WormQTL – Public archive and analysis web portal for C. elegans natural variation data

L.B. Snoek, Y. Li, J.K. van der Velde, D. Arends, A. Beyer, M. Elvin, J. Fisher, A. Hajnal, M. Hengartner, G. Poulin, M. Rodriguez Sanchez, T. Schmid, S. Schrimpf, F. Xue, X. Zheng, R.C. Jansen, J.E. Kammenga, M.A. Swertz

Research output: Chapter in Book/Report/Conference proceedingAbstract

Abstract

WormQTL – Public archive and analysis web portal for C. elegans natural variation data Basten L Snoek¹, Yang Li², Joeri K van der Velde², Danny Arends², Antje Beyer³, Mark Elvin 4, Jasmin Fisher³, Alex Hajnal5, Michael Hengartner5, Gino B Poulin4, Miriam Rodriguez¹,Tobias Schmid5, Sabine Schrimpf5, Feng Xue4, Xue Zheng5 , Ritsert C Jansen², Jan E Kammenga¹, Morris A Swertz2,6 1Wageningen University, Nematology, Wageningen, 7608PB, Netherlands, ²University of Groningen, Bioinformatics Centre, Groningen, 9747AG, Netherlands, ³Microsoft Research, Programming Principles and Tools, Cambridge, CB3 0FB, United Kingdom, 4 University of Manchester, Life Sciences, Manchester, M13 9PT, United Kingdom, 5University of Zurich, Molecular Life Sciences, Zurich, CH-8057, Switzerland, 6University Medical Centre, Genomics Coordination, Groningen, 9700RB, Netherlands Over the past decade increased efforts have been made to explore the model species C. elegans as a platform for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a huge amount of phenotypic and genotypic data across developmental worm stages and environments. To facilitate the accessibility, comparative analysis and meta-analysis of all these data we present WormQTL, a public web portal for the management of all these new data and for integrated development of suitable analysis tools. The web server provides a rich set of data and analysis tools available for direct use, based on R/qtl software. But users can also upload and share new scripts as ‘plugin’ for colleagues in the community. Furthermore, new data can be uploaded and downloaded using XGAP, which is an extensible text format for genotypes and phenotypes (Swertz et al. 2010a). All data and tools can be accessed via web user interfaces and programming interfaces. Large consortia as well as individual researchers can make use of a private area that is under embargo for publication. All software is free for download as MOLGENIS ‘app’ (Swertz et al. 2010b). WormQTL is freely accessible without registration and is hosted on a large computational cluster enabling high throughput analyses. We present WormQTL as an online scalable system for QTL exploration to service the worm community. WormQTL provides many publicly available datasets and welcomes submissions from other worm researchers. Funding: The Centre for BioSystems Genomics (CBSG) and the Netherlands Consortium of Systems Biology (NCSB), both of which are part of the Netherlands Genomics Initiative / Netherlands Organisation for Scientific Research and the EU 7th Framework Programme under the Research Project PANACEA, contract nr 222936.
Original languageEnglish
Title of host publicationAbstracts of papers presented at the Evolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA, 3-6 April 2012
Pages48-48
Publication statusPublished - 2012
EventEvolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA -
Duration: 3 Apr 20126 Apr 2012

Conference

ConferenceEvolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA
Period3/04/126/04/12

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life science
genomics
software
bioinformatics
meta-analysis
analysis
public
accessibility
phenotype
genotype
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research project
scientific research
co-ordination
programme
services

Cite this

Snoek, L. B., Li, Y., van der Velde, J. K., Arends, D., Beyer, A., Elvin, M., ... Swertz, M. A. (2012). WormQTL – Public archive and analysis web portal for C. elegans natural variation data. In Abstracts of papers presented at the Evolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA, 3-6 April 2012 (pp. 48-48)
Snoek, L.B. ; Li, Y. ; van der Velde, J.K. ; Arends, D. ; Beyer, A. ; Elvin, M. ; Fisher, J. ; Hajnal, A. ; Hengartner, M. ; Poulin, G. ; Rodriguez Sanchez, M. ; Schmid, T. ; Schrimpf, S. ; Xue, F. ; Zheng, X. ; Jansen, R.C. ; Kammenga, J.E. ; Swertz, M.A. / WormQTL – Public archive and analysis web portal for C. elegans natural variation data. Abstracts of papers presented at the Evolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA, 3-6 April 2012. 2012. pp. 48-48
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title = "WormQTL – Public archive and analysis web portal for C. elegans natural variation data",
abstract = "WormQTL – Public archive and analysis web portal for C. elegans natural variation data Basten L Snoek¹, Yang Li², Joeri K van der Velde², Danny Arends², Antje Beyer³, Mark Elvin 4, Jasmin Fisher³, Alex Hajnal5, Michael Hengartner5, Gino B Poulin4, Miriam Rodriguez¹,Tobias Schmid5, Sabine Schrimpf5, Feng Xue4, Xue Zheng5 , Ritsert C Jansen², Jan E Kammenga¹, Morris A Swertz2,6 1Wageningen University, Nematology, Wageningen, 7608PB, Netherlands, ²University of Groningen, Bioinformatics Centre, Groningen, 9747AG, Netherlands, ³Microsoft Research, Programming Principles and Tools, Cambridge, CB3 0FB, United Kingdom, 4 University of Manchester, Life Sciences, Manchester, M13 9PT, United Kingdom, 5University of Zurich, Molecular Life Sciences, Zurich, CH-8057, Switzerland, 6University Medical Centre, Genomics Coordination, Groningen, 9700RB, Netherlands Over the past decade increased efforts have been made to explore the model species C. elegans as a platform for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a huge amount of phenotypic and genotypic data across developmental worm stages and environments. To facilitate the accessibility, comparative analysis and meta-analysis of all these data we present WormQTL, a public web portal for the management of all these new data and for integrated development of suitable analysis tools. The web server provides a rich set of data and analysis tools available for direct use, based on R/qtl software. But users can also upload and share new scripts as ‘plugin’ for colleagues in the community. Furthermore, new data can be uploaded and downloaded using XGAP, which is an extensible text format for genotypes and phenotypes (Swertz et al. 2010a). All data and tools can be accessed via web user interfaces and programming interfaces. Large consortia as well as individual researchers can make use of a private area that is under embargo for publication. All software is free for download as MOLGENIS ‘app’ (Swertz et al. 2010b). WormQTL is freely accessible without registration and is hosted on a large computational cluster enabling high throughput analyses. We present WormQTL as an online scalable system for QTL exploration to service the worm community. WormQTL provides many publicly available datasets and welcomes submissions from other worm researchers. Funding: The Centre for BioSystems Genomics (CBSG) and the Netherlands Consortium of Systems Biology (NCSB), both of which are part of the Netherlands Genomics Initiative / Netherlands Organisation for Scientific Research and the EU 7th Framework Programme under the Research Project PANACEA, contract nr 222936.",
author = "L.B. Snoek and Y. Li and {van der Velde}, J.K. and D. Arends and A. Beyer and M. Elvin and J. Fisher and A. Hajnal and M. Hengartner and G. Poulin and {Rodriguez Sanchez}, M. and T. Schmid and S. Schrimpf and F. Xue and X. Zheng and R.C. Jansen and J.E. Kammenga and M.A. Swertz",
year = "2012",
language = "English",
pages = "48--48",
booktitle = "Abstracts of papers presented at the Evolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA, 3-6 April 2012",

}

Snoek, LB, Li, Y, van der Velde, JK, Arends, D, Beyer, A, Elvin, M, Fisher, J, Hajnal, A, Hengartner, M, Poulin, G, Rodriguez Sanchez, M, Schmid, T, Schrimpf, S, Xue, F, Zheng, X, Jansen, RC, Kammenga, JE & Swertz, MA 2012, WormQTL – Public archive and analysis web portal for C. elegans natural variation data. in Abstracts of papers presented at the Evolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA, 3-6 April 2012. pp. 48-48, Evolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA, 3/04/12.

WormQTL – Public archive and analysis web portal for C. elegans natural variation data. / Snoek, L.B.; Li, Y.; van der Velde, J.K.; Arends, D.; Beyer, A.; Elvin, M.; Fisher, J.; Hajnal, A.; Hengartner, M.; Poulin, G.; Rodriguez Sanchez, M.; Schmid, T.; Schrimpf, S.; Xue, F.; Zheng, X.; Jansen, R.C.; Kammenga, J.E.; Swertz, M.A.

Abstracts of papers presented at the Evolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA, 3-6 April 2012. 2012. p. 48-48.

Research output: Chapter in Book/Report/Conference proceedingAbstract

TY - CHAP

T1 - WormQTL – Public archive and analysis web portal for C. elegans natural variation data

AU - Snoek, L.B.

AU - Li, Y.

AU - van der Velde, J.K.

AU - Arends, D.

AU - Beyer, A.

AU - Elvin, M.

AU - Fisher, J.

AU - Hajnal, A.

AU - Hengartner, M.

AU - Poulin, G.

AU - Rodriguez Sanchez, M.

AU - Schmid, T.

AU - Schrimpf, S.

AU - Xue, F.

AU - Zheng, X.

AU - Jansen, R.C.

AU - Kammenga, J.E.

AU - Swertz, M.A.

PY - 2012

Y1 - 2012

N2 - WormQTL – Public archive and analysis web portal for C. elegans natural variation data Basten L Snoek¹, Yang Li², Joeri K van der Velde², Danny Arends², Antje Beyer³, Mark Elvin 4, Jasmin Fisher³, Alex Hajnal5, Michael Hengartner5, Gino B Poulin4, Miriam Rodriguez¹,Tobias Schmid5, Sabine Schrimpf5, Feng Xue4, Xue Zheng5 , Ritsert C Jansen², Jan E Kammenga¹, Morris A Swertz2,6 1Wageningen University, Nematology, Wageningen, 7608PB, Netherlands, ²University of Groningen, Bioinformatics Centre, Groningen, 9747AG, Netherlands, ³Microsoft Research, Programming Principles and Tools, Cambridge, CB3 0FB, United Kingdom, 4 University of Manchester, Life Sciences, Manchester, M13 9PT, United Kingdom, 5University of Zurich, Molecular Life Sciences, Zurich, CH-8057, Switzerland, 6University Medical Centre, Genomics Coordination, Groningen, 9700RB, Netherlands Over the past decade increased efforts have been made to explore the model species C. elegans as a platform for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a huge amount of phenotypic and genotypic data across developmental worm stages and environments. To facilitate the accessibility, comparative analysis and meta-analysis of all these data we present WormQTL, a public web portal for the management of all these new data and for integrated development of suitable analysis tools. The web server provides a rich set of data and analysis tools available for direct use, based on R/qtl software. But users can also upload and share new scripts as ‘plugin’ for colleagues in the community. Furthermore, new data can be uploaded and downloaded using XGAP, which is an extensible text format for genotypes and phenotypes (Swertz et al. 2010a). All data and tools can be accessed via web user interfaces and programming interfaces. Large consortia as well as individual researchers can make use of a private area that is under embargo for publication. All software is free for download as MOLGENIS ‘app’ (Swertz et al. 2010b). WormQTL is freely accessible without registration and is hosted on a large computational cluster enabling high throughput analyses. We present WormQTL as an online scalable system for QTL exploration to service the worm community. WormQTL provides many publicly available datasets and welcomes submissions from other worm researchers. Funding: The Centre for BioSystems Genomics (CBSG) and the Netherlands Consortium of Systems Biology (NCSB), both of which are part of the Netherlands Genomics Initiative / Netherlands Organisation for Scientific Research and the EU 7th Framework Programme under the Research Project PANACEA, contract nr 222936.

AB - WormQTL – Public archive and analysis web portal for C. elegans natural variation data Basten L Snoek¹, Yang Li², Joeri K van der Velde², Danny Arends², Antje Beyer³, Mark Elvin 4, Jasmin Fisher³, Alex Hajnal5, Michael Hengartner5, Gino B Poulin4, Miriam Rodriguez¹,Tobias Schmid5, Sabine Schrimpf5, Feng Xue4, Xue Zheng5 , Ritsert C Jansen², Jan E Kammenga¹, Morris A Swertz2,6 1Wageningen University, Nematology, Wageningen, 7608PB, Netherlands, ²University of Groningen, Bioinformatics Centre, Groningen, 9747AG, Netherlands, ³Microsoft Research, Programming Principles and Tools, Cambridge, CB3 0FB, United Kingdom, 4 University of Manchester, Life Sciences, Manchester, M13 9PT, United Kingdom, 5University of Zurich, Molecular Life Sciences, Zurich, CH-8057, Switzerland, 6University Medical Centre, Genomics Coordination, Groningen, 9700RB, Netherlands Over the past decade increased efforts have been made to explore the model species C. elegans as a platform for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a huge amount of phenotypic and genotypic data across developmental worm stages and environments. To facilitate the accessibility, comparative analysis and meta-analysis of all these data we present WormQTL, a public web portal for the management of all these new data and for integrated development of suitable analysis tools. The web server provides a rich set of data and analysis tools available for direct use, based on R/qtl software. But users can also upload and share new scripts as ‘plugin’ for colleagues in the community. Furthermore, new data can be uploaded and downloaded using XGAP, which is an extensible text format for genotypes and phenotypes (Swertz et al. 2010a). All data and tools can be accessed via web user interfaces and programming interfaces. Large consortia as well as individual researchers can make use of a private area that is under embargo for publication. All software is free for download as MOLGENIS ‘app’ (Swertz et al. 2010b). WormQTL is freely accessible without registration and is hosted on a large computational cluster enabling high throughput analyses. We present WormQTL as an online scalable system for QTL exploration to service the worm community. WormQTL provides many publicly available datasets and welcomes submissions from other worm researchers. Funding: The Centre for BioSystems Genomics (CBSG) and the Netherlands Consortium of Systems Biology (NCSB), both of which are part of the Netherlands Genomics Initiative / Netherlands Organisation for Scientific Research and the EU 7th Framework Programme under the Research Project PANACEA, contract nr 222936.

M3 - Abstract

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EP - 48

BT - Abstracts of papers presented at the Evolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA, 3-6 April 2012

ER -

Snoek LB, Li Y, van der Velde JK, Arends D, Beyer A, Elvin M et al. WormQTL – Public archive and analysis web portal for C. elegans natural variation data. In Abstracts of papers presented at the Evolution of Caenorhabditis and Other Nematodes, Cold Spring Harbor Laboratory, New York, USA, 3-6 April 2012. 2012. p. 48-48