resolution time-series of fermenter-grown samples. RESULTS: Surprisingly, we find that the metabolic switch actually consists of multiple finely orchestrated switching events. Strongly coherent clusters of genes show drastic changes in gene expression already many hours before the classically defined transition phase where the switch from primary to secondary metabolism was expected. The main switch in gene expression takes only 2 hours, and changes in antibiotic biosynthesis genes are delayed relative to the metabolic rearrangements. Furthermore, global variation in morphogenesis genes indicates an involvement of cell differentiation pathways in the decision phase leading up to the commitment to antibiotic biosynthesis. CONCLUSIONS: Our study provides the first detailed insights into the complex sequence of early regulatory events during and preceding the major metabolic switch in S. coelicolor, which will form the starting point for future attempts at engineering antibiotic production in a biotechnological setting.

Authors: Kay Nieselt, Florian Battke, Alexander Herbig, Per Bruheim, Alexander Wentzel, Øyvind M Jakobsen, Håvard Sletta, Mohammad T Alam, Maria E Merlo, Firstname Lastname, Firstname Lastname, Edward R Morrissey, Miguel A Juarez-Hermosillo, Antonio Rodríguez-García, Merle Nentwich, Louise Thomas, Mudassar Iqbal, Roxane Legaie, William H Gaze, Gregory L Challis, Ritsert C Jansen, Lubbert Dijkhuizen, David A Rand, David L Wild, Michael Bonin, Jens Reuther, Wolfgang Wohlleben, Margaret C M Smith, Nigel J Burroughs, Juan F Martín, David A Hodgson, Eriko Takano, Rainer Breitling, Trond E Ellingsen, Elizabeth M H Wellington

Date Published: 28th May 2009

Publication Type: Not specified

The FAIR Guiding Principles for scientific data management and stewardship

Abstract (Expand)

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have … come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

Author: Mark D. Wilkinson, Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E. Bourne, Jildau Bouwman, Anthony J. Brookes, Tim Clark, Mercè Crosas, Ingr Mons

Date Published: 15th Mar 2016

Publication Type: Not specified

The NOVA project: maximizing beam time efficiency through synergistic analyses of SRμCT data

Abstract

Not specified

Authors: Sebastian Schmelzle, Thomas van de Kamp, Michael Heethoff, Vincent Heuveline, Philipp Lösel, Jürgen Becker, Felix Beckmann, Frank Schluenzen, Jörg U. Hammel, Andreas Kopmann, Wolfgang Mexner, Matthias Vogelgesang, Nicholas T. Jerome, Oliver Betz, Rolf Beutel, Benjamin Wipfler, Alexander Blanke, Steffen Harzsch, Marie Hörnig, Tilo Baumbach

Date Published: 7th Sep 2017

Publication Type: Not specified

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud

Abstract

Not specified

Authors: K. Wolstencroft, R. Haines, D. Fellows, A. Williams, D. Withers, S. Owen, S. Soiland-Reyes, I. Dunlop, A. Nenadic, P. Fisher, J. Bhagat, K. Belhajjame, F. Bacall, A. Hardisty, A. Nieva de la Hidalga, M. P. Balcazar Vargas, S. Sufi, C. Goble

Date Published: 2nd May 2013

Publication Type: Not specified

The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels

Abstract (Expand)

The African annual fish Nothobranchius furzeri has over recent years been established as a model species for ageing-related studies. This is mainly based on its exceptionally short lifespan and the … presence of typical characteristics of vertebrate ageing. To substantiate its role as an alternative vertebrate ageing model, a transcript catalogue is needed, which can serve e.g. as basis for identifying ageing-related genes.

Authors: Andreas Petzold, Kathrin Reichwald, Marco Groth, Stefan Taudien, Nils Hartmann, Steffen Priebe, Dmitry Shagin, Christoph Englert, Matthias Platzer

Date Published: 16th Mar 2013

Publication Type: Not specified

The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels

Abstract (Expand)

The African annual fish Nothobranchius furzeri has over recent years been established as a model species for ageing-related studies. This is mainly based on its exceptionally short lifespan and the … presence of typical characteristics of vertebrate ageing. To substantiate its role as an alternative vertebrate ageing model, a transcript catalogue is needed, which can serve e.g. as basis for identifying ageing-related genes.

Authors: Andreas Petzold, Kathrin Reichwald, Marco Groth, Stefan Taudien, Nils Hartmann, Steffen Priebe, Dmitry Shagin, Christoph Englert, Matthias Platzer

Date Published: 16th Mar 2013

Publication Type: Not specified

The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels

Abstract (Expand)

The African annual fish Nothobranchius furzeri has over recent years been established as a model species for ageing-related studies. This is mainly based on its exceptionally short lifespan and the … presence of typical characteristics of vertebrate ageing. To substantiate its role as an alternative vertebrate ageing model, a transcript catalogue is needed, which can serve e.g. as basis for identifying ageing-related genes.

Authors: Andreas Petzold, Kathrin Reichwald, Marco Groth, Stefan Taudien, Nils Hartmann, Steffen Priebe, Dmitry Shagin, Christoph Englert, Matthias Platzer

Date Published: 16th Mar 2013

Publication Type: Not specified

Toward Community Standards and Software for Whole-Cell Modeling.

Abstract

Whole-cell (WC) modeling is a promising tool for biological research, bioengineering, and medicine. However, substantial work remains to create accurate comprehensive models of complex cells.

Authors: Dagmar Waltemath, Jonathan R Karr, Frank T Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J Myers, Pinar Pir, Begum Alaybeyoglu, Naveen K Aranganathan, Kambiz Baghalian, Arne T Bittig, Paulo E Pinto Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S Costa, Joseph Cursons, Tobias Czauderna, Arthur P Goldberg, Harold F Gomez, Jens Hahn, Tuure Hameri, Daniel F Hernandez Gardiol, Denis Kazakiewicz, Ilya Kiselev, Vincent Knight-Schrijver, Christian Knupfer, Matthias Konig, Daewon Lee, Audald Lloret-Villas, Nikita Mandrik, J Kyle Medley, Bertrand Moreau, Hojjat Naderi-Meshkin, Sucheendra K Palaniappan, Daniel Priego-Espinosa, Martin Scharm, Mahesh Sharma, Kieran Smallbone, Natalie J Stanford, Je-Hoon Song, Tom Theile, Milenko Tokic, Namrata Tomar, Vasundra Toure, Jannis Uhlendorf, Thawfeek M Varusai, Leandro H Watanabe, Florian Wendland, Markus Wolfien, James T Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber

Date Published: 24th Sep 2016

Publication Type: Not specified

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