DNA Party workchoppe vol.1

Saturday 18th of July, 2015

The main language of this event will be English

Theme : "A first DNA workshop/workchoppe"

Participants

• Gianpaolo Rando, lead of the BeerDeCoded project email
• Jonathan Sobel email
• Luc Henry email
• Daniel Hernandez email
• Enrico Tenaglia email
• Clément Drévo email
• Alex Hansen [mailto: email]
• Yann Pierson email
• Ruud Hovius email
• Julien Hiblot email
• Yann Heurtaux email
• Brij Sahi email

Goal

Test the key points of our workshop format.

Practical Informations

For how to get there, see the #OpenHackuarium page
Format: 3x 20min presentation, hands-on molecular biology techniques

Schedule

• 10h00-10h20 Welcome. Luc Henry, (citizen science, DIY, science communication and context).
• 10h20-10h50 Visit to UniverCité. Coffee and croissants
• 11h00 - 11h20 Intro molecular biology, Gianpaolo Rando (DNA-tech).
• 11h30 - 13h00 Workshop: DNA extraction from fruit salad, PCR, gel.
• 13h00 - 13h30 Lunch like the monks: Intro bioinformatics (Jonathan Sobel).
• 13h30 - 14h00 Outlook: future steps (Luc, Gianpaolo). Beer surprise.

Questions/free time until 15h30.
Of course, everybody is more than welcome to stay for the rest of the day

Live Documentation

The original live hackpad is here.

The content was transferred below and edited for clarity.

What should be improved?

Below is a list of items that need to be included to the BeerDeCoded DNA workshop and comments about the draft presentations that were given on Saturday July 18th.

10.00 - 10.30 Welcome.

Considering the audience, a short welcome presentation was given, but needs to be structured and expended for later workshops

Introduction to UC (5 minutes) Yann Heurtaux

• General introduction (context, infrastructures)
• Practical informations (*WiFi, WCs, basic rules, how to for smokers

Introduction to Hackuarium (5 minutes), Luc Henry

• Context (Citizen science, DIYbio)
• Story

Questions? "We will talk a lot, so please interrupt"
Introduction (10 minutes), Everybody

• In French/English depending on the audience
• Activate participants: make them present themselves!
• Each participants gives a short introduction. Different possible formats (3 adjectifs qui pour elle/lui représentent ce projet (BeerDecoded). Chaque personne dit son prénom et une caractéristique qui le décrit dont la première lettre est la même que l’initiale de son prénom. Luc commence pour montrer l'exemple.

Introduction to BeerDeCoded (5 minutes), Luc Henry? What is beer?

• "Beer is not an ecosystem!" vs. "Genomically, it is!"
• "Beer was an ecosystem and we can analyze the genetic remains"
• Why BeerDeCoded?
• DNA project (5 minutes)

3 goals:

1. Science -> hypothesis, curiosity, test -> answer (even better with citizen)
2. Scicomm -> technology needs to be explained to the public
3. Community -> challenging multidisciplinary project

• Context for DNA: 23andMe, uBiome, etc..

10.30 - 11.00 Coffee!

11.00 - 11.20 Seminar

Introduction to Molecular Biology (20 minutes) Gianpaolo Rando

The slides can be found here.

Items and comments are in the order of appearance in the original presentation.

• Story - We need a good punchy story of BeerDeCoded -> Slides for the "kickstarter story" (pics !)
• Biology - This part needs to be shorter, beer-related, more metaphores -> one possibility is to use a storified approach. Historical events as introduction to knowledge
  
• The following details need improvement:

• • Many scales, after the intro slide,
  • Sub slides: 1x Ecosystem, 1x Individual, 1x Organ
  • News tools enable molecular descriptions
  • Emphasize visually "description" (cf. slide 4 as an agenda)
  • DNA slide 10: emphasize visually it is the "understanding" thing
  • More slides to illustrate the small line at the bottom "Human genome": 3.2 Gbp
  • Way more slides to explain 4 letters and how bases keep strings attached
  • Add more descriptie title/intro slide to slide 11
  • Why (bonus points for the memorable cat slide :))
  • Intro slide saying "let's rationalize the why". Trying to rationalize with science arguments doesn't talk to non-scientists!
  • Too many examples are far from the BeerDeCoded project. Focus on a couple with positive and negative aspects (lifescanner, 23andMe etc..). cCan we flag them as "they did it right/wrong" with strong message? Cityscale metagenomics slide 15: which city is it a map of? Conclusion: Useful, but needs to be short and clearly separated from our project. And 23andMe/Kuwait examples should probably come in the introduction.
  • Careful: missing the point with "why?" do not talk about bad examples of answering why Life Scanner : explicit biodiversity conservation

In general, needs more focus on beer and sequencing (ecosystem => list in beer)
"People have done it before, we want to do it for beer" -> Why databases were needed?

11.45 - 12.45 Practical DNA Workshop

13.00 - 13.20 Seminar

Introduction to Bioinformatics (20 minutes) Jonathan Sobel

The slides can be found [link here]

The original presentation was a Prezi that can be found here

Items and comments are in the order of appearance in the original presentation.

• Project workflow. When should be have that? Earlier?
• Backer's Survey. Nice plots showing the data behind the campaign. More can be done here. How much money, how many backers? 120 (survey of 60 people). Mention the actual question from the survey e.g. "Where do you come from?" "How did you hear about BeerDeCoded?" etc..
• This needs to be online. Merge with Kickstarter backend data (link to full data)!
• Nanopore sequencing video. Cool but mildly relevant, can we have shorter one for 454 and nanopore? Or simply a slide with "What is sequencing" and a basic explanation. If we plan to show a video, we need a sound system!
• How are we actually going to perform the sequencing? Needs to be clear that this is the only not-DIY step in the project.
• The slide with a sequencing file is great. Shows complexity, but the description of items is too detailed. keep it simple, focus on 3 items (Actual ATGC sequence, unique ID for samples, sample quality. Write on the slide what you are talking about (that line, that zone, that part of the graph...) and split one picture into more slides with boxes highlighted.
• Good slide on metagenomic composition -> typical example needed! love it!
• Great slide on existing database: People have done it before! But add message "Not using DNA like we will, but subjective parameters" So what can we see already using that data?
• Needs to explain PCA without even mentioning the name. "It is a mathematical methods to group items by similarity." It needs an alternate title. This only talks to scientists, be descriptive! "How to compare beers?"
• Results slide for beers ---> One single slide with 1. parameters 2. mathematical method 3. output (PCA of beers)
• Slide "we wouldn't do a family tree beers" you bar it, and explain why, then you explain why this or that display is interesting, describe what it is showing, "In BeerDecoded we will do this and that", "In BeerDecoded we needed to do this differently"... It has to be written on the slide, this is the principal message (insert "tweetable" slides between stuff)

13.30 - 14.30 Lunch

Pizza and discussion about workshop and talk.

14.30 - 15.00 Outlook

Discussion about future steps (Luc, Gianpaolo).

15.00 - 15.30 End of the day

To be done at the end of the day: "keep in touch" UC + Hackuarium part : 1 or 2 links max providing:

• next events
• social media
• calendars