# PEG Lemons Meeting

*Dates: Feb ??th & ??th, 2021*

## Workshop goals

(where do we want to be after workshop)

1. Airing of grievances related to Governance Document violations, broken communication, time wasting (~~ad hominem~~)
2. Identify current bottlenecks which are continuing to slow our progress
3. Reflection & Discussion
4. Reaffirmation of commitment to objectives and proposed revisions to Governance Document

## Agenda Day 1

| AZT MST | EST | Agenda | Lead Personnel | Outcome |
|---------|-----------|-------------|----------------|---------|
| 0900-0910 | 1100-1110 | Welcome |Anne, Arun, Remco, Bryan| |
| 0910-0920 | 1110-1120 | Ice Breaker (Breakout Rooms)| All | favorite Quar food & drinks |
| 0920-0930 | 1120-1130 | Workshop Logistics | Facilitators (Tyson, Laurel) | Use of Website, Zoom, Slack, and GitHub |
| 0930-0945 | 1145-1200 | Overview of GEP project | Anne, Bryan, and Arun, Remco |Four 3 minute Lightning talk for TRIPODS participants w/ 2 minute QA about Year 1 |
| 0945-1000 | 1145-1200 | Tech Breakout | Tyson, Remco, Arun | Rooms focused on ML, Visualization, and Cyberinfrastructure from Year 1 |
| 1000-1015 | 1200-1215 | Break |
| 1015-1030 | 1215-1230 | Data Breakout | David, Pankaj, Ann | Rooms focused on Phenotyping, Genomics, Environmental Data from Year 1 |
| 1030-1045 | 1230-1245 | Science Breakout | Ryan, Gabe, Ishita | Rooms focused on Bayesian Belief Networks, and ML from Year 1 |
| 1045-1100 | 1245-1300 | TRIPODS Q/A Session | All | Tripods participants ask questions about our project |
| 1100-1200 | 1300-1400 | Lunch | |
| 1200-1245 | 1400-1445 | Building our Research Object part 1 | Breakout Rooms | Year 1 Data Inventory and status check (see checklist) |
| 1245-1300 | 1445-1500 | Check-in | All | Review, task assignment |
| 1300-1315 | 1500-1515 | Break | |
| 1315-1345 | 1515-1545 | Building our Research Object part 2 | Breakouts | Year 1 Code, Notebook, Containers Inventory and status check |
| 1345-1400 | 1545-1600 | Wrap-up | All | After-action review (what went well, wrong, could be done better) |

## Agenda Day 2

| AZT MST | EST | Agenda | Lead Personnel | Outcome |
|---------|-----------|-------------|----------------|---------|
| 0900-0910 | 1100-1110 | Briefing | Tyson, Ryan | Overview of day activity |
| 0910-0945 | 1110-1145 | Intro to NEON Data API | TBD NEON science team member | Explanation of how NEON Data are acessed via their API |
| 0945-1000 | 1145-1200 | Intro to CyVerse | Tyson | Working in the CyVerse Workbench with Jupyter & RStudio |
| 1000-1015 | 1200-1215 | Break | |
| 1015-1030 | 1215-1230 | NEON Shiny App | Tyson | Understand downloading of data from NEON into CyVerse |
| 1030-1045 | 1230-1245 | Metagenomics | Ryan | Linking soil metagenomes to environment |
| 1045-1100 | 1245-1300 | | |
| 1100-1200 | 1300-1400 | Lunch | |
| 1300-1315 | 1500-1515 | Machine Learning Applications with NEON Data | Arun and Ishita | Discussion of strengths and weakness |
| 1315-1330 | 1515-1530 | | |
| 1330-1345 | 1530-1545 | | |
| 1345-1400 | 1545-1600 | Break | |
| 1400-1415 | 1600-1615 | | |
| 1415-1430 | 1615-1630 | | |
| 1430-1445 | 1630-1645 | Year 2 Assignments | |
| 1445-1500 | 1645-1700 | Wrap-up | All | After-action review (what went well, wrong, could be done better) |

## Pre Workshop Goals

The ultimate goal of our Harnessing the Data Revolution Idea Lab and Collaborative Research is to run an Institute with other HDR groups. Demonstrating that we are capable of doing so requires that we provide examples of (1) reproducible research, (2) collaboration across discplines, & (3) providing training materials in how to do the former two things.

* Provide evidence of linked data and executable code
+ [ ] Computational Notebooks
+ [ ] Notebooks in GitHub Repository
+ [ ] Version 1.0 Release
+ [ ] Zenodo DOI
+ [ ] Linked data from TERRA REF
+ [ ] Code in GitHub Repository
+ [ ] Version 1.0 Release
+ [ ] Zenodo DOI
+ [ ] Linked data from NEON API
+ [ ] Code in GitHub Repository
+ [ ] Version 1.0 Release
+ [ ] Zenodo DOI
+ [ ] Unique datasets are hosted on CyVerse
+ [ ] Shared Publicly
+ [ ] Data Commons Community Released
+ [ ] Metadata Template Completed
+ [ ] CyVerse DOI
+ [ ] Containers hosted on DockerHub
+ [ ] Run Containers with Notebooks and Data on CyVerse
+ [ ] Run Containers on local hosts or remote servers

* Demonsrate internally a clear understanding of each of the collaborative research team's contributions
+ [ ] Overall Task Abstraction of the project
+ [ ] Ability to describe the contributions of the other groups

* Define achievable goals within the timeline for Year 2
+ [ ] Identify existing datasets

## Milestones

+ [ ] All Year 1 Data are accounted for and are publicly accessible
+ [ ] All Year 1 Notebooks are hosted on GitHub with DOI
+ [ ] All Year 1 Workflows are containerized and hosted on Docker Hub
+ [ ] All Year 1 Workflows are hosted on CyVerse

## Documentation

Adhere to our own Governance Document requirements

Use our Website and ReadTheDocs (RTD) pages for all of workshop documentation

Internal documents are maintained on Google Drive

### ReadTheDocs

Clone CyVerse Tutorial Template into PEG Website RTD

#### Pages

##### CyVerse Account

Copy .rst file for CyVerse Account Creation

##### GitHub Account

##### Google Earth Engine Account

##### NEON Data API Keys

# Pre-meeting materials

Where did we fail in year 1 and how can we improve?
| 0930-0945 | 1130-1145 | Lemons | Breakout Rooms | Identify failures and problems in year 1 regarding, data, code, collaboration |
|:--|:--|:--|:--|:--|
| 0945-1000 | 1145-1200 | Lemon drops | All | The airing of grievances - review and rank problems |
| 1000-1015 | 1200-1215 | Break | |
| 1015-1030 | 1215-1230 | Lemonade | Breakout Rooms | Discuss and identify solutions and changes |
| 1030-1100 | 1230-1300 | (re)Building our common language | All | Update SOP & Governance items |