GCC2022

This session will feature invited and accepted talks.

This session will also be broadcast live to remote participants.

Delphine Lariviere, Dept. of Biochemistry and Molecular Biology, Penn State University, College Park, PA, USA
Giulio Formenti, The Rockefeller University, 1230 York Avenue New York, NY 10065, USA
Alex Ostrovsky, Dept. of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
Cristobal Gallardo, Dept. of Computer Science, University of Freiburg, Freiburg, Germany
Linelle Abueg, The Rockefeller University, 1230 York Avenue New York, NY 10065, USA
Nadolina Brajuka, The Rockefeller University, 1230 York Avenue New York, NY 10065, USA
Marc Palmada Flores, Institut de Biologia Evolutiva, Pompeu Fabra University, Barcelona, 08003, Spain
Anton Nekrutenko, Dept. of Biochemistry and Molecular Biology, Penn State University, College Park, PA, USA
Bjorn Grüning, Dept. of Computer Science, University of Freiburg, Freiburg, Germany
Michael Schatz Dept. of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA

​⇒ Abstract​​​

Monica E. Kruk, University of Minnesota
Subina Mehta, University of Minnesota
Katherine Do, University of Minnesota
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
Reid Wagner, Minnesota Supercomputing Institute, University of Minnesota
Chris Wendt, Minneapolis Veterans Administration Health Care System and University of Minnesota
John B. O’Connor, Ann & Robert H. Lurie Children’s Hospital of Chicago
Theresa Laguna, Ann & Robert H. Lurie Children’s Hospital of Chicago and Northwestern University Feinberg School of Medicine
Pratik D. Jagtap, University of Minnesota
Timothy J. Griffin, University of Minnesota

​⇒ Abstract​​​

Jeremy Goecks, Oregon Health & Science University
Björn Grüning, University of Freiburg

​⇒ Abstract​​​

Andrew T. Rajczewski, University of Minnesota
Efstathios Vryonidis, Stockholm University
Lorena Ndreu, Stockholm University
Gunnar Boysen, University of Arkansas for Medical Sciences
Subina Mehta, University of Minnesota
Pratik D. Jagtap, University of Minnesota
Timothy J. Griffin, University of Minnesota
Isabella Karlsson, Stockholm University
Margareta Törnqvist, Stockholm University
Natalia Y. Tretyakova, University of Minnesota
​⇒ Abstract​​​

Subina Mehta- University of Minnesota
Valdemir M. Carvalho - Fluery Group, Brazil
Andrew T. Rajczewski - University of Minnesota
Björn Grüning- University of Freiburg, Freiburg
James E. Johnson- University of Minnesota
Reid Wagner- University of Minnesota
Olivier Pible -DMT, Université Paris Saclay, Bagnols-sur-Cèze, France
Jean Armengaud- DMT, Université Paris Saclay, Bagnols-sur-Cèze, France
Timothy J. Griffin- University of Minnesota
Pratik D. Jagtap - University of Minnesota

​⇒ Abstract​​​

This session will feature invited and accepted talks.

This session will also be broadcast live to remote participants.

Reid Wagner, Minnesota Supercomputing Institute, University of Minnesota
Benjamin S. Toups, Dept. of Biological Sciences and Museum of Natural Science, Louisiana State University
Zhifeng Deng, Dept. of Mathematics, Florida State University
Thomas McGowan, Minnesota Supercomputing Institute, University of Minnesota
Kyle A. Gallivan, Dept. of Mathematics, Florida State University
Jeremy M. Brown, Dept. of Biological Sciences and Museum of Natural Science, Louisiana State University
James C. Wilgenbusch, Minnesota Supercomputing Institute, University of Minnesota

​⇒ Abstract​​​

Allison Creason, Oregon Health and Science University
Cameron Watson, Oregon Health and Science University
Qiang Gu, Oregon Health and Science University
Daniel Persson, Oregon Health and Science University
Luke Sargent, Oregon Health and Science University
Jeremy Goecks, Oregon Health and Science University

​⇒ Abstract​​​

Helge Hecht, RECETOX, Masaryk University
Martin Čech, RECETOX, Masaryk University
Matej Troják, RECETOX, Masaryk University
Maksym Skoryk, RECETOX, Masaryk University
Jiří Novotný, Institute of Computer Science, Masaryk University
Karolína Trachtová, RECETOX, Masaryk University
Aleš Křenek, Institute of Computer Science, Masaryk University
Elliott James Price, RECETOX, Masaryk University
Jana Klánová, RECETOX, Masaryk University
​⇒ Abstract

​​​Various tools for the processing of mass spectrometry (MS) data exist, though few of them have user friendly GUI interfaces, are built with scalability and robustness in mind, or deliver reproducible results. Many of them are also tied to specific frameworks, e.g bioconductor. There is a need for harmonization in data processing for MS based -omics.The Galaxy framework enables user-friendly access to an expandable set of tools and workflows hosted via compute infrastructure, bringing FAIR data principles to -omics data processing. We extended existing Galaxy resources with R and Python packages (i.e apLCMS, xMSannotator, RIAssigner, matchms, WaveICA , MSMetaEnhancer and RAMClustR) and compiled those into comprehensive end-to-end workflows for non-target analysis (NTA). These tools perform several steps (e.g., peak detection & deconvolution, spectral matching & annotation, batch correction & normalization and metadata curation) to enable end-to-end pre-processing of data acquired via gas chromatography (GC) coupled with MS.Through the demo, we will show how to operate various tools in a data processing pipeline to obtain reproducible and shareable results using an example GC-HRMS dataset. We will show how to choose parameters for peak detection & deconvolution specifically for GC-MS in contrast to LC-MS data and how these parameter choices affect the outputs. Subsequently, we will show how to incorporate retention index information from RIAssigner into the annotation using matchms to improve the chemical annotation. Besides the workflow for compound annotation, we also include tools enabling automated curation and expansion of metadata in associated mass spectral libraries.By applying the knowledge gained from the topics covered in this demo, the participants will be able to process their own MS data using Galaxy. All developments covered are open source and hosted on GitHub providing immediate access and creating a platform for scientific collaborations. Access to those resources is provided to the community by hosting a public instance of Galaxy and by uploading tools to the main tool shed.

Kelly E Nygren, Cornell High Energy Synchrotron Source
Werner Sun, Cornell High Energy Synchrotron Source
Devin Bougie, Cornell High Energy Synchrotron Source
Matt Miller, Cornell High Energy Synchrotron Source
Mehmet Hazar Seren, Cornell High Energy Synchrotron Source
Rolf Verberg, Cornell High Energy Synchrotron Source
Keara Soloway, Cornell High Energy Synchrotron Source
Bob Suter, Carnegie Mellon Department of Physics
Mark Zhuang, Science Gateway Institute. San Diego Supercomputing Center
Mark Miller, Science Gateway Institute. San Diego Supercomputing Center
James Johnson, Minnesota Supercomputing Institute
Jorge Vinals, Minnesota Supercomputing Institute

​⇒ Abstract​​​

Bryan Raubenolt - Genomic Medicine Institute,
Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
Daniel Blankenberg - Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA

​⇒ Abstract​​​

Fabio Cumbo, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
Daniel Blankenberg, Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA

​⇒ Abstract​​​