# Ideas for the EMBARK Autumn Meeting
27./28.09.2022
### Attendees:
Physical:
1. Johan
2. Víctor
3. Svetlana
4. Uli
5. Remi
6. Luis
7. Rabaab
8. Anna
9. Marcus
10. Emil
11. Thomas
12. Faina

New student with Johan?

Remote:
1. Ayaz
2. Etienne
3. Ulrike
4. Sofia

## "Registration form"

- Will you attend EDAR?
- Will you attend the EMBARK meeting physically or remotely?
- When will you arrive to and leave Gothenburg?
- Would you like to participate in an Escape room activity?
- Would you like a boat tour (Paddan) around Gothenburg harbour?
- Food preferences

## Meeting structure
**Aims:** *Papers, protocols, party*

### Very non-fixed schedule

**DAY 1** Starting in the afternoon after EDAR lunch
*Location: Room Utsikten, 7th floor in the Chalmers Chemistry Building*
- [x] *Johan* checks venue capacities (~20 participants + remote capacities)
- [x] *Johan* checks Chalmerska huset for Day 2
- [ ] *Johan* ask other PIs about potential collaborative publications

14:00 – Socializing activity - *something that would bring physical participants together with the remote participants*

14:30 – **Paper discussions**
* Broad overarching papers involving almost everyone
* Responsibles of the papaers should lead the discussion

1) Method comparison paper: **Comparison of methods to monitor antibiotic resistance in the environment** (No manuscript drafted, data exists, basically everyone is involved)

2) Big data re-analysis paper: **Normal background levels of antibiotic resistance genes in the environment** (No manuscript drafted, basically everyone is involved)

18:00 Social activity: Escape room

20:00 – **Party** – EMBARK Dinner at Heaven 23

**DAY 2**
9:00 **Protocols**
* *Open for EMBARK Monitoring Group?*
* What stage are the different protocols in?
* What do we want to change?
* What recommendations do we think can be carried over to "routine" monitoring?
* How do our methods for monitoring integrate with other monitoring initiatives?
* Protocol paper: **A suggested protocol for resistance gene analysis in environmental samples** (No manuscript drafted, basically everyone is involved, **someone** should be assigned to take the lead)

12:00 - **Lunch**
13:00 - **Papers**
* Smaller group EMBARK collaborations
* Two paralell tracks: Bioinformatics vs. wet lab
* One session before coffee break + photo shoot, potentially one session after

1. Metagenomics method comparison paper: **Evaluating methods for ARG annotation in metagenomes** (data exists, no manuscript drafted — led by Svetlana + Luis, Johan, Victor?, Remi?, Etienne?, Marcus?)
2. Tax-to-ARG paper: **Prediction and inference of resistance gene abundance from taxonomic composition** (No manuscript drafted, data exists, analysis needs to be performed - led by Ulrike + Luis, Svetlana, Victor, Sofia, Johan?, Anna?)
3. Incubation temperature optimization paper/study: **Effects of incubation temperature on the detection of microbial abundance and diversity from environmental samples through selective plating** (No manuscript drafted, some data exists, future experiments needed, analysis needs to be performed - led by Faina/Thomas/Uli + Anna?, Emil?)

14:30 – **Team photo shoot**

15:00 - Paper discussion session two

16:00 - Wrapping up, thinking about future funding

17:00 – *Optional* [Paddan boat tour](https://www.stromma.com/en-se/gothenburg/sightseeing/sightseeing-by-boat/the-paddan-tour/)

19:00 – **Party** - Dinner at Blackbird restaurant.

## Themes and activities
TBC

## Social activities

- **Guess Who?** Ice breaker game: guessing who is who from the young me photos

- **Academic bingo** if you get a line, a row, or a diagonal - you get to shout "Bingo!"

- **An Escape Room**
https://gotescape.se/en/start
Max 6 people per room, precheck interest!

### Bingo board ideas:

- [BINGO](https://myfreebingocards.com/bingo-card-generator)
- mini project pitches [past/upcomming projects not necessarily EMBARK] (2min/5min?) by all participants
- BINGO cards will be generated beforehand
- every BINGO wins a shot