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Handbook to organize a Gallantries event |
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We're thrilled you've choosen to run a Gallantries event!
We hope this guide will help you navigate the logistics of the event organization. If anything is unclear or you have more questions, feel free to add comments in [GitHub]({{ site.github.repository_url }}/issues/new), or reach out to us on Gitter. We're here to help!
Several recent surveys highlight the need and demand from early-stage researchers for training in management and analysis of their High Throughput Sequencing (HTS) data. Given the gap in the education currently offered by traditional providers, there is a distinct push to create and provide high quality, decentralized, accessible, scalable, and practical training in bioinformatics.
The Gallantries team aims to address this gap by preparing training material for the computational analysis of HTS data, starting from the raw data and leading up to the development of publication ready visualizations of the analyzed results, using the Galaxy platform as the underlying infrastructure. This is a representative training scenario as it covers themes and practices common in the vast majority of data analysis pipelines in life sciences:
- User-friendly data analysis in Galaxy, from the raw sequencing data to the downstream count tables
- Downstream analysis & visualisation in Rstudio with manipulation and visualization of the results within R, including an introduction to R using RStudio
Beyond the curriculum, Gallantries team aims to address the scalability of training delivery via hybrid training events, i.e. pairing-up on-site helpers with remote instructors across multiple sites simultaneously:
With this model, we aim to bring training events to the trainees while reducing the environmental impact of instructor travel.
To illustrate a typical Gallantries event and the different roles (1 person can have several roles), we have decided to share a story with several fictional characters
Max is a training coordinator of an international research consortium. They recently surveyed researchers in the consortium on their need in HTS data analysis. The results were overwhelming: over 60 scientists at the several locations would like to learn how to analyze their own RNA-seq data. To fulfill this demand, Max decided to organize a Gallantries event: a 3-days workshop with 4 different locations simultaneously (Greece, Estonia, France and Spain). Max is the global organizer of this event, in charge of finding the date, contact and coordinate with the local hosts, advertize the event, find the instructors, etc. After the event, Max will aggregate all feedback from participants, helpers and hosts and share them.
Max first contacted 4 local hosts (1 at each site):
One of them is Imani who is based in Greece. Imani is in charge of finding a suitable room (preferably with computers), checking the local setup, recruiting local helpers, advertizing the event locally to participants, and organizing the local catering and social event. Imani will also give the introduction and wrap-up on each day, and collecting feedback from participants.
Imani recruited 2 local helpers for each day. One of the helpers, Casey, has some previous experience with RNA-seq data analysis and Galaxy. Before the workshop, they went through the training material and tested it. They will help participants during the workshop when they are stuck or get different results than the instructors. They will also give direct feedback to the instructor about the pace, any possible local issues etc.
Max also recruited 4 instructors, Farah among them. Farah is a trained bioinformatician and experienced instructor, regularly giving training to scientists on HTS data analysis. They will teach in the morning of the 2nd day (introduction and the first steps of RNA-seq data analysis). Farah is located in Germany and teaches from a room at their institute in front of their computer. During their session, they will adapt their pace given the feedback they receive from the local helpers, check the status of participants job on a dedicated page, and will also answer questions from participants written on chat.
Alex is a PhD student in molecular biology based in Greece. They would like to learn about RNA-seq data analysis to be able to analyze the data they generated. They heard about the workshop and join one site for the workshop close to their institute. As a participant, Alex will actively participate in the workshop by running their first RNA-seq data analysis given the instructor's instructions, ask for help from local helpers when stuck, will raise their questions on the participant chat, and will give feedback using sticky notes and the dedicated feedback form.
An example Gallantries event covers the computational analysis of HTS data from raw data to the development of publication ready visualizations of the analyzed results within 3 days of hands-on training:
- The first day is usually an introduction to Galaxy, quality control and, if time allows, mapping.
- On the second day, the training covers HTS data analysis, e.g. reference based RNA-seq analysis from raw sequences to differential expression analysis.
- The third day is dedicated to downstream analysis & visualisation of generated results with Rstudio in Galaxy, after an introduction to R.
Every day the workshop usually run from 8:30-10:00 to 17:00-18:30 (give or take, depending on questions at the end). Be sure to confer with your sites to determine reasonable start and end times that fit everyone's schedules. The suggested schedule is following
| Time | Topic | Material | Speaker |
|---|---|---|---|
| 1st day | |||
| 9:00 - 9:30 | General introduction: round of introductions from participants, helpers and local hosts, explanation of sticky notes and hybrid training | slides | |
| 9:30 - 10:00 | Introduction to Galaxy | slides | Local hosts |
| 10:00 - 12:30 | Galaxy 101 | tutorial | One instructor |
| 12:30 - 13:30 | Lunch | ||
| 13:30 - 15:30 | Quality control | slides, tutorial | One instructor |
| 15:30 - 17:00 | Mapping | slides, tutorial | One instructor |
| 17:00 - 17:30 | Recap of the day | Local hosts | |
| 2nd day | |||
| 9:00 - 9:30 | Recap of the previous day | Local hosts | |
| 9:30 - 10:00 | Introduction to RNA-Seq | slides | One instructor |
| 10:00 - 12:30 | Reference-based RNA-seq, part I (QC + mapping) | tutorial | One instructor |
| 12:30 - 13:30 | Lunch | ||
| 13:30 - 17:00 | Reference-based RNA-seq, part II (Differentail expression analysis) | tutorial | One instructor |
| 17:00 - 17:30 | Recap of the workshop + feedbacks | Local hosts | |
| Evening | Social Dinner | All sites | |
| 3rd day | |||
| 9:00 - 9:30 | Recap of the previous day | Local hosts | |
| 9:30 - 10:30 | Introduction to RStudio in Galaxy | tutorial | One instructor |
| 10:30 - 12:30 | Introduction to R programming | tutorial | One instructor |
| 12:30 - 13:30 | Lunch | ||
| 13:30 - 17:00 | Post-processing RNA-seq data using R | tutorial | One instructor |
| 17:00 - 17:30 | Recap of the workshop + feedbacks | Local hosts | |
| {:.table.table-striped} |
Breaks (10-15 minutes, with ideally drinks and snacks) are recommanded every hour to help participants to stay focus and let instructors to rest a bit. Breaks are difficult to pre-schedule, but could be done while a tool is running or if there are some technical issues.
With the hybrid training model, the cost of organizing and participating in the workshop are minimized: the instructors do not need to travel to the venue and the event can be the closest as possible to participants (e.g. in their institute).
We recommend that local hosts organize drinks and coffee for the breaks and, if possible, lunch. These will be the major costs of hosting such an event.
To cover those costs, local hosts can ask for a small participation fee. This will also increase the number of registered participants showing up.
To help you organize a Gallantries event, we have created some checklists, by timing but also by role. Most of the items in these checklists are not specific to Gallantries events.
{% include handbook/organizer-before.md %}
{% include handbook/host-before.md %}
{% include handbook/helper-before.md %}
{% include handbook/instructor-before.md %}
Templates for chat How chat works emphasize communication between helpers put sticky notes there quickly
{% include handbook/organizer-during.md %}
{% include handbook/host-during.md %}
{% include handbook/helper-during.md %}
{% include handbook/instructor-during.md %}
Debrief Sticky notes collection from sites share experience back: feedback from sites (extract form from issue in github) form feedback from instructors + helpers
{% include handbook/organizer-after.md %}
{% include handbook/host-after.md %}
{% include handbook/helper-after.md %}
{% include handbook/instructor-after.md %}
{% include handbook/organizer-before.md %}
{% include handbook/organizer-during.md %}
{% include handbook/organizer-after.md %}
{% include handbook/host-before.md %}
{% include handbook/host-during.md %}
{% include handbook/host-after.md %}
{% include handbook/helper-before.md %}
{% include handbook/helper-during.md %}
{% include handbook/helper-after.md %}
{% include handbook/instructor-before.md %}
{% include handbook/instructor-during.md %}
{% include handbook/instructor-after.md %}
- Event webpage
- Registration form
- Certificates
- Starting slides
- Collaborative document to collect questions from participants and document answers
- Instructors - Helpers Chat
- Wrap up slides for daily recap
- Wrap up slides for the end of the workshop
- Feedback form for participants
- Feedback form for helpers, hosts, instructors
We hope this guide gave you an overview of how to organize a Gallantries event, and will help you manage the logistics of the event organization.
The checklists has been adapted and extended from Galaxy and The Carpentries workshop checklists.