BioStrike: Open Antibiotics Discovery

BioStrike
Open Antibiotics Discovery
biostrike.jpg
founder: denisakera
depends on:
interested: denisakera
software license:
hardware license:
status: active

Dedicated to Albert Schatz, who discovered streptomycin and saved millions from tuberculosis, our Nobel prize martyr-laureate. This project is trying to purify science through soil bacteria, which we hope will return research to people like him and find cure against big pharma greed. Read the story of Experiment eleven

Global open biology project supporting the ideals of open science, in which we screen soil bacteria, such as Actinomyces, Streptomyces and Micromonospora for antibiotic properties and to explore the user experience of sharing and discussing open data. It is initiated by DIYbio Waag in 2012 during the first DIYBIO Europe meeting in Paris (Dec 2012) and developed into a global project in October 2013 during a workshop in the Lorentz center in Leiden. It is a part of larger DIYBIO Europe project called BugID on bioprospecting of soil bacteria. The implementation started in October 2013 in a workshop called Innoculab session, by the Waag Society Open Wetlab and BiologiGaragen during the Re-new Festival in Copenhagen Biologigaragen.

Antibiotics have saved millions of lives over the last century. However, many microbes have evolved new mechanisms to withstand these once powerful medicine.

Participate in the BioStrike challenge to hunt for new antibiotics and learn about microbiology starting in your own backyard and kitchen.

There are microbes all around us and everywhere on the planet. They are constantly competing and battling to survive and evolve. Some microbes produces compounds that are toxic to other microorganisms, and these compounds can be used as antibiotics in medicine. The microbes and antibiotics are different all over the world and also depending on what the microbes are growing on, what medium. We invites individuals, high schools and communities to participate in the search for new antibiotic producing microorganisms. It’s up to the participants to find the optimal conditions and measure the capability of their strain to inhibit the growth of the reference strain. The results and strains will be collected and ranked on a global ladder. The data will be openly peer-reviewed by the organizing community.

Goals

A fun gamified competition and participatory community

Open participatory experiential learning

Low barrier to enter the challenge, but a potential of a gradually increasing learning curve as the participants progresses

Global scientific collaboration

Potential of discovering new antibiotics through Open drug discovery

There is an ongoing discussion on the hierarchy of goals in this project: bioprospecting, education, engagement, science communication, open science rituals & interpretation of science history, bioart- citizen science experiment. Pieter offered a good summary: “To me, it's more about engagement and education. You never know what you might find in the process. Just working with microbiology is an exciting to many people in itself. The project has a low entry level, and encourages collaboration, discussion and self education. It can be done as a workshop in groups, or by individuals in many different settings. It could be a nice answer to the many “where do I start”-topics on the global DIYBio discussion group, as it offers a guideline along which one learns what materials and equipment need to be acquired for what purpose. Furthermore, it explores the infrastructure that is needed to set up a true international collaborative DIYBio project, ultimately leading the way towards open drug discovery. Although the likelihood of finding a new antibiotic may be theoretically slim, it might be that this project will breed a new generation of scientists that will actually achieve that goal.”

Status

Phase 1: Defining the Protocol

Google Drive Results of the first workshop in Copenhagen

Synbiota collaboration on the protocol Protocol Discussions

Zotero links for articles Links

Google group discussion General discussion

Science Issues

Biosafety issues Isolating bacteria from soil

How to train people outside of a lab to understand and take proper measures against the health risk of dealing with soil isolates, such as Aspergillus mold?

1. Train people in professional microbiology safety procedures and building a BS2 lab. Maybe in collaboration with microbiology department and DIYbio labs in hackerspaces.

2. Designing the growth medium properly: Streptomyces selective medium preventing the growth of other organisms (mix the medium with antifungal cream?), treating the sample with heat (Streptomyces spores are mildly heat resistant, many other bugs are not).

3. Define basic rules, such as “You do not inhale and touch anything that grows on the plate” or “You dispose the medium by cooking it for x minutes under x temperature”

Logic behind this: “BSL1 restrictions are too abstract and not useful for an the average amateur. How is growing plates with diluted mud any different from leaving your dinner leftovers in a bin for 2 weeks at room temperature? The idea behind this project is to join the forces of science and people, not turning everyone into scientists.”

Basic rules: wearing gloves so you don't contaminate your plates with human pathogens, incubating at room temperature rather than body temperature, working underneath a tupperware box to provide a bit of a physical barrier to contamination, etc.

October 2013 guidelines Roskilde document

Original guidelines DIYbio EU guidelines

Evaluation of antibiotics

How to increase the chance of discovering some novel antibiotics?

Streptomyces have been mined for antibiotics for decades, how to bias the selection in favour of novel parts of the antibiotics spectrum?

How to support inexpensive way to screen tons of isolates, characterize their antibiotics, and identify the novel ones?

Phase 2: Design of Interaction over Agar Plates

Design Issues

1. The challenge is to use agar plates with inhibition zones from various locations to motivate people to take a lot of samples and share. Should it be a hunt, adventure, tournament, cross-platform (mobile, online, offline)?

2. What if the whole process is a form of science purification ritual, returning innocence to science against big pharma money industry? Connection with our soil is full with symbolic meaning, which we can use for some interaction ideas. Should we add this more “serious” dimension to the activities, so people get diploma with special bacterial ink or other paraphernalia related to being motivated friends of good bacteria or something? Helping science to remain open one bacteria per time?

3. Infographics explaining and helping the amateurs to work with agar plates and practice basic science protocols & safety.

User Experience ideas

How to use game elements (collecting, badges, tournaments)?

How to turn the images of inoculated plates and the zones of growth inhibition into game mechanics or some novel user experience?

1. Badge or Pokemon style collection with various “killers” in forms of photos, people name their agar plates/strains

Typical Badge Model Florcaching:

Badges associated with particular activities are placed on the virtual profile pages of users. Each badge is linked to an activity that has been identified as a motivation for gamers: fun, community involvement, competition or personal performance. For example, the Invasive Patroller badge requires users to create a cache of an invasive species, and the Friendly Floracacher requires players to check in with another person. Some of our badges relate to collecting a certain number of different plants, uploading images of plants that the Encyclopedia of Life needs photos of, validating the identification of other people’s caches, and being the first to find a new species…

Challenges in the badge model Gamification of Citizens science issues:

How can gamified apps be built to appeal to an audience that enjoys game-like interfaces, and an audience that may find them distracting?

How can gamification enhance the experience of an audience that already displays powerful intrinsic motivations?

How should gamified apps be modified when supporting data quality is a crucial task?

It seems like the badge model is good for supporting activities you do for the first time, but how good is it for tedious, everyday work? Maybe collections are better model for that, like collections of plates representing various strains and building something of an army.

2. Tournaments: every month the two strongest strains will compete and it is documented as stop animation

3. Cross-platform interaction

Actions of the microbes change some virtual world, people create their own narrative under certain mechanisms/systems/worldviews, people can win prizes from bioartist, so we connect citizen science with bioart.

Simon Park has a nice piece on textiles with Streptomyces http://exploringtheinvisible.com/2012/11/13/biogenic-designs-patterned-panacea/, maybe some fashion items from the most successful strains, which we will identify? The textiles infused with such bacteria have a forest soil smell and nice colours, velvety feeling.

4. Soil rituals http://en.wikipedia.org/wiki/Ritual_purification

APIs

How to integrate the various services with Synbiota?

Define API requirements for Synbiota.

Phase 3: Impact

How to sequence the successful strains?

Cooperation with some big sequencing company?

Metagenomic analysis and more open search for bacteria?

What licences to use in Open Science? Proposal http://creativecommons.org/licenses/by/3.0/

Research Questions

How can citizen science support open science and vice versa?

What collaborative mechanisms and user experience design strategies can improve sharing, crowdsourcing and discussing of data?

How to support open drug discovery with gamification, crowdsourcing and user experience design?

How to manage issues of biosafety, standardization of protocols and quality control on a global level?

What are the opportunities and issues in involving amateur and professional actors and stakeholders in the various stages of the project?

What roles can CC and similar open licenses play in open drug discovery?

How such project supports science communication and education, public participation in science and policy deliberation, but also the actual production of scientifically valuable data?

Documentation

Original BioStrike.odt proposal 2012

Simon Park Biprospecting proposal 2013 Despite this, the number of new antimicrobial compounds reported to have been isolated from this group has declined in recent years and is predicted to fall to zero in the next 1-2 decades. The Streptomyces, as a group, are predicted to be capable of producing at least 100,000 antibiotics, and only a minute fraction of this therapeutic diversity has been unearthed so far.

Lorentz center proposal 2013

Labitat Re-new digital arts festival Makerspace 2013

October 2013 Re-new digital arts festival Agar plates

Summary October 2013 Roskilde Festival

 
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