hexylena
commented
3 years ago Agenda & Minutes
(Please feel free to add any points you would like to discuss today in the list below)
- Welcome & Introductions
- Communication Channels
- Can everybody access all the links above?
- Teams
- Anyone you're working with or will be helping?
- Anthony: 1
- Bérénice: Bea, Cristobal (November)
- Yvan: Coline
- Anybody who should be added to Gitter/GitHub/other? Let us know!
- Anyone you're working with or will be helping?
- Meeting Schedule
- Suggestion: monthly partner-wide telcos.
- When? This time ok structurally? Yes! It seems to be
- First Monday of the month, 15:00-16:00 CET (starting > December 7)?
- Suggestion: monthly partner-wide telcos.
- Report of Erasmus+ Kickoff Meeting (06-10-2020) [Saskia & Helena]
- Slides (mostly in Dutch)
- Mobility Tool (Project Management/Reporting tools from EC for coordinators, partners can view)
- Focus on impact
- Impact was 30/100 points on proposal, 40/100 on final assessment
- They seem very open to changes in plan if motivated by impact
- Impact tool to help define/articulate/assess impact, to help guide the project
- We must have EU logo visible on any activities related to Gallantries
- Added image to Gdrive
- Added to Gallantries website [Helena]
- Add to GTN logo list [Saskia]
- Given pandemic, digital signatures are fine for now (e.g. for timesheets), they might ask for "wet" signatures down the road.
- Monitoring by EC
- Risk-based (based on our reporting) and random spot checks
- EC may decide to attend our project meetings and events (Annex III)
- Yearly + Midterm + End reports
- Sept 1st start date
- they can reduce the money they give based on the final score.
- never happened before in NL
- Control of our paperwork up to 5 years after project.
- "Association link"
- All y'all are formal employees of your institutions right?
- EMC receives, then disburses to Institutes, then they can subdivide
- Any changes in how we're spending, must be passed on
- Up to 20% may be transferred between budget posts without formal amendment.
- First Six Months - Project-wide activities
- Events
- Course in February (15-19) as first event for IO1/2
- Goal: Assess whether this format works for us in lieu of hybrid training format.
- Second one for IO3/4 to be planned
- Course in February (15-19) as first event for IO1/2
- Develop feedback/impact assessment surveys
- Align with ELIXIR, others?
- Dissemination Channels
- Create a mailing list for our stakeholders?
- Social Media? Twitter! [Fotis]
- Update Gallantries website [Helena working on it]
- Anything else?
- Events
- First Six Months - Detailed IO Plans!
- IO1 - [CERTH, EMC] Introduction to data analysis and management, statistics, and coding
- (Stretch) Intro to Programming Concept
- What are functions
- What are variables
- Slower w/ more exercises, some ROSALIND type exercises?
- Coding in R
- a lot is done with R code. GTN modules are OK.
- do we need to update these? (I know of 1 broken link)
- we did the demo ggplot2, maybe include that?
- Update w/ new tidyverse
- Make it a bit bigger? more exercises, starting from scratch maybe?
- Coding in Python3
- Consider RStudio w/ Python? (shows variables/datastructures/etc)
- pedagogically better to unify on one platform, not switch?
- FP: If you want to increase impact, maybe use jupyter
- Avoid viz in python? Discuss later.
- BB: anne was working on jupyter? Can we coordinate?
- https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/jupyterlab/tutorial.html
- https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/galaxy-intro-jupyter/tutorial.html
- FP: Reuse the R for python? Advanced replicating the advanced R maybe.
- Consider RStudio w/ Python? (shows variables/datastructures/etc)
- Intro to Command line
- New interactive tool for an Ubuntu Desktop (Or Rstudio! That's easy)
- Bash
- Practical tools
- Github/git?
- (Stretch) Make a PR?
- Stretch goal: Scientific Collaboration (how to review code/PR, work together.)
- AS: use case focused development maybe? Something getting increasingly more complex with similar datasets or analyses as a thread/link between them?
- (Stretch) Intro to Programming Concept
- IO2 - [EMC/ALU-FR] Large-scale data analysis, and introduction to visualization and data modelling
- Intro to Scaling
- collections: update the tutorials / tips n tricks (\@shiltemann?)
- how to work on workflows (editor, subworkflows, collections, test expression tools & tuto if working.) (\@hexylena)
- Rule based, nametags, group tags (\@hexylena)
- Tutorials need to be more real world (\@shiltemann)
- Workflow Reports (\@hexylena)
- Intro to human microbiome
- Expand intro slides
- 16s with Mothur (\@shiltemann)
- stretch: 16s w/ QIIME 2? (\@shiltemann)
- Advanced Microbiome analysis
- Shotgun metagenomics (\@bebatut)
- Add more visualizations
- Metatranscriptomics one to metagenomics? (\@bebatut)
- Work with GalaxyP there?
- Oleg (Freiburg) is working to make automatic gifs of the snippets?
- Miaomiao WF (\@shiltemann)
- Nanopore ABR tutorial (\@shiltemann, willem, astrid)
- Update nanopore to WF helena made? (\@hexylena/astrid)
- Shotgun metagenomics (\@bebatut)
- Other
- Considering metagenomics related content, We (MNHN) are thinking creating a Interactive Tool based on Ranacapa R shiny app https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6305237/ dedicated to eDNA data analysis
- Virus?
- Intro to Scaling
- IO3 - [INRAE/EMC] Data stewardship, federation, standardisation, and collaboration
- Intro to Genomics and GA
- lots of content needed
- Data management (histories, naming, tagging, data storage, etc.?) (\@hexylena)
- Data sources (genomics?)
- Adapt GA introduction slides (remove euk slides)
- FAIR (andrew)
- Intro to Proks / biology
- Collaborative Curation (everyone on one test org \@hexylena)
- Apollo working on EU and everything flowing enough to work for events. (\@hexylena)
- Apollo : check permissions + name collisions
- Review Prokka tutorial, + add more functional annot ?
- Finish pending apollo pull request
- Some Python coding to compute stats on annotated genes ?
- (Started work on a shortened Maker tuto for later too)
- Discussion
- FP: Maybe overlap with IO1 for their Python3 module?
- Crossmap?
- Yvan: maybe a link to do between IO3 and \"ELIXIR Community-led Implementation Study 2020 PROPOSAL Strengthen Data Management in Galaxy\" querying metadata contents of an exported history file https://github.com/usegalaxy-no/nels-galaxy-api
- Yvan: Research Objects / Discussions on that with Nicola/Hadley
- Andrew: link it back to elixir projects like aai?
- https://github.com/inab/EPICO-data-model/blob/fairtracks/model-docs/general-schema.pdf
- https://github.com/fairtracks/fairtracks\_standard
- Intro to Genomics and GA
- IO4 - [MNHN/ALU-FR] Data analysis and modelling for evidence and hypothesis generation and knowledge discovery
- Biodiversity data handling and visualisation
- Raw data to analyses through modelling approach (GLM)
- WF is complete already !
- Rstudio flavour?
- Biodiversity data handling and visualisation
- IO5 - [ALU-FR/CERTH] TtT & Mentor Programme
- Most of the work will start after February when Bérénice is
back full time
- What can we do to help with this before then?
- Discuss with the freiburg folks (Bea/Christobal)
- Train-the-Trainer program
- Feedback form for the trainers
- Discuss the contents of this form
- Disseminate to the trainers/helpers during event
- Course builder
- Provide some example schedules based on our own experiences?
- Tool to let you build your own (using metadata on prerequisite and follow-up tutorials, expected length, etc)
- (Maybe a masters project? VueJS, machine learning 😭)
- Maybe TeSS is an option to integrate with, we'll have to keep in touch with them.
- Most of the work will start after February when Bérénice is
back full time
- IO1 - [CERTH, EMC] Introduction to data analysis and management, statistics, and coding
- Communications
- GitHub
- Bérénice: is reading her emails (gh issues on monday)
- Yvan: email.
- Meeting Schedule
- Suggestion: monthly partner-wide telcos. When? This time? First Monday of the month, 15:00-16:00 CET (starting December 7)?
- Paperwork
- Timesheets (per person, per IO)
- Template in reports folder of Gdrive
- We'll place ours in gdrive
- Final grant agreement (\@shiltemann will put in GDrive for your records)
- Timesheets (per person, per IO)
- Quizzing students
- https://kahoot.it was used in kickoff meeting with EC, which was quite nice. We could consider doing similar things in our events (you just joined with a phone/browser, it was relatively privacy preserving, and we can use it to gauge knowledge maybe??)
- Please record all our dissemination activities in this document in Gdrive any blog posts, emails to mailing lists, presentations, etc\
- GitHub
- AOB?
- Any other business anybody would like to raise?\
- Next Meeting: TBA
Action Items
| Action | Who |
|---|---|
| Update Gallantries website | Helena |
| Add EU logo to GTN website | Saskia |
| Go through impact tool in next meeting, what impacts we expect/how | H |
| Rename org | H |
| Blog post | H |
| Coordinate with CINECA on impact/feebdack | Saskia |
| Coordinate with Elixir | H |
| Twtitter Account Create + share with us? | Fotis |
| Can freiburg use HiWis? | Saskia / EMC |
| Fotis will invite us to the TeSS club | Fotis |
| FAIR workshop | Andrew |
| Timesheet/paperwork | Saskia / EMC |
saskia
Our Kickoff Meeting is October 26th, 15-17 CET
Minutes document: https://docs.google.com/document/d/1k8daES74rpeFK9roQDGWxotEPHURto-fYZBJlpIFZ8k/edit?usp=sharing
Agenda