Open-Food-DNA - Revision history

Talia S: /* Current status */

2019-12-13T16:39:37Z

Current status

Talia S: /* Current status */

2019-12-13T16:39:16Z

Current status

Talia S: /* Current status */

2019-12-13T16:38:43Z

Current status

Talia S: /* Team */

2019-12-13T14:21:55Z

Team

Talia S: /* Team */

2019-12-13T14:09:34Z

Team

Talia S: /* Team */

2019-12-12T16:25:00Z

Team

Talia S: /* Current status */

2019-12-09T12:54:02Z

Current status

Talia S: /* Why DNA? */

2019-12-09T12:42:56Z

Why DNA?

Talia S: /* Why food? */

2019-12-09T12:40:42Z

Why food?

Talia S: /* Why citizen science? */

2019-12-09T12:39:49Z

Why citizen science?

@@ Line 59: / Line 59: @@
 The informatics pipeline will be in a public repository on GitHub.
-This is the summary of the sequencing run from the second workshop: [[191102report.pdf]]
+This is the summary of the sequencing run from the second workshop: [[File:191102report.pdf]]
 ===Similar projects===

@@ Line 59: / Line 59: @@
 The informatics pipeline will be in a public repository on GitHub.
-This is the summary of the sequencing run from the second workshop: [[File:191102report.pdf]]
+This is the summary of the sequencing run from the second workshop: [[191102report.pdf]]
 ===Similar projects===

@@ Line 58: / Line 58: @@
 Results will be posted here shortly - if you are impatient you can write to dna@foodrepo.org!
 The informatics pipeline will be in a public repository on GitHub.
 ===Similar projects===

@@ Line 83: / Line 83: @@
 '''Marcel Salathé''' (head of Digital Epidemiology lab, EPFL) works at the interface of biology, computational and social sciences. Driven by open science and innovation, Marcel has been committed to making this project happen from the get-go, providing a home for it in his lab within the FoodRepo project and championing it to funders, partners and the media.
-'''Talia Salzmann''' (Project Manager at Digital Epidemiology Lab, EPFL) trained in Life Sciences and in Public Health. She coordinates the project and is enthusiastic to see it develop. Besides being excited by the advanced science involved, she believes it can improve health through food transparency and awareness as well as bring together a vibrant community gravitating around Hackuarium.
+'''Talia Salzmann''' (Project Manager at Digital Epidemiology Lab, EPFL) trained in Life Sciences and in Public Health. She coordinates the project and is enthusiastic to see it develop. Besides being excited by the scientific progress involved, she believes it can improve health through food transparency and awareness as well as bring together a vibrant community around Hackuarium with an interest in food.
 <u>Useful links: </u>

@@ Line 71: / Line 71: @@
 ==Team==
-'''Paulina Martinez''' (Field Application Scientist at SwissDeCode, PhD biochemistry) and '''Pietro Cattaneo''' (Product Development Scientist at SwissDeCode, PhD molecular plant biology) joined their forces to develop the first protocols for democratizing genetic sequencing of food samples under the helm of Gianpaolo Rando.
+'''Paulina Martinez''' (Field Application Scientist at SwissDeCode, PhD biochemistry) and '''Pietro Cattaneo''' (Product Development Scientist at SwissDeCode, PhD molecular plant biology) joined forces to use their expertise to develop the first protocols for genetic sequencing of complex food samples and produce a large dataset of food DNA, under the helm of Gianpaolo Rando. They also guided participants through both versions of the protocol when they were piloted in a community setting (v1: Pietro, v2: Paulina).
-'''Gianpaolo Rando''' (CEO at SwissDeCode) is one of the initial instigators of the project to sequence food using NGS with an open science approach and was part of the ancestor project: BeerDeCoded. Gianpaolo holds a Ph.D in biotechnology and has 10 years of experience at the interface between genomics and nutrition. He is a proud member of Hackuarium and has a passion for food and drinks.
+'''Gianpaolo Rando''' (Founder and CEO at SwissDeCode) is one of the initial instigators of the project to sequence food using NGS with an open science approach and was part of the ancestor project: BeerDeCoded. Gianpaolo holds a Ph.D in biotechnology and has 10 years of experience at the interface between genomics and nutrition. He is a proud member of Hackuarium and has a passion for food and drinks.
 '''Luc Henry''' (co-founder of Hackuarium) holds a DPhil in chemical biology and has a strong interest in the impact of new technologies on society, in particular in the fields of biotechnology and health. He is scientific advisor to the presidency at EPFL and wants to promote an open approach to science and innovation. Luc is also one of the first to have conceived the project and was part of BeerDeCoded.
-'''Rachel Aronoff''' (president of Hackuarium) is biosafety officer and project manager at Hackuarium, in which she has been involved since 2015. Rachel is a passionate biologist who has worked on a wide range of projects since her PhD in microbiology, including founding the non-profit, AGiR! Action for Genomic integrity through Research!, focussing upon dynamic cellular processes and making wiser choices to improve public health.
+'''Rachel Aronoff''' (president of Hackuarium) is biosafety officer and project manager at Hackuarium, in which she has been involved since 2015. Rachel is a passionate biologist who has worked on a wide range of projects since her PhD in microbiology, including founding the non-profit, AGiR! Action for Genomic integrity through Research!, focussing upon dynamic cellular processes and making wiser choices to improve public health. She has provided a lot of support to the project including hosting the workshops.
-'''Olivier Emery''' is an expert bioinformatician who has been active at Hackuarium for several years, especially for his project BeeMos which was connected to his PhD on bee gut microbiota. Olivier took part in the first Food DNA workshop and then took on an active role as the project's bioinformatician and coordinator for the second part of the project.
+'''Olivier Emery''' is an expert bioinformatician who has been active at Hackuarium for several years, especially for his project BeeMos which was connected to his PhD on bee gut microbiota. Olivier took part in the first Food DNA workshop and then took on an active role as the project's bioinformatician and Hackuarium, coordinator for the second stage of the project.
 '''Marcel Salathé''' (head of Digital Epidemiology lab, EPFL) works at the interface of biology, computational and social sciences. Driven by open science and innovation, Marcel has been committed to making this project happen from the get-go, providing a home for it in his lab within the FoodRepo project and championing it to funders, partners and the media.
-'''Talia Salzmann''' (Project Manager at Digital Epidemiology Lab, EPFL) trained in Life Sciences and in Public Health. She coordinates the project and is enthusiastic to see it develop and improve health through food transparency and awareness.
+'''Talia Salzmann''' (Project Manager at Digital Epidemiology Lab, EPFL) trained in Life Sciences and in Public Health. She coordinates the project and is enthusiastic to see it develop. Besides being excited by the advanced science involved, she believes it can improve health through food transparency and awareness as well as bring together a vibrant community gravitating around Hackuarium.
 <u>Useful links: </u>

@@ Line 54: / Line 54: @@
 ===Current status===
-The first protocol developed by SwissDeCode will be piloted at Hackuarium by a group of volunteers who will provide feedback. The 10 participants are biohackers, scientists, open science and consumer rights advocates. The first workshop took place in May 2019, and the second is planned for 2 November!
+The first protocol developed by SwissDeCode was applied to 370 products, generating DNA datasets for > 200 products. This protocol was also piloted in a community setting during a workshop in spring 2019. An open bioinformatics pipeline (WIMF) was set up to analyse this data. While some showed clear ingredient identification, there remained a lot of ambiguity with closely related species. To try and solve this challenge, a second protocol was designed with different primers. This was tested for the first time in a second workshop in autumn 2019, and is being tested in a professional lab at SwissDeCode to provide a large enough dataset to examine in detail. In parallel, the bioinformatics pipeline is being expanded to accommodate the new markers.
 ===Similar projects===

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 ==Why DNA?==
-We cook and eat animals (meat, fishes), plants (vegetables, spices) and fungi (mushrooms, yeast). These are all life forms, so they all contain DNA - thus our food is full of DNA. With DNA, it could be possible to identify, classify and count all the species present in a food serving.. In a portion of lasagna, ground beef and horse meat may look similar, but their DNA differs and can be identified through sequencing. Scientists have identified short sequences that are conserved in each category ( animal, plants, mushrooms) that change a tiny bit between species - which effectively can be used like a barcode to identify different species. The consortium barcodeoflife.org has made a list of unique DNA identifiers for 300,000 species collected around the world. We have access to this data and to the technology to interrogate thousands of different DNA species in a complex sample.
+We cook and eat animals (meat, fishes), plants (vegetables, spices) and fungi (mushrooms, yeast). These are all life forms, so they all contain DNA - thus our food is full of DNA. With DNA, it could be possible to identify, classify and count all the species present in a food serving. In a portion of lasagna, ground beef and horse meat may look similar, but their but that contain small differences between each species. This sequence can be used like a barcode to identify different species, and infact these sequences are referred to as DNA barcodes. The consortium barcodeoflife.org has made a list of unique DNA identifiers for 300,000 species collected around the world. We have access to this data and to the technology to examine thousands of different DNA species in a complex sample.
 ==Why Open Data?==

@@ Line 30: / Line 30: @@
 ==Why food?==
-The project initially turned to food as a tool to explain genetic technology while avoiding  the many pitfalls related to health data, such as privacy and regulatory issues. However, this has since taken on a life of its own as food transparency is a crucial issue in today’s industrialized and globalized  food chains. ood concerns everybody. Some people have health, religious or ethical reasons for avoiding certain types of food. Others just want to choose healthy, natural, or local ingredients. But how can we know? As previous studies and whistleblowers have shown, the food industry is a complex black box of sorts - where additives and relabelling often lead consumers to eat something they would otherwise have stayed away from. We have limited knowledge about what exactly composes our diet. Today's information comes from the suppliers who themselves rely on their suppliers. Does a dish really contain what is written on the label? Where do the ingredients really come from? Does the food contain allergens, pesticides, GM crops, etc.?
+The project initially turned to food as a tool to explain genetic technology while avoiding  the many pitfalls related to health data, such as privacy and regulatory issues. However, this has since taken on a life of its own as food transparency is a crucial issue in today’s industrialized and globalized  food chains. Food concerns everybody. Some people have health, religious or ethical reasons for avoiding certain types of food. Others just want to choose healthy, natural, or local ingredients. But how can we know? As previous studies and whistleblowers have shown, the food industry is a complex black box of sorts - where additives and relabelling often lead consumers to eat something they would otherwise have stayed away from. We have limited knowledge about what exactly composes our diet. Today's information comes from the suppliers who themselves rely on their suppliers. Does a dish really contain what is written on the label? Where do the ingredients really come from? Does the food contain allergens, pesticides, GM crops, etc.?
 How much more complex is it than what the label says?

@@ Line 24: / Line 24: @@
 # Produce an open access knowledge database.
-==Why citizens?==
+==Why citizen science?==
 Switzerland is amongst the world’s most productive countries in terms of research and innovation. Citizens have a direct impact on the future role of genetic technologies in our economy and society. Our project demystifies DNA science and stimulates public interest for topics usually confined to R&D departments. We want to let people engage in science and make more informed decisions.