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SI Deliverables

A running tally of activity for Blake Joyce during his tenure as a CyVerse Science Informatician.

1. Discovery Environment Applications

Genetics Apps

  1. 2017.05 Sickle
  2. 2017.07 Fastq_screen
  3. 2017.10 SimPrily

2. Agave Applications

 

3. Scientific Workflows

  1. 2017.02 Connecting downstream annotation analysis tools to upstream CyVerse assembly and annotation tools
  2. 2017.02 Hitchhiker's Guide to Parallelizing Scientific Analysis

4. Atmosphere Images

  1. 2016.05 Trinity & Trinotate image for de novo transcriptomics
  2. 2017.10 Kaldi Speech Recognition Image

5. Bisque Modules

 

6. Public Datasets

  1. 2016.08 Population genetics of cancer Nathan Ellis and Gaius Augustus √
  2. 2017.01 EpiDB in CoGe and CyVerse
  3. 2017.02 Phenotyping data from James Schnable
  4. 2017.01 Stefan Rensing - Physcomitrella

7. Documentation & Tutorials

  1. 2016.08 De novo transcriptomics with non-model organisms

  2. 2017.07 Best Practices for Setting Up a Workshop on CyVerse

8. Outreach & Training

Webinars & Workshops

  1. CoGe methylation and epigenetics webinar
  2. 2016.12 UA EEB CyVerse + R workshop
  3. 2016.11 PLOTCON
  4. 2017.01 Society for Integrative Biology Non-model Comparative Transcriptomics in CyVerse workshop
  5. 2017.03 Non-model organism comparative transcriptomics
  6. 2017.06 Animal Genome 2 Phenome RCN & CyVerse Training
  7. 2017.06 Journey to the Compute - Two day Data Science Meetup

Community Building

  1. 2016.08 Research Bazaar Arizona

Peer-to-Peer Training

  1. 2016.08 Ashley Maynard - Oyster pop gen
  2. 2016.12 David Jones - Master's student
  3. 2016.12 Benchtop science to Bioinformatics - Carlos and Blake Training
  4. 2017.01 Ecological Modeling of Human Demographics - Ariella

  5. 2017.02 ISTA Capstone Project - Advanced Visualizations

Conferences

  1. 2017.02 Phenome 2017

Links to Calendar of Events

  1. 2016 Events
  2. 2017 Events

9. Extended Community Support

Edit View

  1. Animal Genome to Phenome RCN
    1. JIRA
    2. Overview of Major Activity
      1. SICB 2016 White paper
      2. SICB 2017 Workshop
      3. 2017 Sustainable Community Cyberinfrastructure Maymester
  2. iAnimal
    1. Feb 2017 - : EpiDB - James Koltes
  3. Database and pipeline development for field-based high-throughput plant phenotyping (JIRA)

10. Product Champion

  1. 2016.09 User portal update
  2. 2016.11 Genome services revamp
  3. 2017.02 Atmosphere/Jetstream instance benchmarking and visualization in GUI
  4. 2017.05 Interactive analysis and visualization in CyVerse
  5. 2017.05 User experience update
  6. 2017.05 BisQue platform
  7. 2017.06 ElasticSearch Integration in CyVerse

11. Publications

  1. Mykles, Donald L; Burnett, Karen G; Durica, David S; Joyce, Blake L; McCarthy, Fiona M; Schmidt, Carl J; Stillman, Jonathon H. 2016. Resources and recommendations for using transcriptomics to address grand challenges in comparative biology. Integrative and comparative biology. DOI: https://doi.org/10.1093/icb/icw083
  2. B.L. Joyce, A. Haug-Baltzell, S. Davey, M. Bomhoff, E. Lyons. 2016. FractBias: a graphical tool for assessing fractionation bias following polyploidy. Bioinformatics. DOI: 10.1093/bioinformatics/btw666.
  3. B.L. Joyce, A. Haug-Baltzell, J. Hulvey, U.K. Devisetty, F. McCarthy, and E. Lyons. 2016. Leveraging CyVerse resources for de novo comparative transcriptomics of underserved (non-model) organisms. Journal of Visualized Experiments. DOI: http://dx.doi.org/10.3791/55009

12. Grants

  1. 2016.08 USDA AFRI Animal Breeding, Genetics, and Genomics - Yang Da
  2. 2016.12 NSF Training-based Workforce Development for Advanced Cyberinfrastructure (Cyber-Training) - Prasun Dewan

Other

  1. 2016.12 Update to data policy and CyVerse submission forms
  2. 2017.03 Update to CyVerse Main Webpage
  3. User Support
    1. Ask iPlant Responses
    2. JIRA tickets submitted
    3. RT Tickets
  4. Meetings and Talks

Professional Development

  1. 2016.08 SDSC Supercomputing Summer Institute
  2. 2016.08 Plant Functional Traits Course
  3. 2016 MAC High-throughput Phenotyping Workshop
  4. 2017.02 Fundamentals of Project Management
  5. 2017.02 NVIDIA Machine Learning Workshop

 

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Page: 2016.10 User Portal Update Page: 2016.12 Update to data policy and CyVerse submission forms Page: 2017-08-03 A GWAS image for the International Rice Research Institute (IRRI) Page: 2017.02 Data Commons Phenotyping Dataset from James Schnable Page: 2017.03 Update to CyVerse Main Webpage Page: Animal Genome to Phenome RCN - Blake Joyce Page: Ask iPlant Responses - Blake Joyce Page: Atmosphere/Jetstream instance benchmarking and visualization in GUI Page: Atmosphere Product Champion Page: Best Practices for Setting Up a Workshop on CyVerse Page: Blake Joyce - Meetings and Talks Overview Page: Cannabis genome version 2 reannotation Page: Connecting downstream annotation analysis tools to upstream CyVerse assembly and annotation tools Page: CyVerse BisQue Platform Page: Database and pipeline development for field-based high-throughput plant phenotyping (Alison Thompson, ECS JIRA - CS-913) Page: ElasticSearch Integration in CyVerse Page: EpiDB - James Koltes Page: Extended Community Support Page: Fundamentals of Project Management Page: Genome services Revamp Page: Integrating Circos in the DE Page: Interactive analysis and visualization in CyVerse Page: Interactive Analysis and Visualization in DE or Atmosphere Page: Jaguar BisQue Project - Susan Malusa Page: JIRA Tickets - Blake Joyce Page: Kaldi Speech Recognition Image Page: Meeting reports Page: NVIDIA Machine Learning Workshop Page: Phenome 2017 - Tucson Page: Physcomitrella genome version 3 Page: Portrait of Harbor - Visualizing Data - Noble Menchaca Page: Research Bazaar Arizona Page: RT Tickets Closed - Blake Joyce Page: SimPrily Page: SRA pipeline submission of two datasets for the Animal Genome to Phenome NSF RCN - Stillman Lab Page: The Hitchhiker's Guide to Parallelizing Scientific Analysis Page: User Experience Update