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The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.
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Thursday, June 29 • 15:40 - 17:00
P25: Galaxy and the full spectrum of needs in a small-scale cancer study

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Authors
Christin Lund-Andersen 1, Ståle Nygård 2,3, Stein Larsen 4, Eivind Hovig 1,3  , Kjersti Flatmark 1,3,4  

1 : Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
2 : Bioinformatics Core Facility, Institute for Medical Informatics, Oslo University Hospital.
3 : University of Oslo, Oslo, Norway
4 : Department of Gastroenterological Surgery, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway


Abstract
In small research groups with limited bioinformatics capabilities, there is a need for analyzing various forms of sequencing data in a simple, comprehensive, time and cost effective manner. Galaxy potentially offers the ideal solution for such a situation, providing standardized workflows for a variety of analytical scenarios in a unified framework. However, in a given institutional context, there may be a variety of practical obstacles.

We will in the poster present analytical needs and practical obstacles faced in a concrete small-scale research project concerning a patient with peritoneal mesothelioma that responded extremely well to chemotherapy but needed additional treatment options. We performed exome, RNA and miRNA sequencing on tumor samples, and ran a variety of bioinformatics analyses, e.g. detection of somatic variants, copy number variation, mutational signatures, and differential gene and miRNA expression. While the needed bioinformatics methods are available in public Galaxy server(s), one is still dependent on experience with all involved methodologies to make appropriate choices of methods and parameters according to the specifics of the data and research questions. The required competence is available locally through collaboration with various bioinformaticians, where only some offer to provide their analyses through a (public or local) Galaxy platform. This may be due to personal inclinations or technical challenges like running Galaxy within a secure environment. The poster will present the analyses performed for the case, and argue that to truly reach the potential for simplification and streamlining, it is crucial that Galaxy can be used for all involved bioinformatics analyses.

Presenters
CL

Christin Lund-Andersen

Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway


Thursday June 29, 2017 15:40 - 17:00
Le Corum Le Corum

Attendees (1)