Loading…
GCC BOSC 2018 has ended
The 2018 Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference 2018 (BOSC2018) are meeting together in Portland, Oregon, United States, June 25-30, 2018.  There will be two days of training, a two+ day meeting, and four days of intense collaboration.  The meeting features joint & parallel sessions, shared keynotes, poster & demo sessions, birds-of-a-feather, and social events.  GCCBOSC is organized by Oregon Health & Science University and will be at Reed College.

avatar for Arthur Eschenlauer

Arthur Eschenlauer

University of Minnesota
Postdoc
Twin Cities, MN
Poster Abstract:
Untargeted metabolomics contrasts metabolome-scale analyses of samples without first identifying individual metabolites. Workflow4Metabolomics (W4m) provides a suite of Galaxy tools for untargeted metabolomics including univariate and multivariate statistical tools and tools for preprocessing LC-MS, GC-MS, and NMR spectra. W4m Data Subset (w4mclassfilter) conditions data for statistical analysis by providing:
- feature- and sample-selection;
- metadata-filtering;
- intensity-thresholding;
- log-transformation;
- elimination of zero-variance data;
- imputation of missing values to zero.

We have created four additional tools to simplify or extend the use of W4m in our lab: W4m Data Subset, OPLS-DA Contrasts, Join +/- Ions, and w4mkmeans. We have also "adopted" the Query Tabular tool to further simplify and extend our data workflows. The tools are available in the public Galaxy Toolshed.
We demonstrate how these tools complement W4m with a data-processing workflow assessing the effect of pathogen inoculation on resin-collection by honey bee colonies.
Wednesday, June 27
 

9:01am PDT

Keynote: Fernando Pérez--"Sustainable development of scientific open source tools: a view from Jupyter" Vollum Lecture HallFernando Pérez

10:00am PDT

10:50am PDT

10:51am PDT

11:10am PDT

11:30am PDT

11:50am PDT

11:56am PDT

12:02pm PDT

1:40pm PDT

1:41pm PDT

2:00pm PDT

2:20pm PDT

2:40pm PDT

3:01pm PDT

4:20pm PDT

 
Thursday, June 28
 

9:00am PDT

9:40am PDT

10:00am PDT

10:50am PDT

10:51am PDT

11:10am PDT

11:30am PDT

11:50am PDT

11:56am PDT

12:02pm PDT

12:30pm PDT

1:40pm PDT

1:41pm PDT

2:10pm PDT

2:16pm PDT

2:46pm PDT

2:52pm PDT

3:01pm PDT

B22: Code is Science: a manifesto for open source code in science PAB AtriumYo Yehudi B36: Understanding reproducibility of bioinformatics workflows PAB AtriumSehrish Kanwal B40: Running portable workflow and container specifications at production scale in the cloud: strategy & best practices PAB AtriumGeet Duggal B42: The GA4GH/DREAM Workflow Execution Challenge PAB AtriumJames Eddy D02: Adding R shiny apps as Galaxy interactive environment. A Galaxy-E demo PAB AtriumValintin Chambon D06: Distributed execution of bioinformatics tools on Apache Spark with ADAM and Cannoli PAB AtriumMichael Heuer G02: Testing Wide-Area Lustre File Systems for Sharing load in Galaxy PAB AtriumCarrie Ganote G06: Galaxy2Shiny2Galaxy - Combining Galaxy with Shiny (and doing other bad things) PAB AtriumHans-Rudolf Hotz G12: Canada's Integrated Rapid Infectious Disease Analysis Platform (IRIDA) PAB AtriumThomas Matthews G18: CRAVAT (Cancer-Related Analysis of Variants Toolkit) integration into Galaxy-P and extension towards proteogenomic studies PAB AtriumRay Sajulga G24: New tools to enhance the Galaxy-based metabolomics workbench PAB AtriumArthur Eschenlauer G26: ISAcreate: a Galaxy tool for Prospective Data Management with ISA format support - Application to Metabolomics Datasets PAB AtriumPhilippe Rocca-Serra G28: EDAM: the ontology of bioinformatics operations, types of data, topics, and data formats (2018 update) PAB AtriumHervé Ménager G32: Results of an Extended Developer Support consultation with the CloudLaunch project PAB AtriumMarcus Christie

4:01pm PDT

5:00pm PDT

 
Friday, June 29
 

9:00am PDT