Handbook to organize a Gallantries event

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, or reach out to us on Gitter. We’re here to help!

What is a Gallantries event?

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:

  1. User-friendly data analysis in Galaxy, from the raw sequencing data to the downstream count tables
  2. 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:

Hybrid training diagram, a single remote instructor broadcasts training to multiple sites

With this model, we aim to bring training events to the trainees while reducing the environmental impact of instructor travel.

A typical Gallantries hybrid training event

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.

Curriculum and schedule for an event

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

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.

Cost of an event

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.

Workshop Checklists

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.

Before the workshop

Global organizers

  • Contact and identify situable locations

    We recommend no more than 2 different time zones as the days are full.

  • Identify and contact instructors

    Some recommendation: an instructor should teach at maximum half day in a row. So at least 2 instructors per day are needed.

  • Choose a date in coordination with local hosts and instructors

  • Create a registration form, e.g. by copying our template

    Such a registration form should include: participant details, email, affiliation, location for the workshop, accessibility requirements, motivation for participating, participation on social event, dietary requirements, agreement on privacy statement.

  • Setup a webpage to advertize the event

    This page should include:

    • general information about the event, its format
    • registration details and deadline
    • draft schedule
    • what participants need to do before
    • details about the venues, including travel details, accomodation and meal suggestions
    • details about the instructors, helpers, hosts
    • sponsors (if any)

    We created a template of such a page that can easily adapted.

  • Identify places you can promote your event. Galaxy Hub or Carpentries Discuss List are the primary places to do this

    You should do this 1-3 month in advance of your event (if you can).

  • Collect contact details of the local hosts and instructors in case of last minute changes

  • Arrange the schedule given the content, the instructor availability and the different time zones

    Days are usually full-days. Starting times will depend on audience, if they travel and the different time zones, and should be chosen with the local hosts.

  • Identify the tool for call, e.g. Zoom

  • Arrange a conference call(s) with instructors and hosts in order to:
    • Meet in advance of the workshop
    • Divide and document the responsibilities
    • Share contact details
    • Test the technical infrastructure
    • Test the local set ups

    To avoid audio issues (full vs empty room), the test should be hearable at 75% volume (so room to go up if need be)

  • Request TiaaS infrastructure if using usegalaxy.eu
  • Remind instructors to arrange microphone/headphones

  • Create name badges, with space for people to specify pronouns, and send them to local hosts

    Name badges for attendees (and helpers) are important for participants as well. At busy venues, it can help attendees to find each other and remember each others’ names. For the helpers, usually with a different color border so attendees can identify people who can help them with any issues they encounter.

  • Prepare sign-in sheet for each location
  • Contact participants to remind them of the workshop webpage where you have written location/directions, start/end times, and contact information
  • Prepare the different slides:
    • Starting slides, including instructor presentation, different locations, etc
    • Wrap up slides for daily recap, including 5 minutes dedicated for filling the post-it feedback
    • Wrap up slides for the end of the workshop, including 5 minutes dedicated for filling the general feedback, remind of gitter/help/etc
  • Create the collaborative document to collect questions from participants and document answers, e.g. by copying our template
  • Create the collaborative document for the communication between the instructors and helpers, in order to get direct feeback from sites, e.g. by copying our template
  • Prepare the feedback form for participants, e.g. by copying our template
  • Prepare the feedback form for hosts, helpers and instructors, e.g. by copying our template

Local hosts

  • Identify a suitable room (ideally a computer room)
    • Check for stable internet connection
    • Make sure the workshop space is accessible to all individuals
      • Check if the building, room and restrooms are wheelchair accessible (ramps, elevators, etc.)
      • List any gender-neutral toilet options
      • Check that the screen is large enough and bright enough to be read easily
      • Offer extra chair if people bring a listener/signer
  • Make reservations of the room on the chosen dates
  • Identify and contact local helpers
  • Collect emergency contact details (emergency phone number, nearest hospital, pharmacy, police, on-site emergency contact)
  • Print sign-in sheets
  • Print name badges
  • Arrange a sound system in the classroom
  • Make sure wifi or wired internet connection in the classroom is of sufficient speed
  • Test the screen with different light intensity
  • Arrange required materials and equipment
    • Set up extension cords or power strips
    • Get sticky notes in two contrasting colors. Make sure the colors are distinguishable by color blind people.
    • Get extra pens and paper in case people want to take notes by hand
    • Get pens for blackboard, whiteboard or flipboard
  • Arrange for beverages, snacks, and meals
    • Remember about dietary requirements
    • Ensure that your catering service will label the food for contents/allergens (e.g. for vegetarian/vegan/allergens like gluten, etc.)
    • Make a reservation for a social dinner, if any.

    Catering can be expensive. If you choose to have participants fund their own lunch, you should add nearby lunch location ideas to the workshop webpage. If your workshop is a multi-day workshop, you should include dinner options on the workshop webpage.

Local helpers

  • Test the training material

Instructors

  • Decide on the order of the lessons and who will teach which modules
  • Help the organizer set up the workshop webpage
  • Share emergency contact information with the organizer in case of last minute changes
  • Review the training material and suggest changes at max 2 days before
  • Make sure good quality wifi or wired internet connection in the room
  • Prepare microphone/headphones
  • Help organizer to create the recap slides for the end of each day (including newly learned file formats, usual HTS data analysis workflow)

During the workshop

Templates for chat How chat works emphasize communication between helpers put sticky notes there quickly

Global organizers

  • Prepare the participation certificates, e.g. by copying our template, and send them to local hosts

Local hosts

  • Ensure that the room is set up with all necessary materials and equipment.
  • Arrange drinks and snacks for each break
  • Be inclusive
  • Distribute 2 sticky notes (one of each color) per participants
  • Make the first presentation
    • Remind the Code of Conduct when starting
    • Indicate restroom location
  • Collect sticky notes (one for good thing., one for things to improve) at the end of each day. Minute Cards
  • Print the certificates

Local helpers

  • Indicate to instructor if they should speed up or slow down, or if there is a technical issue and need, using the instructor - helper chat
  • Help answer procedural questions like “where is this button that I should click”
  • Direct technical/biological questions to the participant chat

Instructors

  • Introduce yourself
  • Explain and show the use of participant chat
  • Remind learners to use post-it notes to give feedback
  • Answer questions on the participant chat
  • Publish Galaxy history regularly, for the participants who might be left behind
  • Check the instructor - helper chat regularly and adapt the pace in function

After the workshop

Debrief Sticky notes collection from sites share experience back: feedback from sites (extract form from issue in github) form feedback from instructors + helpers

Global organizers

  • Collect the participant feedback forms
  • Collect the sticky notes
  • Collect the host, helper, instructor feedback form
  • Setup a call with the instructors to discuss feedback.
  • Report the feedback and notes via the Gallantries GitHub issue

Local hosts

  • Collect and send to organizer the participant feedback form
  • Transcript the sticky notes and send them to organizer
  • Ask helpers to fill the helper feedback form

Local helpers

  • Fill the helper feedback form

Instructors

Checklists by role

Global organizers

Before the workshop

  • Contact and identify situable locations

    We recommend no more than 2 different time zones as the days are full.

  • Identify and contact instructors

    Some recommendation: an instructor should teach at maximum half day in a row. So at least 2 instructors per day are needed.

  • Choose a date in coordination with local hosts and instructors

  • Create a registration form, e.g. by copying our template

    Such a registration form should include: participant details, email, affiliation, location for the workshop, accessibility requirements, motivation for participating, participation on social event, dietary requirements, agreement on privacy statement.

  • Setup a webpage to advertize the event

    This page should include:

    • general information about the event, its format
    • registration details and deadline
    • draft schedule
    • what participants need to do before
    • details about the venues, including travel details, accomodation and meal suggestions
    • details about the instructors, helpers, hosts
    • sponsors (if any)

    We created a template of such a page that can easily adapted.

  • Identify places you can promote your event. Galaxy Hub or Carpentries Discuss List are the primary places to do this

    You should do this 1-3 month in advance of your event (if you can).

  • Collect contact details of the local hosts and instructors in case of last minute changes

  • Arrange the schedule given the content, the instructor availability and the different time zones

    Days are usually full-days. Starting times will depend on audience, if they travel and the different time zones, and should be chosen with the local hosts.

  • Identify the tool for call, e.g. Zoom

  • Arrange a conference call(s) with instructors and hosts in order to:
    • Meet in advance of the workshop
    • Divide and document the responsibilities
    • Share contact details
    • Test the technical infrastructure
    • Test the local set ups

    To avoid audio issues (full vs empty room), the test should be hearable at 75% volume (so room to go up if need be)

  • Request TiaaS infrastructure if using usegalaxy.eu
  • Remind instructors to arrange microphone/headphones

  • Create name badges, with space for people to specify pronouns, and send them to local hosts

    Name badges for attendees (and helpers) are important for participants as well. At busy venues, it can help attendees to find each other and remember each others’ names. For the helpers, usually with a different color border so attendees can identify people who can help them with any issues they encounter.

  • Prepare sign-in sheet for each location
  • Contact participants to remind them of the workshop webpage where you have written location/directions, start/end times, and contact information
  • Prepare the different slides:
    • Starting slides, including instructor presentation, different locations, etc
    • Wrap up slides for daily recap, including 5 minutes dedicated for filling the post-it feedback
    • Wrap up slides for the end of the workshop, including 5 minutes dedicated for filling the general feedback, remind of gitter/help/etc
  • Create the collaborative document to collect questions from participants and document answers, e.g. by copying our template
  • Create the collaborative document for the communication between the instructors and helpers, in order to get direct feeback from sites, e.g. by copying our template
  • Prepare the feedback form for participants, e.g. by copying our template
  • Prepare the feedback form for hosts, helpers and instructors, e.g. by copying our template

During the workshop

  • Prepare the participation certificates, e.g. by copying our template, and send them to local hosts

After the workshop

  • Collect the participant feedback forms
  • Collect the sticky notes
  • Collect the host, helper, instructor feedback form
  • Setup a call with the instructors to discuss feedback.
  • Report the feedback and notes via the Gallantries GitHub issue

Local hosts

Before the workshop

  • Identify a suitable room (ideally a computer room)
    • Check for stable internet connection
    • Make sure the workshop space is accessible to all individuals
      • Check if the building, room and restrooms are wheelchair accessible (ramps, elevators, etc.)
      • List any gender-neutral toilet options
      • Check that the screen is large enough and bright enough to be read easily
      • Offer extra chair if people bring a listener/signer
  • Make reservations of the room on the chosen dates
  • Identify and contact local helpers
  • Collect emergency contact details (emergency phone number, nearest hospital, pharmacy, police, on-site emergency contact)
  • Print sign-in sheets
  • Print name badges
  • Arrange a sound system in the classroom
  • Make sure wifi or wired internet connection in the classroom is of sufficient speed
  • Test the screen with different light intensity
  • Arrange required materials and equipment
    • Set up extension cords or power strips
    • Get sticky notes in two contrasting colors. Make sure the colors are distinguishable by color blind people.
    • Get extra pens and paper in case people want to take notes by hand
    • Get pens for blackboard, whiteboard or flipboard
  • Arrange for beverages, snacks, and meals
    • Remember about dietary requirements
    • Ensure that your catering service will label the food for contents/allergens (e.g. for vegetarian/vegan/allergens like gluten, etc.)
    • Make a reservation for a social dinner, if any.

    Catering can be expensive. If you choose to have participants fund their own lunch, you should add nearby lunch location ideas to the workshop webpage. If your workshop is a multi-day workshop, you should include dinner options on the workshop webpage.

During the workshop

  • Ensure that the room is set up with all necessary materials and equipment.
  • Arrange drinks and snacks for each break
  • Be inclusive
  • Distribute 2 sticky notes (one of each color) per participants
  • Make the first presentation
    • Remind the Code of Conduct when starting
    • Indicate restroom location
  • Collect sticky notes (one for good thing., one for things to improve) at the end of each day. Minute Cards
  • Print the certificates

After the workshop

  • Collect and send to organizer the participant feedback form
  • Transcript the sticky notes and send them to organizer
  • Ask helpers to fill the helper feedback form

Local helpers

Before the workshop

  • Test the training material

During the workshop

  • Indicate to instructor if they should speed up or slow down, or if there is a technical issue and need, using the instructor - helper chat
  • Help answer procedural questions like “where is this button that I should click”
  • Direct technical/biological questions to the participant chat

After the workshop

  • Fill the helper feedback form

Instructors

Before the workshop

  • Decide on the order of the lessons and who will teach which modules
  • Help the organizer set up the workshop webpage
  • Share emergency contact information with the organizer in case of last minute changes
  • Review the training material and suggest changes at max 2 days before
  • Make sure good quality wifi or wired internet connection in the room
  • Prepare microphone/headphones
  • Help organizer to create the recap slides for the end of each day (including newly learned file formats, usual HTS data analysis workflow)

During the workshop

  • Introduce yourself
  • Explain and show the use of participant chat
  • Remind learners to use post-it notes to give feedback
  • Answer questions on the participant chat
  • Publish Galaxy history regularly, for the participants who might be left behind
  • Check the instructor - helper chat regularly and adapt the pace in function

After the workshop

Templates

Conclusion

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.

References

The checklists has been adapted and extended from Galaxy and The Carpentries workshop checklists.