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Finalise schedule
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‎docs/2025/README.md‎

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The summer school will be held between 4th-8th August 2024, 09:00-17:00 CEST (Berlin Time).
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Applications for the 2025 Introduction to Ancient Metagenomics Summer school are now **closed**!
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Note the following additional dates:
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- **Applications open**: 31st March 2025
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- **Applications close**: 30th May 2025
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- **Decision notifications**: from second to third week of June 2025
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To see the provisional schedule, please see the [here](2025/schedule.md).
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To see the schedule, please see the [here](2025/schedule.md).
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## Where
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‎docs/2025/schedule.md‎

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## Overview
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The PROVISIONAL schedule for the summer school is as follows:
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The schedule for the summer school is as follows:
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| **Time** | **Session Type** | **Day 1** | **Day 2** | **Day 3** | **Day 4** | **Day 5** |
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| ----------- | ---------------- | ----------------------------------------------------------------------- | ------------------------------------------------------------------------------- | ------------------------------------------------- | ---------------------------------- | ----------------------------------------------------------------------------------- |
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| 12:30-13:30 | | Lunch | Lunch | Lunch | Lunch | Lunch |
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| 13:30-15:30 | Practical | Introduction to R and the tidyverse & Introduction to Python and Pandas | - Introduction to Git(Hub) (1h)<br>- Introduction to AncientMetagenomeDir (1hr) | Genome mapping | Phylogenomics | - Authentication at Scale Practical (1h) <br>- Ancient Metagenomic Pipelines (1h) |
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| 15:30-15:45 | | Break | Break | Break | Break | |
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| 15:45-17:00 | Roundtable | TBC | TBC Activity | TBC | Instructor Office Hours | Dinner (Leipzig Only) |
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| 15:45-17:00 | Roundtable | Lightning talks | Team activity (your perfect bioinformatic tool) | Instructor Office Hours | Instructor Office Hours | Dinner (Leipzig Only) |
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Lectures and Practical sessions are typically 2 hours, and round-table discussions 1 hour.
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- **Practical** Introduction to R and the tidyverse / Introduction to Python and Pandas: _Clemens Schmid and Keri Burge_ / _Rémi Denise and Freya Steinhagen_
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- How to read/write files and run statistical analyses? How to make figures with ggplot2/plotnine
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- (Note: Parallel sessions participants can choose which to attend based on their prior experience)
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- **Round table** TBC
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- **Round table** Lightning talks
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- To get to know each other, all students will give a 1 minute lightning talk about themselves and their research topics and interests.
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### DAY 2
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- **Practical** AncientMetagenomeDir: _James Fellows Yates and Megan Michal_
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- Where to get ancient metagenomic comparative data, and why is metadata important?
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- Git practice
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- **Round table** TBC
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- **Round table** Team activity
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- To building networks amongst your peers, students will put into groups
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- They will have to think what is their biggest issues in bioinformatics, design a the 'perfect' tool to solve it, and come up with a fun naming scheme (and logo!)
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### DAY 3
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- Python practice. How to normalise OTU tables and perform microbial ecology analyses.
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- **Practical** Genome mapping: _Tessa Zeibig and Alexander Herbig_
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- Why and how do we map against a reference? What parameters are important for aDNA?
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- **Round table** TBC
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- **Round table** Instructor open hours
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- An opportunity for students to ask the instructors any questions about the content they have learnt so far, or to get advice on their own research.
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### DAY 4
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- De novo methods for obtaining metagenomically assembled genomes (MAGs). What are the best pipelines and parameters for ancient DNA?
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- **Practical** Phylogenomics: _Arthur Kocher and Aida Andrades Valtueña_
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- How to perform phylogenetic analysis. What to consider when dealing with low coverage data
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- **Roundtable** Instructor Office Hours: Ask the instructors anything about you learnt during the week or to get advice on your own research!
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- **Round table** Instructor open hours
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- An opportunity for students to ask the instructors any questions about the content they have learnt so far, or to get advice on their own research.
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### DAY 5
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‎docs/organisers/milestones.md‎

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- [ ] **Organisers:** spin up nodes for each person; mount volumes; set all teachers as admins
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- [ ] **Participants:** send final reminder about organisational details
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- [ ] **Organisers:** make dinner reservations (don’t leave to 1 week before!)
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- [ ] **Organisers:** request EVA WiFi vouchers
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## T-Minus 1 week before (JULY/AUGUST)
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