prgm-bioreactor

There was a recent change in the template and that is not reflected in the current layout.

Please click the link below for the complete updated project submission.

https://docs.google.com/document/d/1ho2kqETR3HEMr810e-MaQIFVknhwcr6aLd0Yrn7DFjk/edit?usp=sharing

to find our JOGL project submission.

The actual Slack Channel for the Bioreactor project was created in the early days directly in Slack. It would be good to try to move it but that there were many priorities so it's still like that.

Until then we created a placeholder under the main JOGL group: #bioreactor

https://open-covid19.slack.com/archives/C011RDAQG69

So you can join the https://join.slack.com/t/prj-bioreactor/shared_invite/zt-d0o2x5g6-rElluC8xXfRvwwSGK6__PQ or just message Adrian direcly.

Detecting the virus or create treatments like vaccines require reagents (chemicals).

In order to ran the reactions you need reagents for each test. Reagents are expensive and many are unavailable due to current demand. There is an imperious need to create an abundant yet qualitative alternative inexpensive source for these reagents. There are several labs working on this, notably the FreeGenes to mention one of the leaders.

The only way to produce reagent of quality in usable quantities is to use a bioreactor. Commercial bioreactors cost thousands or tens of thousands. That does not reflect manufacturing costs. Existing open source designs are not usable, abandoned prototypes, work in progress or they accommodate only some types of cells .

That's why this this is important. A cheap alternative to commercial bioreactors that would cost less than Euro 200 would solve this and also make possible the rest of the other initiatives.

A bioreactor is a container where cells are grown under very specific conditions. For instance temperature, Oxygen, pH, Optical Density, Weight etc.

We will do a wave bioreactor. Here is a non-exhaustive comparison of industrial and non-industrial bioreactors. Only wave bioreactors can reliably produce high quality results for advanced types of cells.

One of the mos critical needs at this point is reagents, Without reagents detection and research is blocked. Most reagents are produced by a handful of companies that can not cope with demands orders of magnitude higher than their capacity. Not only that the reagents are not available but their cost is prohibitive for many labs or large scale detection. We need a way to produce those reagents at a decent price in sufficient quantity. There are several groups already working on finding new protocols and reagents. However we still need a cost efficient, productive, qualitative way to produce organic reagents and that is only possible using bioreactors. They are growth chambers where reagents can be produced in a reliable fashion in a controlled environment. At this point there are very few open source projects and most of them are not usable or finished or fail to ensure mandatory requirements. We started building a Wave Bioreactor that will address this needs.

People interested in this project should join the Slack channel. After that we usually start with familiarizing with the team by going to the introduction channel and checking out the introductions of the other members and adding one for yourself. Then send us a message so we could do a short 5 minute on-boarding as a video session where we would discuss skills, needs and we will carve out concrete task for you.

We normally use Zoom for video communication and Meetings. We use GitHub for source code and documents that require version control.

We use Google Docs for documents that require simple concurrent editing. We also use many of the features offered by JOGL.

For convenience and clarity we added all relevant links to a plain web page so we only need to know the one link.http://specyal.com/diybio/bioreactor.html.

As for a code of conduct we follow common sense and we adhere to Google's https://abc.xyz/investor/other/google-code-of-conduct/.

Please understand that not only that you contribute to a crucial project but you will also acquire new interdisciplinary knowledge.

You will collaborate with enthusiastic and exceptional people and you will get from this project more than you put in the project. Be proactive and respectful of other people's time.

Detecting pathogens like the SARS_COVID2 virus or creating treatments or vaccines require reagents.

In order to run the reaction you need reagents for each test. Reagents are expensive and many are unavailable due to current demand. For some countries the cost is totally prohibitive given the number of infections.

Reagents are also essential for any type of biological research targeting other current major health and environmental issues.

There is an imperious need to create a quality alternative inexpensive source for these reagents. There are several labs working on genes for this. Notably, FreeGenes that is doing a great job pioneering this. Genes though are not enough when it comes to production.

Organisms can produce protein reagents however producing that on Petri dishes or flasks using manual procedures does not produce sufficient quantity. The environment is hard to control in a manual operating setting so it's hard to assure quality and consistence.

To produce quality inexpensive reagents we need a device called a bioreactor, a controlled environment growth chamber.

This is a standard industrial solution to the needs and it's employed by the industry. With few exceptions, labs, including academic and industrial do not have bioreactors because they buy the reagents. That left them vulnerable to situation like this where the industry does not have the capacity to produce the quantity of necessary reagents.

This project is about creating a quality Open Source Bioreactor comparable or better in terms of functionality and quality with the most advanced industrial devices yet for a fraction of the cost.

This will serve current needs of researchers around the world as well as creating a solution for inexpensive reagents not only for the current crisis but for future research.

This bioreactor would not be limited to primary organisms cell. Besides production of bacteria it will allow producing yeast, insect cells and even mammalian cells required for production of antibodies, phage based vectors or some complicated proteins. That requires a special type of agitation that does not break cells which is where wave solutions are superior. Apart for some other bioreactors that are not geared towards high quality products, this bioreactor needs to be sterile and reusable. Sterilization is required so cells don’t get contaminated and die. Also reagent purity is assured. For that we need to ensure the components are autoclavable. 

A specific challenge is creating this solution at a fraction of the cost of industrial bioreactors making this affordable even for small labs, community labs or labs in developing countries.

We will be using other Open Source projects when possible for different hardware, electronics and software modules. We are in contact exchanging information and ideas with authors or previous similar devices.

Since some of the operations will be done in a lab environment we'll observe the biosafety rules as mandated by local regulation.

We have several characteristics that make us stand apart from other solutions:

We use a Wifi controller which allows us at move the UI from the device to a laptop or any device with a browser. That will allow us to:

• display charts in real time
• monitor the process from everywhere in the world. Useful when researchers are in lockdown or remote
• run AI algorithms for optimization of the process
• paradoxically will make the device cheaper because we will not need to buy keyboards or specialized electronics for the device itself

We use a silicon bag instead of a glass jar. That will allow us to:

• simplify the manufacturing process of drilling holes for the hoses
• removes the need for expensive, toxic filament 3D printing that requires special 3D printers
• makes shipping easier and cheaper by reducing volume and fragility

We use an induction control system. That will allow us to produce enzymes that are toxic to host in large quantities

We use external agitation. That will allow Oxygenation without the need to insert shafts and propellers in the media. That will allow growth of mammalian cells and also simplify the design and enhance modularity.

There is no Open Source system even close to this.

We created a spreadsheet comparing different information on bioreactors and bioreactors.

https://docs.google.com/spreadsheets/d/1x3HjwaHuI_y1nTg_eBZIuizAPXirYkmAepSiM0xiFSg/edit?ts=5e4c5190.

Literature research- done

Comparative analysis of existing industrial solutions - done

Comparative analysis of existing open source attempts - done

Order Parts - Partially done

Create use cases for software, 50% done

Build the Optical Density module - 60% done

Several 3D printed Optical Density module parts versions finalized

Optical Density module software beta done

Calibration and adjustments - 4 weeks

UI software - 4 weeks

Controller software - 4 weeks

Main chamber design and assembly- 2 weeks after receiving parts

Additional device assembly - 3 weeks after all parts in

Testing on simple plasmids - 4 weeks after parts are in

Testing for RT polymerase starts 4 weeks after parts are in

Testing protocols produced by detection group start- 6 weeks

Shipping to participating labs - 6 weeks

Optimization and enhancement phases- 8 weeks

Documentation - 2 weeks

We have contacted and discussed with a number of labs that are interested to use this device for production of reagents for their research.

We have talked to people from other JOGL initiatives about the use of the bioreactor as a way to produce the reagents and execute their protocols therefore enabling other projects

We will enlarge the number of client labs once we'll have prototypes and we'll demonstrate real time online the operation of the device.

We have members actively working that started researching and creating plasmids and organisms to produce the reagents. Fortunately the labs of these members are still active.

We assembled a team with exceptional skills in the domain space. We are developing different parts and modules independently in iterations. Once modules become available they are integrated in the solution. We start with prototypes. We monitor and evaluate the delivery of these modules and we evaluate modules in a divide and conquers strategy. We test early and we apply parallelism in our development efforts whenever possible. The goal is clear: Provide inexpensive quality reagents for all research labs that look for a solution to current and future problems.

We work with labs and include them early in the iterations to make sure the product meets their needs. Short term goal, supply the much needed reagent for researchers. Provide cheap reliable reagents for further solutions for labs in research and medical use where legal requirements are met. In long term we want to continue to provide inexpensive qualitative reagent while adding new protocols for treatments like genetic diseases via vectors, antibodies, nanotechnology etc.

As the bioreactor will produce inexpensive affordable reagents it could change the tools available to researchers and health experts in third world countries making treatments possible therefore resulting in significant number of lives affected. 

As the bioreactor wil be able to produce not only reagents but vectors and nanoparticles will be a priceless tool for research in cure of genetic diseases including Cancer.

Production of reagents will follow standard biology procedures including sterile techniques and proper manipulation and disposal of materials. 

By producing these reagents in a reusable container we will avoid producing waste.

By producing these reagents in a controlled environment we will avoid manual procedures that results in significant waste like plastic Petri dishes, lab gloves, different size tubes and all the normal lab disposables that accompany manual procedures.

This is not project to fill an important yet temporary need. It's a project that will offer significant value beyond the next several months.

As there are no finalized competing projects with the same capabilities it should be relevant for a long term. There are many potential enhancements. Many of short term enhancement will focus on hardware in monitoring of additional parameters. The larger enhancements will be in optimization and using AI in optimization of the products.

A constant stream of new protocols and new organisms designed to expand the number of reagents for years to come.

Adding production of vectors for treatment of genetic diseases.

We are contacting other labs around the world asking for their input in terms of capabilities and their needs.

We will use our connections like participants in the MIT Medial Lab BioSummit, governmental players and Universities to present and promote this important new capability.

We will contact researchers around the world to ask what reagents to add next to the list of tested protocols.

Funding

This project is not funded. Some of the members advanced personal money to allow it to exist. We need to find grants to continue otherwise the project will probably stall.

Based on previous projects, we expect to need to build 2 versions of the prototype to settle on a good functional product. We expect the BOM parts, laser cutting and 3D printing to cost about 200 Euro per prototype. See BOM https://drive.google.com/open?id=1OglE-9ybC1iGGKNqzX2OSMWbrmI4yl8A

We need to ship 3 working prototypes to international labs to collaborators for testing and optimizations at a cost of 200 euro each. We have international members with labs in three countries.

We expect reagent costs for several plasmid construction, transformation, PCR, Gel electrophoresis and sequencing for producing two reagents to be 400 Euro.

We expect consumables for testing and optimization: Gloves, Petri plates, PCR tubes, etc to cost about 100 Euro for all three labs

We have 2 PCR machines with 96 wheels and a dozen of Gel Electrophoresis boxes to do the testing and other devices in other labs.

Total 1500 Euro.

Normally designing and creating a device like this in an industrial environment would cost two orders of magnitude more but we rely on our talented volunteers and cheap components to lower it down so much.