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SDA 7: A modular and parallel implementation of the simulation of diffusional association software

Abstract

Not specified

Authors: Michael Martinez, Neil J. Bruce, Julia Romanowska, Daria B. Kokh, Musa Ozboyaci, Xiaofeng Yu, Mehmet Ali Öztürk, Stefan Richter, Rebecca C. Wade

Date Published: 5th Aug 2015

Publication Type: Journal

Analyzing Complex and Structured Data via Unsupervised Learning Techniques

Abstract

Not specified

Authors: K. L. Polsterer, F. Gieseke, N. Gianniotis, S. D. Kuegler

Date Published: 1st Aug 2015

Publication Type: Journal

Type Ia supernovae from exploding oxygen-neon white dwarfs

Abstract

Not specified

Authors: Kai S. Marquardt, Stuart A. Sim, Ashley J. Ruiter, Ivo R. Seitenzahl, Sebastian T. Ohlmann, Markus Kromer, Rüdiger Pakmor, Friedrich K. Röpke

Date Published: 1st Aug 2015

Publication Type: Journal

Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation

Abstract

Not specified

Authors: Nadinath B. Nillegoda, Janine Kirstein, Anna Szlachcic, Mykhaylo Berynskyy, Antonia Stank, Florian Stengel, Kristin Arnsburg, Xuechao Gao, Annika Scior, Ruedi Aebersold, D. Lys Guilbride, Rebecca C. Wade, Richard I. Morimoto, Matthias P. Mayer, Bernd Bukau

Date Published: 1st Aug 2015

Publication Type: Journal

ExaML version 3: a tool for phylogenomic analyses on supercomputers

Abstract

Not specified

Authors: Alexey M. Kozlov, Andre J. Aberer, Alexandros Stamatakis

Date Published: 25th Jul 2015

Publication Type: Journal

SEEK: a systems biology data and model management platform.

Abstract (Expand)

BACKGROUND: Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools … and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing biological data of a particular type, for example transcriptomics or proteomics, and there are several model repositories. However, this silo-type storage of data and models is not conducive to systems biology investigations. Interdependencies between multiple omics datasets and between datasets and models are essential. Researchers require an environment that will allow the management and sharing of heterogeneous data and models in the context of the experiments which created them. RESULTS: The SEEK is a suite of tools to support the management, sharing and exploration of data and models in systems biology. The SEEK platform provides an access-controlled, web-based environment for scientists to share and exchange data and models for day-to-day collaboration and for public dissemination. A plug-in architecture allows the linking of experiments, their protocols, data, models and results in a configurable system that is available 'off the shelf'. Tools to run model simulations, plot experimental data and assist with data annotation and standardisation combine to produce a collection of resources that support analysis as well as sharing. Underlying semantic web resources additionally extract and serve SEEK metadata in RDF (Resource Description Format). SEEK RDF enables rich semantic queries, both within SEEK and between related resources in the web of Linked Open Data. CONCLUSION: The SEEK platform has been adopted by many systems biology consortia across Europe. It is a data management environment that has a low barrier of uptake and provides rich resources for collaboration. This paper provides an update on the functions and features of the SEEK software, and describes the use of the SEEK in the SysMO consortium (Systems biology for Micro-organisms), and the VLN (virtual Liver Network), two large systems biology initiatives with different research aims and different scientific communities.

Authors: K. Wolstencroft, S. Owen, O. Krebs, Q. Nguyen, N. J. Stanford, M. Golebiewski, A. Weidemann, M. Bittkowski, L. An, D. Shockley, J. L. Snoep, W. Mueller, C. Goble

Date Published: 15th Jul 2015

Publication Type: Journal

Deflagrations in hybrid CONe white dwarfs: a route to explain the faint Type Iax supernova 2008ha

Abstract

Not specified

Authors: M. Kromer, S. T. Ohlmann, R. Pakmor, A. J. Ruiter, W. Hillebrandt, K. S. Marquardt, F. K. Röpke, I. R. Seitenzahl, S. A. Sim, S. Taubenberger

Date Published: 1st Jul 2015

Publication Type: Journal

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