Governance Open Discussion: Why and When?

January 21, 2016 Leave a comment

Why is governance important?

These are notes on a discussion on 21 January, 2016, at Open Tools and Infrastructure for Biology 2016 held at Newcastle University.

  • Governance is for a common goal.
  • Provide structure and effective coordination – trying to reduce the “cost” of conflict resolution (conflict reduction). It is important that all know that there is a way things are supposed to work within the community.
  • It increases efficiency and decreases friction. Poor governance results in the opposite effect, and there does need to be iterative development of the governance methodology itself (the governance itself needs to be evaluated and modified).
  • It is an expression of the values within your community (e.g. how the community is represented and structured).
  • An open governance model means that feedback from within the community (3 people in a pub creating an add-on) can be quickly incorporated and made use of. It aligns well with modular design principles.
  • If the solution space is limited, then you don’t actually need much governance. If your goal is focused (and therefore so is the solution space), then a lack of governance might be best.
    • Governance provides a socio-political framework. If you don’t have many social or political requirements, you may not need governance.

As an example, the SBOL governance process has changed over time. One of the useful things it has provided is a framework of expectations and responsibilities of the various academics and companies. SBOL seems to be getting more open over time, and the changes in governance method has likely helped increase this openness.

If a community is too small, it could become closed because of “accidental obscurity”. You don’t want the governance structure to become an excuse for the standard not progressing.

Is it helpful to have a benevolent dictator?

Perhaps a better question than “Do we need governance” is “When do we need governance?”

In projects that are open and have more than one person, how do these people interact – what are the rules of interaction?

  • What does “open” mean, and who gets to choose its definition?
  • With “open”, you have to find the appropriate mixture (for you) of freedom and community consensus.
  • Does openness need to be imposed upon a newcomer? When someone wishes to participate in a group, you let them know what the rules/governance of the community are, and ask if they want to be a part of it. There is a distinction here in that people make the choice to be part of a community, and therefore the openness is not an imposition, as such.

For open science, we need governance. Openness implies some restrictions or rules, even if it’s just to state the (type of) openness itself. Governance doesn’t mean you are mandating behavior (necessarily). For instance, in SBOL you can extend it however you like (the freedom to extend) but you gain additional benefits if you follow the rules (a privilege if you follow the rules rather than using governance to mandate the use of the rules).

Example: Governance states a list of recommended formats. Users create open data files – if they are not in a format from the list, they don’t get the benefits of the other tools in the community which follow the governance policies. If they do use the format, you get immediate benefits wrt reproducibility and community.

What happens when there are multiple governance frameworks? The way you set up your governance may be incompatible for some people who are under a contradictory governance framework.

Do you need metrics to figure out how well your governance model is working as well as how well your community is developing? Or should such metrics be closely aligned / identical?

Who are all the players that have a say in governance? What do we exclude? Governance is ultimately the definition of who is the “in” group and who is the “out” group. The “in” group are the community, defined by their agreement to be governed according to the governance framework. However, a community needs to remain open to external input, otherwise bad decisions may be propagated.

How does governance began and how does it change over time?

  • How do decisions get made? You can organize your project to disperse your decision making to a greater or lesser extent. This results in either greater or lesser exclusivity of such decision making.
  • Various government strategies are dependent upon time and money resources – so some form of governance are only available to certain types of people.
  • How does governance pursue openness? There are very few ways in which communities devoted to openness actually get (monetary, social) credit for such commitment.
  • Different groups of people prefer different methods of communication, and this may have an effect on the governance method.
  • You need to have a singular goal or view, or it doesn’t matter what the governance method is, you will not be able to resolve anything. Deciding what the problem is, is a deeply social issue – without this, you can’t decide what is valuable and what your goal should be.

Please note that this post is merely my notes on the discussion. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be m

The OpenPlant Project

January 20, 2016 Leave a comment

Jenny Molloy

This is a presentation given on 20 January, 2016, at the Open Tools and Infrastructure for Biology 2016 held at Newcastle University.

Plants provide proven, global, low-cost technology for gigatonne scale bioproduction. Synthetic biology offers breakout technologies. Plants are useful because they are faster but still simple multicellular systems for engineering form and metabolism. Plant biotechnology is often beset by restrictive IP practices that threaten to constrain innovation. Creating open tools and technologies for plant experimentation will be very useful for future research. For instance, many parts of a typical plant expression vector are under patent. And once you start engineering entire metabolic pathways, the worry is that such patents will be an increasingly problematic issue. In seed patents, a small number of large players hold most of the information.

In plant biotechnology, most applications are IP protected. What would be useful to have is a shared toolset to promote innovation, and might allow smaller players to enter the market. More importantly there would be a social benefit WRT agriculture, drug production and greater openness. OpenPlant would be completely free and available to everyone, but leave some room to allow people to also go through the patent process if they choose. There are currently very few plant “parts” or biobricks available at the moment (compared with microbial parts).

There are a number of work programmes that the Open Plant initiative is trying to build: open technology EZ-MTA / Open MTA, a common syntax for DNA parts, low-cost automated assembly, marchantia (a simple plant chassis), genome-scale DNA engineering, and shared libraries of biological parts and resources. There are also core laboratories in Cambridge and Norwich, and the OpenPlant Fund (funding specifically for small-scale interdisciplinary projects).

Foundational Technology: Chassis, DNA Assembly, Gene expression, Genome engineering, open source software and modelling. Trait engineering projects include photosynthesis, carbohydrate engineering, natural products, nitrogen fixation, and virus-based methods for bioproduction.

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

The Bento Lab

January 20, 2016 Leave a comment

Bethan Wolfenden

This is a presentation given on 20 January, 2016, at the Open Tools and Infrastructure for Biology 2016 held at Newcastle University.

The Registry of Standard Biological Parts isn’t necessarily very user friendly (e.g. to newcomers), but the actual parts that are inside the registry are exciting. What she noticed with the Registry, is that unless you were an academic or associated with iGEM, it wasn’t easy to get a hold of these biological parts. In 2012 they investigated ways to give the public access to biobricks. https://biohackspace.org (@londonbiohack) was a part of this effort. Their work was summarized in Wired magazine. See also hackteria.org.

The Bento Lab is an affordable, user-friendly biotechnology laboratory. You should then be able to connect it to your laptop. Their first prototype was a “biolab in a suitcase” (Darwin toolbox). Now they have a functional 3kg DNA analysis lab. It has gel electrophoresis, PCR and a centrifuge. With it, they’ve demonstrated how you might go about doing lab work related to, e.g. the horsemeat in burgers scandal. Other ways to use it might include wildlife sampling (e.g. mushrooms), flavor identification, science competitions etc. Other examples: beer decoded (analysing yeast strains from beer). Helps people explore what might be possible when the technology is less of a barrier.

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

(Temporary Autonomous) Lab Building

January 20, 2016 Leave a comment

Brian Degger

This is a presentation given on 20 January, 2016, at the Open Tools and Infrastructure for Biology 2016 held at Newcastle University.

Trained in molecular biology, then transitioned to art and science instead of taking a post doc. Has seen the rise of bio-art, but not much biology resulting from that. Tools (e.g. Arduino) and a growing community (maker fairs, hack days, hackteria in 2009) led to increasing collaboration. He is going to cover TALs (Temporary Autonomous Labs). TALs are meant to be essentially zero budget. Work would range from basic DNA extraction through to putting a webcam into a digital microscope. You can perform some nice observations on things like complex lifecycles, quorum sensing etc.

DIY BIO Coding Europe 2011 – resulted in a Draft code of ethics from the European Congress. In Europe, the technology is regulated more than the output, whereas in America the questions arise later, e.g. when you’re ready to go to market.

TALs are labs set up in unconventional spaces for research or to run workshops. They last only a short time, for instance 1 day to 3 weeks. Some lab spaces might be a bar or cultural venue. In many cases, the chance of getting some of these things actually working were slim, but it was more about the journey. TALs are also meant to be cheap (use of micro controllers and sensors) and performed in a way that there is a high level of overlap with related experiments. TALs also have bespoke materials and protocols which respond to local conditions. This may mean that there are many local substitutions and some hacking involved. For instance, WRT basic microbiological media, they used domestic yeast extract instead of lab grade.

TALs still need to have an appropriate safety awareness and lab rules which are contingent upon the experiment. BS0 (biosafety zero) experiments are those that pose no or limited risk to the experimenter. Also, one-way culturing, e.g. microbial kisses and octopus dissection (looking/experimenting/eating). With a TAL, you can “roll your own lab”, and see lab building as a process. This highlights the importance of labelling and questioning. What is the lab for? What are the parts? Workshops run with TALs include daphnia hacking, octopus dissection, kinchi making, sima making, spice detectives, glowing squid, glowing wood, glowing…everything! Degger then described Gjino Sutic’s work on building a “beating heart” by stitching cellulose together. They do outreach through maker fairs and libraries rather than through their own lab.

Workshop-o-logy… There has been some “cross-pollination” with Hackterias. There are also workshops run in labs themselves. In 2014 they had a “make your own” hackteria, e.g. what kind of lab shaking equipment can you make from commonly-found motors? He spent some time doing transitlab.org in 2011. There are some groups which take slack time in other organizations, e.g. Field Notes. Other interesting projects: OpenPump.org, OpenTrons.

What are the TALs place WRT more academic/permanent labs? Are low cost labs better for teaching bioscience? Interesting questions…

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

OpenDrop: an ecosystem of open digital microfluidics

January 20, 2016 Leave a comment

Eugenio Battaglia, @battagliaem

This is a presentation given on 20 January, 2016, at the Open Tools and Infrastructure for Biology 2016 held at Newcastle University.

OuiShare, OpenDrop.

OpenDrop is made by a group of labs and individuals. In order to increase reproducibility and lower errors, automation is a common solution to as many of the (pipetting mixing splitting, labelling and handling) steps in the lab as possible. In microfluidics in biology there are, broadly speaking, two categories: channel microfluidics and electrowetting.

Wheeler Microfluidics Lab in Toronto are developing a machine called DropBot. They are interested in openness where possible. Then, via their digital biology uResidency, they looked into producing something that was like, but cheaper than, the DropBot. They came up with their “Open Science Digital Bio Device”. They studied the 50 most used and labor instensive protocols in biological labs, and tried to come up with was to apply these protocols to their design. The result is OpenDrop. Then DropBot people were happy with the collaboration, and blogged about OpenDrop and its relationship to DropBot. The Waag Society (see Pieter’s talk from earlier today) also organized a microfluidics hackathon. This was just the start – there are a number of other similar efforts.

For the future, the idea is to have people really involved in certain areas of future tasks because they are interested in that area. Contributions are ad hoc, as the people have time. The mixing between engineering and biology has really accelerated, and the DIY BIO movement is popular. However, some projects are not sustainable, and why is this? Is it money? Is it when the community is more of a bazaar or a cathedral (Eric S. Raymond)? Perhaps it’s less about being a cathedral or a bazaar, and more of a simple design issue – is it a good design, or a bad design?

“Platforms are essentially bureaucracies for the networked age” (I lost the owner of this quote). Deloitte (The Value Multiplier) says there are 4 business models in history: asset builders, service providers, technology creators and, more recently and perhaps more importantly, network orchestrators. He describes how a project will be responsive and collaborative when there is both a high alignment of goals and a high level of autonomy. The governance model he really likes is Liquid Organization (the cocoon project). The governance meetings are a mixture of weekly coordination, monthly catch up, quarterly kick off, and global jam (twice yearly).

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

Promoting open notebook science in an institutional biotech lab

January 20, 2016 Leave a comment

Speaker: Rahmi Lale

This is a presentation given on 20 January, 2016, at the Open Tools and Infrastructure for Biology 2016 held at Newcastle University.

PhotoSynLab: working with Mesophiles, psychrophiles (some of these can grow at -10 degrees) and eukaryotic algae. Built a plasmid pTA-Mob and published in PLoS One, which allows you to do conjugation – the host can work as a donor in conjugation. It has a broad host range, practically all gram negatives.

When discussing the openness aspect of his work, he begins with the four essential elements of the scientific method: characterization, hypotheses, predictions, experiments (and of course, publishing). He will be focussing on reproducibility. With respect to publishing, “you have to understand human nature”. In publishing and sharing, there is a tension between cooperation and competition. Many believe that those scientists who make the greatest contribution often behave the worst, and vice versa.

In a 2014 Nature Methods editorial where they tried to stress the importance of the methods section of papers, they say that an open implementation provides confidence in the performance of a method, but also increases the likelihood that other researchers can build upon it.

An article about computer science in a publication is not the scholarship, but merely the advertising of the scholarship (Jon Claerbout). The inability to reproduce experiments indicates the possible limits of big science, and that without verification there is no science (Garfield, 1990).

A researcher moves from experiment to publishing, while a reader moves in the opposite direction. Having your data free isn’t such a big deal, but having a standard method of how you got your data there is more of an issue.

On their lab website, they give access to the raw data and the analysis (using wordpress). The latest version uses (is?) Benchling. The idea behind all of this is to aid reproducibility by giving access to all data and analysis. They also wish people to publish negative as well as positive results. This should aid career development by involving students in scientific writing. It is important to teach students how to communicate their science.

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

 

The BioStrike Project

January 20, 2016 Leave a comment

The BioStrike Project, or how to hack your way out of antibiotic resistance.

Pieter van Boheemen

This is a presentation given on 20 January, 2016, at the Open Tools and Infrastructure for Biology 2016 held at Newcastle University.

Technology is not neutral. It is always tailored towards a certain world view or opinion. The choices are made between competition and collaboration, and centralized versus grass roots. This research group works with a variety of people (including artists) performing “creative research”, mixing art, science and technology.

In their projects they bring a number of different attitudes, one of which is MAKER. Making is crucial to understand and act in our world. The best producers of technology are the users themselves. The Makers are brought together with artists. An example of this is the “Fat Project”, examining the role of fat in society. They strongly believe in “engaged citizens”, and involving everyone in what they do.

Pieter is trained in biology / biotechnology. He has set up the Open Wetlab, where they can try and build their own tools and their own experiments in a new layout and setup (e.g. they’ve made their own bioprinter). A couple of years ago they started up a Meetup community, where you can come into the Open Wetlab to do your own experiments. Every Tuesday people get together to work on community projects. “Do it Together Bio” includes making your own superfoods, bioprinting and all sorts of other things. One workshop was making competent cells (CLab) trying to show the community what can be done in the lab.

They also worked on the Bio Solar Ensemble, which combined bio art and performance art. At a festival, you could inject zebrafish embryos with algae to start a discussion in the community.

Lately he’s been working on the BioHack academy, which organizes all of the stuff they’ve been doing in the Open Wetlab into a single course. They also teach people about what it means to be a hacker – it’s an attitude, a subculture. It means:

  • Create & share,
  • freedom of inquiry,
  • hostility to secrecy,
  • sharing as ideology and strategy,
  • the right to fork,
  • emphasis on rationality,
  • distaste of authority, and
  • playful cleverness.

Everything in the BioHack academy is freely available – all course material, lab work etc. There are a number of BioHack Academy partner labs as well. There have been two years now of the BioHack Academy. BHA3 (the current one) has an even bigger set of partner labs.

BioStrike has been going on in the “biohack scene” for a while, and revolves around the issue of antibiotic resistance. NESTA is handing out a prize of £10 million to develop new diagnostic tools – the Antibiotic Resistance Challenge. They have a current project called the Art of Impact.

About 65% of all antibiotics that we have are derived from Actinomyces. The simpler antibiotics have largely been found (vancomycin and daptomycin). Most microbes cannot be screened and therefore cannot be tested – in theory there is a lot to be discovered. They have built their own version of the iChip called the Double Sandwich Diffusion System – these tools are used in metagenomics. The PetShop Project allows people in the community to buy microbes, and buy tools related to it. They’ve got a “DIY” approach to try to find antibiotics.

The industry claims that there is a 23 year delay between antibiotic creation and profit. They suggest new types of patents, product development partnerships, reimbursement to the industry after AB development, tax discount for AB development, and loosening of regulations… Where is the “open” in the development of AB by the industry? He says that if you search, you can find suitable companies…

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

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