Systematic tools for reprogramming plant gene expression in a simple model, Marchantia polymorpha.
Sauret-Güeto S, Frangedakis E, Silvestri L, Rebmann M, Tomaselli M, Markel K, Delmans M, West A, Patron NJ, Haseloff J.
ACS Synth. Biol. 2020, 9, 4, 864–882
We are a small, merry band of newbie Biomakers and amateur homebrewers and have started a project to monitor the progression of our fine brews in real time. By day we are two research scientists and a Biology teacher.
We are looking to develop a piece of kit which allows us to see how quickly our homebrew is turned from a mixture of sugars in the initial malty extract into alcohol in beer. As sugars are converted to alcohol by the yeast, the density, or Specific Gravity (SG), of the liquid decreases and this is traditionally monitored by the means of a hydrometer. The SG decreases over time until it reaches a final plateau, at which point all of the sugars have been turned into alcohol. We are interested in monitoring how quickly this happens and how we can monitor it in real time.
Sam’s Biomaker Starter Kit arrives “what an exciting package to find on my desk first day back in the lab in 2019!”
An alcohol meter, testing beer immediately after brewing but before fermentation.
Image by Jeena on Wikipedia, shared under CC BY-SA 3.0
Getting started…
As two of us have absolutely no prior knowledge of using Arduinos the first challenge has been to work out which end of the lead plugs into the laptop and which end into the Arduino. One of us has much more experience of programming, but not huge experience with Arduinos. It’s pretty much a ragtag skillset, held together with a Whatsapp group, copious mugs of tea, soup, swearing and an overarching dedication to the cause of better homebrew.
The learning curve of getting the Arduinos, laptops and components to talk to each other was incredibly steep. A few pointers from the ever-helpful Colette Matthewman helped immensely. Gratifyingly learning the XOD aspect of the project has been pretty straightforward. The online tutorials have stepped us through what we need to do in a logical manner.
Our initial design has been modified, from just monitoring the height via the height sensor supplied, to attaching a Hall Sensor to the Arduino and attaching magnets to the hydrometer. We have developed ideas which can spring from this once we’ve got the basics in place and are quite excited (an overused word), about the potential scope of what we’re playing with.
We are still very much in the early stages of the project, but are learning and have welcomed the opportunities to work towards a common goal (better beer), whilst acquiring new skills. This project has some way to run and will, no doubt, be adapted, modified and changed over time.
Follow our progress (intermittently) via twitter @dewhurst_ben, @popupcamptrout, @LP_Alwyn, @AutoBrewControl
More information about the Biomaker Challenge can be found at www.biomaker.org
The 2018 Summer Biomaker Challenge was wrapped up in October with a showcase event, but it not all over. Biomaker activities are still going strong! Below is a summary of activities as well as a write up of the Biomaker Fayre and the winning teams….
Winter Software Challenge (apply by 16 December 2018): Interested in programming? Low-cost hardware for science? Learning new skills with a team? We provide the hardware, you develop software nodes for integrating hardware with new graphical programming interface, XOD. More information at www.biomaker.org/apply-now - a quick, rolling application process so you can receive your kit and start playing ASAP!
Norwich Biomakers - An interdisciplinary network exploring the cross-over of biology with design, technology, engineering, electronics, software, art and much more. A place to learn about the latest technologies, share ideas and skills and shape projects. We meet up on a monthly basis.
Cambridge Synthetic Biology meetups - A clearing house for a wide variety of regular open meetings like Cafe Synthetique, Science Makers and the SRI Forums - with a particular focus on building tools and interdisciplinary research.
Cambridge Biomakespace - Scientists, engineers, students and entrepreneurs are developing the new Cambridge Biomakespace - an innovation space for building with biology in the historic MRC Laboratory of Molecular Biology building.
On Saturday 29 October, over 100 attendees came together in the University of Cambridge Department of Engineering to showcase and celebrate open-source technologies in research and education. The day consisted of a morning of talks followed by the Biomaker Fayre, where this year's ten Biomaker Challenge teams exhibited their projects alongside industry leaders and independent makers.
We started the day with some inspiring talks: Paolo Bombelli & Alasdair Davies on open tools for animal conservation and the "Powered by Plants" project, Grey Christoforo on hacking 3D printers to create better solar cells, Helene Steiner on OpenCell and teaching the next generation of designers to work with scientists, Richard Hayler on citizen science and education with Raspberry Pi and Julian Stirling on open instrumentation for Africa.
After a coffee break and lunch, we headed upstairs for the Biomaker Fayre. There was a festive feel to the space- gold balloons marked each exhibit, 3D-printed trophies were on display to be given out at the end of day, and attendees filled the space, excited to get involved and try out some hands-on demos.
Exhibits covered everything from a cartesian coordinate robot for dispensing fruit fly food to a wearable biosensor for monitoring vaginal discharge and a temperature-controlled container for sample transportation. Among the exhibitors were the ten Biomaker Challenge teams. In June, each team were given a £1000 grant and four months to turn their ideas for open source and DIY research tools into a reality.
The Biomaker Challenge judges were very impressed by each one of the projects and ended up deliberating for over an hour. In the end, the 3D-printed trophies (low-cost and DIY of course) were presented to the following teams:
Dual-View Imaging in a Custom-Built Light Sheet Microscope
Stephanie Hohn, Hannah Sleath, Rashid Khashiev, Francesco Boselli, Karen Lee
"The large variety of Biomaker projects was very inspiring. We had a lot of fun during the challenge and the feedback from people in different fields was really helpful. It was great to get in touch with programmers, engineers and designers. We received a great confidence boost for future more technical projects."
Stephanie Hohn (University of Cambridge)
Spectre, Low-cost whole-cell biosensors for environmental and medical surveillance.
Feng Geng, Boon Lim, Xiaoyu Chen, Jimmy Chen
"The Biomaker Challenge has provided us a great opportunity to extend our research into real-world application. As most of us come from a biological background, we faced a lot of difficulties on assembling the electronics and programming our Arduino kit. With three months of perseverance and constant guidance from our advisor Tony, we managed to come up with a customised, miniaturised spectrophotometer which can be used in conjunction with our whole-cell biosensor. We received an Arduino kit and sufficient funding to get us through the proof-of-concept stage of our project and from here, we are planning to further develop and optimise our device into a start-up company. It is amazing to think that it all starts with a small Biomaker Challenge Summer Project!"
Boon Lim, University of Oxford
Wearable biosensor for monitoring vaginal discharge
Tommaso Busolo, Giulia Tomasello, Michael Calabrese, James Che
"We all really enjoyed the multidisciplinary nature of the challenge, working with people from all sorts of backgrounds. We feel we now have a much clearer, hands-on insight into how the more diverse a collaboration is, the more relevant, impactful and exciting the results of ideas brainstorming can be!"
Michael Calabrese, University of Cambridge
Biomaker Challenge and Open Technology Workshop aimed to show the value of open, low-cost and DIY technologies as convening points for interactions between biologists and engineers. They are also important educational tools for those who are interested in developing technical skills and have great potential for improving the quality of science and increasing productivity in the lab for lower costs. With the proliferation of digital designs for 3D-printing and easily available consumer electronics like Arduino which has a huge community of users and lots of online help, designing your instrumentation around your experiment rather than vice versa has never been more possible.
Check out more photos from the day!
The descriptions of all prototypes are available at www.hackster.io/biomaker. To find out more about the most recent and upcoming competitions go to www.biomaker.org/biomaker-challenge to be kept up to date with developments.
Biomaker Challenge 2018 was funded by OpenPlant, a BBSRC/EPSRC Synthetic Biology Research Centre Grant BB/L014130/1. The Biomaker Challenge and Open Technology Workshop were coordinated by University of Cambridge's Synthetic Biology Strategic Research Initiative
Aleksandr Gavrin pitching his proposal.
Friday 1 December 2017, Norwich, was the day of the pitches for the 5th round of OpenPlant Fund proposals – and what an exciting set of proposals they were. Eleven proposals were pitched, ranging from development of plant tools and methods, to cell-free protein production, software and hardware development, training, and development of resources for schools in Ghana.
The OpenPlant Fund is rapidly building a dynamic community of early career plant synthetic biologists. The Fund has awarded over 60 micro-grants between 2015 and 2017 to projects facilitating exchange between University of Cambridge, the John Innes Institute and Earlham Institute in Norwich and a range of external collaborators for the development of open technologies and responsible innovation in the context of synthetic biology. Through these awards, OpenPlant aims to promote plant synthetic biology as an interdisciplinary field. This latest round of “high quality, innovative and novel ideas” – as judge Richard Hammond of Cambridge Consultants put it – highlights the engagement, motivation and drive the is present within the local community. More information on the Fund can be found at www.openplant.org/fund and documentation of OpenPlant Fund projects can be found at www.biomaker.org.
Fern gametophyte photographed by Dr Jennifer Deegan using her focus stacking photography platform. More information, images and project documentation can be found through http://chlorophyllosophy.uk/
The first talk, coming to us via skype, pitched for funding to further develop a focus stacking photography platform for teaching and publication in plant sciences. Impressive images of fern gametophytes showed the current scope of the platform developed through the Biomaker Challenge. Presenter Jennifer Deegan (University of Cambridge) made full use of skype by demonstrating the hardware setup, explaining how it would be further developed to expand its scope, and how it would be adapted to build a cheap system for schools.
Next up, Aleksandr Gavrin (Sainsbury Laboratory, University of Cambridge) presented a proposal to make stable transgenic Medicago truncatula lines in which actin is tagged with a reporter gene as a tool for legume researchers. In another legume-focused project, Abhimanyu Sarkar (John Innes Centre) proposed to establish a transformation system for the orphan crop Grass-pea. While there were some challenging legal questions surrounding the shareability of the system, the judges recognised the urgent need for new developments in transformation.
Image by Pablo Ramdohr, shared under licence CC BY 2.0
Proposing to compare cell-free and plant expression systems for protein expression, Susan Duncan (Earlham Institute) pitched a project that would analyse synthesis of proteins, focussing specifically on transcription factors. New collaborations between groups in Norwich and Cambridge will provide Susan with a variety of transcription factors to test.
In a related, but “very independent” project, Quentin Dudley (Earlham Institute) proposed to compare protein synthesis in two different cell-free systems, E.coli and wheat germ lysates. The project aims to gather data on yield vs cost of the two systems. He extended on open invitation for people to ask him “can you try my protein”. So, get in touch if you’d like your plant protein to be tested in Quentin’s cell-free systems.
The third cell-free proposal came in via skype, with Clayton Rabideau (University of Cambridge) rubbing the sleep from his eyes to pitch from the US in the early morning hours. Clayton pitched for funding to develop a hardware system called Open-Cell, using machine learning together with microfluidics-based cell-free screening assay technology for screening of enzyme activity.
A third theme that came out through the pitches, was the need for computation, software development and training. Chris Penfold (University of Cambridge), who had arrived straight off a plane from Venice, proposed an ambitious project to develop a suite of computational tools to simulate large gene regulatory networks in plants and mammals. These tools aim to improve rational design and predictability in synthetic biology.
Jan Sklenar (The Sainsbury Laboratory, Norwich) presented a proposal to bring together proteomics experts and bioinformaticists with expertise in R software. To do this, the group propose a series of workshops for knowledge exchange and training to help both disciplines understand each other. Following these workshops, the team will work together to integrate the ‘R for Proteomics’ package, developed at the University of Cambridge, into Norwich proteomics workflows and further develop the software suite. Jan’s driving motivation for the project is to “be more efficient” and require “less manual interference” for proteomics analysis.
A final computational project was pitched by Aaron Bostrom (Earlham Institute) who talked about mutant worms and Raspberry Pi’s in a proposal to develop a training programme designed around sensing hardware for data collection and machine learning for plant synthetic biology projects.
An artistic representation of a plant-microbial fuel cell, submitted in Paolo Bombelli's proposal
Two energetic presenters pitched projects focussed on engaging directly with an international group. Paolo “the plant electrician” Bombelli (University of Cambridge) pitched for match-funding to enable him to run an international biodesign competition for the development of prototypes for a plant-microbial fuel cell to be used in remote jungle regions as an environmentally friendly power supply for a sensor and camera-trap to be used by Zoologists.
Waving his hands as he introduced himself, PhD student Hans Pfalgraz (University of East Anglia and John Innes Centre) proposed a project, working with Kumasi Hive innovation hub and the Lab_13 Ghana practical science education project, to take inspiration from previous OpenPlant projects and develop open source practical teaching activities, testing these in Ghana and then making more widely available for schools in other low-resource settings.
“This was a great event and I thoroughly enjoyed it. It felt like we visited all four corners of science in a couple of hours. The proposals were of a high standard and well presented with some fascinating new ideas to understand and discuss. Well done to all involved.’”
“It was a great day, very good science, creativity and a warm welcome. Thanks for the invite!”
“We heard a number of compelling and original ideas, the majority being led by early career researchers. It was particularly impressive to see so many new collaborations and networks being built, both between the Open Plant Research Institutes and with external partners.”
The eLife Innovation Sprint is a two-day challenge on 10-11 May 2018 for developers, designers, technologists and researchers to collaboratively prototype innovations that bring cutting-edge technology to open research.
The eLife Innovation Initiative have been working to improve research transparency and accessibility, and accelerate discovery in the life sciences, by developing open-source technologies in collaboration with the wider community. They have heard many excellent ideas for transforming how the latest science is shared, built upon and recognised, and they want to create a space that would help translate these ideas into action.
By bringing ideators, creators and users together for the Innovation Sprint, they hope to provide space, time and access to diverse skill sets for the community to develop their ideas into prototypes and forge new collaborations.
eLife invite you — whether change maker or web wrangler, UX champion or data tinkerer — to apply to participate in person.
Applications will close at 9am GMT on March 5 2018, and we aim to communicate the outcome of each application by March 23 2018.
OpenPlantand The Synthetic Biology SRI, Public Policy SRI and Faculty of Law co-organised a workshop held on 28 January 2016 on the openness of large bioresources in synthetic biology and genomics. The resulting report by Dr John Liddicoat and Dr Kathy Liddell has now been published on SSRN.
Research in synthetic biology and genomics depends on the use of collections of tissue and data, commonly known as bioresources. Substantial amounts of time and money are being spent on creating these bioresources and it is likely that significant scientific breakthroughs and development of end-products may be missed or delayed if the tissue and data in these resources are not shared. Accordingly, the ‘openness’ of these bioresources — in other words, the ability for other researchers to access, use, and share these resources (which is typically recorded in a bioresource’s IP and access policy) — is a key issue for the success of bioresource initiatives and the progress of synthetic biology and genomics.
There are, however, many different approaches to openness, and the development and dissemination of new knowledge are not necessarily advanced by distributing material at low cost or without any restrictions; time-limited rights of control (e.g. IP rights) may provide a useful incentive. It is a significant challenge to develop a fit-for-purpose openness policy that balances the advantages (and disadvantages) of different approaches to openness. The Workshop addressed this challenge by: reviewing openness policies adopted by large bioresources; eliciting ideas about access and intellectual property; debating the applicability of different openness policies; and identifying relevant areas for future research.
The report can be accessed here, and thanks and acknowledgments go to the Welcome ISSF and OpenPlant Fund. Both the Synthetic Biology SRI and OpenPlant were involved with co-organisation of funding along with Public Policy SRI and LML.
For more information please click here.
Image credit: Holly Gramazio via Flickr, licensed under CC-BY-SA 2.0
via Flickr, licensed under CC-BY-SA 2.0
Betty and Gordon Moore Library Wilberforce Road Cambridge CB3 oWD
OpenCon 2016 is the student and early career academic professional conference on Open Access, Open Education, and Open Data being held in Washington, DC.
The OpenCon 2016 Cambridge satellite event will bring together students, early career academic professionals and open advocates from around Cambridge (although anyone from the surrounding areas are welcome to join us!)
This year’s theme is Building Impact Through Openness.
Our goal is to support and build the open community in Cambridge. We want to empower attendees to make a difference in their respective fields through open research, data, education and access.
This year’s committee have brought together a sensational program of world leading speakers but there is also time scheduled for focus group discussion around actions that we can take to make a change in the world.
Furthermore there’s ample time set aside in the day to ensure all the attendees will be able to share their ongoing activities (in the “silent” unconference) and hopefully build new collaborations for the future.
You can follow the main OpenCon event in held in Washington DC #OpenCon, and you can join the discussion around the Cambridge satellite event at #OpenConCam2016.
We look forward to seeing you there! Please reach out if you have any questions.
For more information and booking, click here.
The event is organised by Kirstie Whitaker, on behalf of the OpenCon Cambridge organising committee
The OpenPlant-supported Cambridge-JIC iGEM Team are exploring open source synthetic biology tools for chloroplast engineering in algae. The following was authored by Cambridge JIC- iGEM team member Claire Restarick and is reposted with permission from the Cambridge Consultants blog.
Since our initial blog post, we’ve spent many hours finalising designs for our genetic assemblies, which are now in the process of being synthesised. Once these are complete, we will begin the challenging task of completing four rounds of experiments before our deadline in September.
While our biologists are making significant headway in the lab, there have also been advancements on the hardware and engineering side. Our designs for low-cost, open-source lab equipment to support our Chlamydomonas transformation protocol have started to take shape – with the first stages of assembly taking place. This equipment will include a growth facility with light control, temperature regulation and imaging capabilities (linked to a dedicated Twitter account, @RPi_camigem2016), as well as a gene gun which, if successful, will transform cells by firing DNA-coated tungsten microparticles directly into them at high pressure.
The decision to make our hardware low cost and open source developed from recent trips to publicise our project at synthetic biology conferences in Paris and Norwich. At the Bio NightScience event hosted by the Centre de Recherches Interdisciplinaires (CRI) at the Cité des Sciences et de l’Industry, we presented our project to the conference and heard from many projects originating from Makespaces – collaborative community labs with little-to-no budget. We found its use of plant synthetic biology was hindered by the high cost of commercial equipment to culture and transform plant and algal cells. This inspired us to design low-cost equipment, which could make the area of plant synthetic biology more accessible to these creative workspaces, and other small research institutions.
The issue of documentation for open-source hardware for synthetic biology was raised repeatedly during the Open Plant Forum, hosted by the John Innes Centre in Norwich. A lack of clear, detailed protocols online makes it near impossible for the average novice builder to construct these devices. Having struggled ourselves to find appropriate parts and clear designs online, we have placed a focus on thoroughly documenting our designs, to make our open-source designs truly accessible for everyone.
To support both the hardware and biology aspects of the project, we have also continued our work on mathematical modelling, developing an open-source, integrated, kinetic model of Cas9-mediated gene insertion. We also held our first meeting with the director of the Cambridge-based Centre for Global Equality, to begin developing the human practices element of our project – understanding its impact and integrating this within the design and aims of the different parts.
Now past the halfway point of our project’s timeline, we feel well on track to meeting our project’s ambitious goals. Thanks to the continued support of our advisors at the Plant Sciences Department, and specialist advice from Cambridge Consultants, all aspects of our project are developing the potential to have an impact on both the scientific and non-scientific communities.
Note from Cambridge Consultants
Synthetic biology has huge potential to solve many of today’s critical challenges in healthcare, agriculture, energy and the environment. That’s why Cambridge Consultants has decided to sponsor the Cambridge University team at iGEM 2016 – the international genetically engineered machine competition run by MIT. As part of our sponsorship, we are acting as mentors – giving the team access to more than 700 Cambridge Consultants engineers and scientists worldwide to help solve problems during this year’s project.
The iGEM team is also grateful for support from:
Source: Open Source Hardware from the PLOS SynBio Community, licensed under CC-BY 4.0
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by Tobias Wenzel, who received an OpenPlant Fund grant to develop DokuBricks
Open Source Hardware is an exciting new trend
Figure 1: OpenFlexture Microscope by Richard Bowman, UK, 3D printed and operated with a Raspberry Pi computer.
“This microscope is one of the cleverest pieces of open source hardware for laboratory use that I have seen so far” said Prof. Jim Haseloff in the Plant Science Department at the University of Cambridge, as he learned about a design by Richard Bowman. Richard, a fellow in the Department of Physics, was frustrated about the difficulty of working with conventional technologies for some of his experiments. For example fitting a growth chamber into a microscope can be a major challenge. Many conventional scientific instruments are designed to be incompatible to possible extensions and are not co-developed by the user community, leading to impractical designs. Thus he built his own digital microscope from a 3D printed chassis and a simple Raspberry Pi computer. The main challenge to solve for high-quality microscopy results was to position and stabilise the sample. He solved this with a one-piece 3D printed flexing mechanism in plastic. Now the microscope is ready for all sorts of adaption, it can even be placed inside commercial incubators or used in education and field uses – all at a tiny fraction of the price of conventional digital microscopes. What a great demonstration of the uses that are enabled by rapid prototyping methods! Increasingly available methods are e.g. 3D printing and laser cutting along with accessible electronic units such as Arduino microcontrollers or Raspberry Pi computers.
Figure 2: OpenTrons pipetting robot for open source liquid handling, designed by junior MIT scientists, USA
Richard is not alone in his desire to make experiments more reproducible, and customisable as well as automated. In the last few years, Open Ephys and Backyard Brains started providing tools for electrophysiology measurements, OpenTrons and open syringepump designs target the automation of liquid handling, the electrochemical potentiostat Cheapstat was a creation of an iGEM team and was published in 2011, a different iGEM team in 2015 created a fluorescence microscope adaptation of Richard’s initial design to join the ranks of another popular fluorescence microscope by Tom Baden and Andre Chagas from the University of Tuebingen, Germany. The last mentioned scientists also curate the PLOS Open Source Hardware collection where many other examples can be discovered.
Sharing equipment plans is an opportunity for experimental science, especially Synthetic Biology
Another noteworthy collection that demonstrates the fast raising popularity of Open Source Hardware is Joshua Pearce’s Appropedia and his book Open-source Lab. He illustrates the benefits of open scientific information sharing to the reader in depth. Beyond the arguments of openness, Open Source Hardware works well in science since many experimental set-ups are prototypes that are suitable for manual or rapid manufacturing methods and because technical training is widely available in science. Furthermore, it is a job requirement to demonstrate impact in this profession. Extending the publication-like sharing philosophy to hardware has worked well for the pioneers.
Synthetic Biology specifically can benefit from the open community engineering approach to bring the users and designers of complex interdisciplinary equipment closer together. The exchange of designs and protocols comes hand in hand with an increase of reproducibility of experiments, which is a major challenge of the field. The reproducibility is further enhanced by the additional number of eyes that can spot errors in protocols and improve processes without additional development cost. Open Source Hardware works well in businesses too, when equipment is expensive and specialised as is the case for most synthetic biology instruments. For example: OpenIOlabs is a young Cambridge company that (among others) is in the process of open sourcing many expensive equipment parts from the supply chain, in order to make their key products more accessible and IO Rodeo offers open source laboratory equipment for which the user can decide how many parts he wants to buy and what to build on their own. Users then often contribute improvements for free, which has most prominently driven the development cycles of 3D printers.
Many designs come from the DIY community. Are the bio laboratory designs good enough?
Figure 3: NinjaPRC, a thermocycler design for open source DNA amplification, by Shingo Hisakawa, Japan
A lot of existing open source designs come from the do-it-yourself (DIY) and maker community, as the trend only recently reached academia and business more widely. A group of scientists and makers in Cambridge, UK, tried to replicate open source designs for biology laboratory equipment to kickstart a DIY biolab and evaluate the designs along the criteria of safety, quality, adaptability and ease of build. Funded by a mini-grant of the Synthetic Biology Strategic Research Initiative, they attempted designs for electrophoretic gel boxes, a centrifuge, PCR thermocyclers, tube holders, syringe pumps and a 3D printer (more to be found online, soon). Unfortunately, the team discovered more problems than solutions: even in the documentation sets that looked good, essential parts were missing. Some designs referred to specific parts that are not generally available and that had to be shipped from the US for high costs. Most design files where difficult to adapt to other sizes of e.g. acrylic sheets when build from a metric rather than US-imperial material stock. Assembly sets that could be ordered commercially were complete and had decent to good assembly instructions, but the documentations were usually not sufficient to build the hardware without buying the set, thus not fully deserving the label ‘Open Source Hardware’.
Open Source Hardware + good documentation; it just got easier with DocuBricks
There is a lesson to be learned from the incompleteness of commercial assembly-set documentations: Open Source Hardware is more than an assembly instruction. It is also about documenting design files and decisions along its functionality and in a modular fashion, complete with testing and calibration instructions. A good documentation enables the project to grow and improve without the doing of the inventor. Only in this way most projects can enfold their benefit well to society and technology companies. To be sure, documenting a hardware project is not easy and requires time. For this reason a handful scientists at the University of Cambridge (including the author), all with a background in technology and biology, recently started the DocuBricks initiative. DocuBricks is an open source and free software that makes documenting hardware and usage procedures easier. The name is a reference to modularity in the same way as Lego or BioBricks. As the name suggests, the editor part of the software guides the user through a modular documentation structure with relevant fields in a standardised, yet general format. The user can create a hierarchy of documentation bricks, explaining their function, implementation and assembly while referring to a parts library. The result is a XML document and a folder with construction and media files that is displayed with the viewer part of the software (a style sheet and script to enable interactivity).
Figure 4: DocuBricks* logo, the new open source tool for easy generation of high-quality hardware and procedure documentations. (*Image rights: Tobias Wenzel)
Over the database with the same name, DocuBrick.com, the projects can be shared and found. The team puts emphasis on impact tracking and acknowledgement, to make engagement in Open Source Hardware not only easier, but also more promising to the scientific community. Projects can also be cited via DOI’s, which are internationally curated short links and the standard way of referencing scientific literature. The new initiative is growing fast: Richard Bowman’s microscope from the beginning of this article can already be found. The wireless communication designs of Shuttleworth Fellow and collaborator Luca Mustafa will be released soon, just like several projects of the OpenPlant Initiative in Cambridge and a number of other scientific interest groups. Even a journal on Open Source Hardware from the Ubiquity Press will be launched and intends to use DocuBricks as the preferred documentation format. When will you join the effort to make science more open and reproducible?
Tobias Wenzel is a PhD candidate at the University of Cambridge and DocuBricks founder. This blog is a summary of a presentation given at Cafe Synthetique in November 2015.
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The EU is a Party to the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilisation. The EU ABS Regulation, which transposes into the EU legal order the compliance pillar of the Protocol, became applicable as of 12 October 2014. The principal obligations of the Regulation – i.e. Article 4 on due diligence, Article 7 on monitoring user compliance and Article 9 on checks on user compliance – will become applicable as of 12 October 2015. In this context it is important that those who utilise genetic resources (i.e. conduct research and development on the genetic and/or biological composition of genetic resources, including through the application of biotechnology) are aware of the obligations arising from the Regulation, and that they can take the necessary measures to ensure their activities are compliant.
The workshop aims at providing the participants with knowledge about their obligations under the EU ABS Regulation and what they practically imply for their everyday work. In the first part of the workshop, the new legal framework will be explained, providing insight into the main provisions of the EU ABS Regulation. In the second part of the workshop, participants will have a chance to put the knowledge gained into practice through interactive case studies, based on real-life examples and realistic scenarios. The workshop should allow participants to better understand their obligations under the EU law, and to establish which steps they need to follow and which practical measures they should take when dealing with genetic resources originating from Parties to the Nagoya Protocol.
The workshop is targeted at senior academics and experienced researchers conducting research and development on genetic resources who have an interest in gaining an essential understanding of the new legal framework in the EU, in view of the ABS Regulation becoming fully operational later this year.
Scientists with an expertise in the ABS regulation are not targeted by this basic training workshop
We are working on a methodology for accelerating open source hardware development, and we are calling out open hardware practitioners to collaborate
To increase our effectiveness in open hardware development, we are creating an Open Source Ecology Working Team on development workflows and standards. This is our Development Method Working Team. To do this, we are collating prior work on the topic of open hardware development and documentation by reaching out to existing open source hardware efforts. We are interested in the comprehensive process of open development, everything from documentation best practices, development workflows, and versioning strategies – to social and economic aspects of the process – such as team building, production engineering, open hardware enterprise development, and many others. If you are involved in open hardware development – please fill out this Survey of Development Workflows and Practices to provide feedback on what tools and processes you use. These results will be mede available to the rest of the open source hardware community.
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Open Source Hardware Development Method | Open Source Ecology.
Useful-source is a step beyond open-source for hardware, focusing on empowering, enabling reproduction and the use of such freely available designs by large populations. We are proposing this concept, to improve the current best practices and to make sure our developments are as useful as possible.
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