Apply here for GOSH’s 2022 Collaborative Development Program! (Phase 2)

GOSH 2022 Collaborative Development Program (GOSH CDP) - Phase 2

Hi, everyone! :raising_hand_man: Welcome to GOSH CDP - Phase 2! Due to some unforeseen circumstances, we had to push back the start of the second phase later than expected. We are officially open to applications for the second phase of the collaborative development program.

Collaborative Development Program Goals

The GOSH Collaborative Development Program is designed to facilitate the production of high-quality open science hardware by building collaboration. The goals of this program are as follows:

  • To move forward existing OScH projects to achieve higher quality or more relevant results’
  • To incorporate and experiment with a range of documentation best practices
  • To match up new hardware projects with expertise from across the GOSH community
  • To experiment with collaborative models in working with professionals who have expertise presently missing or scarce within the GOSH community
  • To learn from these professionals to improve the OScH design and development process.

The collaboration itself will involve participation from professionals within and outside the GOSH community and will result in an improved piece of OScH with published open software and hardware designs, along with any calibration information, standards, safety information, and guidelines for use.

This program feeds directly into our efforts to support and grow the OScH community by experimenting with collaborative models and disseminating best practices in documentation, design and testing, as prioritized in the GOSH Roadmap. Additionally, the results and lessons learned from these exercises will be useful in other initiatives.

The application tracks and phases are outlined below:

New Project Track - This track provides funding for individuals and groups looking to build their first prototype or to significantly improve a prototype. The project should aim to fill a gap not currently filled by an established open science hardware project. A core part of this grant is collaborative development.

In Phase 1, teams have been working on a collaboration plan to build or improve their prototypes. In Phase 2, teams are expected to execute the collaboration plan and disseminate the results and documentation to GOSH Community.

Established Project Track - This track provides funding for established Open Science Hardware projects looking to advance their project to the next stage (e.g. creating a new fabrication technique for mass manufacturing, passing certification, establishing quality control, creating technical documentation, etc.) through collaborative development with professionals who are presently not involved in OScH collaborations in an academic and community-based context, such as professional electronic test engineers.

In Phase 1, teams have been sourcing and hiring external experts (freelancers, consultants, etc) and writing a detailed plan for implementing their objectives. In Phase 2, the team is expected to execute the detailed plan to achieve their objectives and disseminate the results and documentation to GOSH Community.

Funds

The total funding for the program is $110,000 USD.

Thirty percent (30%) of the total, or $33,000 USD, is allocated to the New Project Track, and seventy percent (70%) of the total, or $77,000 USD, is allocated to the Established Project Track.

Phase 1 funding breakdown:

  • New Project Track: Up to $2,000 USD per project, for a total of up to five projects (up to $10,000 USD awarded in total).
  • Established Project Track: Up to $4,600 USD per project, for a total of up to five projects (up to $23,000 USD awarded in total)

Phase 2 funding breakdown:

  • New Project Track: Up to three projects from Phase 1 will be approved for Phase 2 funding based on progress evidenced by the submission of an interim report. Up to $7,600 USD per project, for a total of up to three projects (up to $23,000 USD awarded in total).
  • Established Project Track: Up to three projects from Phase 1 will be approved for Phase 2 funding based on progress evidenced by the submission of an interim report. Up to $18,000 USD per project, for a total of up to three projects (up to $54,000 USD awarded in total).

The source of these funds is a grant from the Alfred P. Sloan Foundation held by GOSH Inc., a non-profit organization in the United States. The GOSH Community Council and the wider GOSH community have designed the Collaborative Development Program and will manage the selection and support of projects while GOSH Inc. will manage the financial administration and funding agreements.

Eligibility criteria

General information: All organizations and groups are eligible to apply as long as their proposed projects are aligned with the GOSH Manifesto, code of conduct, and ethos. The physical hardware or hardware design must meet the OSHWA Open Source Hardware Definition. Projects have or plan to have open source licensing (i.e. OSHWA-compatible licenses for hardware, free software licenses for software, and CC BY 4.0 or CC BY-SA 4.0 for others)

Phase 2: Only the projects below are eligible to apply for additional funding.

New Project Track (in no particular order):

  1. Shazam for Bats - @audevuilli
  2. Liquid handling robot - @naikymen
  3. Reuse of spectrophotometer - @juul

Established Project Track (in no particular order):

  1. PCR Project - @FranQuero
  2. Governmental Framework to strengthen the market of Enzyme made in Cameroon - @thomasmboa
  3. Open Science Shop - @Nat_Irwin
  4. Friendzymes - @jeremycahill

How to apply

The application consists of a well-detailed report about the collaboration plan, progress in Phase 1, and expected results for Phase 2. Applications are submitted by responding to this thread and they will be evaluated in the following sections:

General information

  • Name of the project
  • Track (New Project Track / Established Project Track)
  • Contact name
  • Contact email

Proposal

  1. Identified problem or need in OSH Community and lessons learned about this gap in Phase 1 - 1500 characters max.
  2. Project proposal and upgrades from Phase 1 - 1500 characters max.
  3. User profile and/or market and lessons learned about end-users in Phase 1 - 1500 characters max.
  4. Current state of the project (idea or prototype) with focus on progress done in Phase 1 - 1500 characters max.
  5. Team Description (Per member: Name, Role, Motivation, Experience). Please, highlight the new members in Phase 2.
  6. Project objectives, expected results, and potential limitations for Phase 2 - 1500 characters max.
  7. Gantt chart (Milestones, tasks, deliverables, responsible, time frames) - A link must be shared - File format: Calc, Excel, PDF, or any Gantt tool
  8. Budget (Bill of materials and other resources) - A link must be shared - File format: Calc, Excel, or PDF
  9. BONUS: Link to the public project repository

Timeline for Phase 2:

  • Deadline: 5 August 2022 at 23.59 hrs (PST) - Submit your application
  • 26 August 2022 - Grant awardees notified; due diligence process begins
  • 9 September 2022 - Successful applications announced to the community (public announcements may be delayed if due diligence checks are still pending).
  • 9 September to 9 December 2022 - Work on your projects

Review Process

Reviewers

Proposals will be reviewed by the GOSH CDP Working Group set by the Community Council in Phase 1. This group included at least one Community Council member. They will select projects based on the review criteria. If a member of this review panel has a conflict of interest with an application, they will recuse themselves from reviewing it.

Review criteria

The rubric for evaluating the applications will be posted soon. We shall note any changes once this is posted.

Budget

Please include a well-detailed list of direct costs in Calc, Excel, or PDF (a link must be shared), with the amount and justification for each, using the following categories:

  • Personnel
  • Supplies
  • Subcontracts
  • Travel
  • Equipment
  • Other expenses

Below is an example of a budget line item:

Cost Category Details Units Estimated Cost in USD Why it’s needed
Subcontract Professional electronic test engineer 1 $1000.00 Needed to learn how to assemble pre-production hardware
Other Shipping costs for prototype 1 $30.00 To send the prototype to professional test engineer

Project Withdrawal

We understand that projects don’t always go as expected or planned. Sometimes this leads to unanticipated success, and sometimes, it means that project members cannot complete the work as outlined in their proposal.

In the event members are faced with canceling or withdrawing their project after funds have been dispersed (for instance, due to illness, natural disaster, or unforeseen circumstances), we ask that the project team a) communicates to the GOSH Council in writing as soon as possible; b) returns any unused funds; c) submits documentation that includes the challenges that prevented them from meeting their objectives and/or responsibilities.

Responsibilities

Responsibilities of selected proposals:

  • Attend scheduled check-ins with the Collaborative Development Funding Working group
  • Make a post on the GOSH forum about your project at the conception of the grant
  • Post at least one update on this forum at the beginning of each phase
  • Post at least one update on this forum after each phase and before launching into the subsequent phase
  • List the open source hardware design principles your project will follow
  • Provide detailed project documentation at the end of each phase
  • Publish at least one mature documentation output that will tangibly benefit the open science hardware community

Applications are submitted by responding to this thread. If you have a question about this funding or a related discussion, please post in the other thread!

3 Likes

@biomakers_lab thanks for putting this out and I am very happy to see this continue. Is there some confusion with “Round 2” (has so far been used for a second round to apply for a funding opportunity) and “Phase 2” (as for the next phase for the projects that have already completed phase1 ).

Hi @gaudi, thank you for pointing it out! Yes, the term Phase makes more sense. Following your comment, I updated “Round 2” to “Phase 2” in the post. :+1:

Pipetting bot’s application to round 2 :partying_face:

General information

  • Project name: “OScH micropipette set for standard and automated laboratory assays”.
  • Track: New Project Track
  • Contact name: Nicolás Méndez
  • Contact name: nmendez.ar@gmail.com

Proposal

1. Identified problem or need in OSH Community and lessons learned about this gap in Round 1

The overall project is about making a liquid handling robot, to automate molecular biology protocols of low to moderate complexity, on a tight budget.

However, the current pipette tool currently has some pros and cons:

  • The project relies on pipettes supplied by the user. This can be desirable or not, depending on whether there is a spare pipette set at the lab.
  • So far only the Pipetman micropipettes are supported by our adapter, because they are the most popular model at our workplace. There are cheaper micropipettes. These pipettes are easily serviceable locally, but have high acquisition and maintenance costs.
  • The adapter is good enough, but several mechanichal compromises were made to accomodate them (some range is lost, motors are oversized, etc.), and callibration is cumbersome.

We believe that a low cost, open source hardware micropipette set can be benefitial for labs on low budgets, and is essential to overcome the current performance limitations of our pipetting robot.

Secondly, while our software is functional and nice, we thank the suggestion about having interoperability with the OpenTrons software. It must be on the roadmap.

During round 2 we expect to add compatibility of the software to drive our and other CNC pipetting machines, whithout the need to rely so tightly on the electronic components on the OT2, but benefitting from their great open source software project.

2. Project proposal and upgrades from Round 1

The project proposal is twofold:

  • Develop OScH low-cost electronic micropipettes.
  • Adapt the OT2 protocol designer to our machine.

By making our own micropipettes, we aim to overcome the following limitations of our current design:

  • Maximize volume range, reduce weight and size, simplify callibration greatly.
  • Enable the user to make their own electronic micropipettes.
  • Reduce acquisition and maintenance costs.

Secondly, by adapting OT’s protocol designer, we hope to benefit from their quality software, and by enforcing interoperability, we hope to enable other pipetting robots to join and contribute to the growing OT2 ecosystem of protocols in in scientific publications.

Finally, by focusing on free and thorough documentation, we hope that the growing assembly instructions will enable individuals or groups with limited resources to automate pipetting protocols.

3. User profile and/or market and lessons learned about end-users in Round 1

Target users are early stage scientists and institutions who would benefit from automating preparations for routine assays (such as DNA cloning, screenings assays of several types, growth cruves, etc.), especially labs from regions with less funding.

4. Current state of the project (idea or prototype) with focus on progress done in Phase 1

The award from round 1 set the project on its way. So far we’ve spent on parts 10-20 times less than the cost of acquiring a full commercial solution, well under the 1000 USD mark.

Development and documentation are still under way, and will continue until the 31st of August (by an extension).

As posted on the forum, the prototype is under construction, and waiting for the toolchanging system to be completed.

5. Team Description (Per member: Name, Role, Motivation, Experience)

Most team members from round 1 remain:

  • Nicolás Méndez (IFIBYNE-UBA, CABA, Argentina).
  • Gastón Corthey (TECSCI S.A.S. and UNSAM, Buenos Aires, Argentina).
  • Martin Gambarotta (TECSCI S.A.S., Buenos Aires, Argentina).

We also plan to keep the new collaborators from round 1 in the team:

  • Renan and Solomon: open hardware machine design and CNC control.
  • Felipe: industrial designer.

Finally, we will also need a new collaboration with a Python software engineer.

6. Project objectives, expected results, and potential limitations for Phase 2

Our main objectives are:

  • Develop, prototype and document a free hardware micropipette set, that lowers initial investment and maintenance costs.
  • Adapt the OT2 protocol creator software to our machine. In this way pusblished open protocols could be used directly on a different machine.

The main challenges are precision in parts and chemichal compatibility with organic solvents. Fortunately TECSCI is well equipped to face them with Gastón’s chemistry expertise, and the available manufacturing equipment.

The main lesson learnt from Round 1 is that hardware development takes substantially more time than expected, especially documentation. Using GitBuilding is still of interest, and we will soon migrate the documentation on the repo’s README files to that platform.

7. Gantt chart (Milestones, tasks, deliverables, responsible, time frames)

Find our draft Gantt chart by following this link to an online spreadsheet.

8. Budget

Cost Category Details Units Estimated Cost in USD Why it’s needed
Subcontract Industrial designer and/or mechanichal engineer. 1 2220 Ergonomics of the micropipettes
Parts Prototyping parts and manufacturing costs. 1 1500 Development of the micropipettes.
Subcontract Programmer 1 3500 Adapt the OT2 protocol software to a generic CNC machine.
Fiscal sponsoring 5% fee charged by FUNDACEN. 1 380 To manage the funding and make payments.

Total budget: 7600 USD

9. Link to the public project repository

Gladly :slight_smile:


Best!

1 Like

General information

  • Name of the project
    • Friendzymes - Open Colony Picker
  • Track (New Project Track / Established Project Track)
    • Established Project Track :white_check_mark:
  • Contact name
    • Friendzymes - Jeremy Cahill; Scott Pownall
  • Contact email

Proposal

Item 1

Many organizations (e.g. academic labs, startups, community labs) around the world desire low cost automation to increase the throughput of their capabilities. The success of the low cost Opentrons pipetting robot shows this. There are many other commercial laboratory automated tools that are beyond the means of many.

Colony picking robots are automated machines that can detect microbial (e.g. bacterial or yeast) colonies on agar plates, then pick and inoculate the discrete colony into liquid media for growth or replicate colonies on another agar plate. Some robots can distinguish between fluorescent and non-fluorescent colonies. Automation of the process of colony picking allows high throughput and frees up expensive manual labor.

Item 2

Friendzymes received round 1 funding in the Established Project Track for our project whose goal is to create a low cost open automated colony picking robot to facilitate molecular cloning of assembled DNA parts from Freegenes, iGEM, and other open wetware sources as well as for colony screening of strains for desired assemblies and behavior.

The focus of our round 1 application was on developing some of the subsystems required to realize a complete automated colony picking robot. This included designing and building the Colony Picking Head Subsystem, the Raspberry Pi-based FluoPi Imaging Subsystem and ideation of the completed robot.

Phase 2 goals are to integrate those Phase 1 sub-systems along with some new subsystems to be designed and built in Phase 2. All of these subsystems will be integrated with the OpenWorkstation cartesian system using the Klipper 3D framework. All of the subsystems for the final colony picking robot are:

  • Cartesian System based on OpenWorkstation
  • Adapted FloPi subsystem
    • Bright field and fluorescent plate imaging
    • Discrete colony identification
    • Map agar surface height
  • Colony Pick Head Subsystem
    • Sterilization Unit
    • Filament Cutting Subsystem
    • Head Transport
  • Agar Plate Management Subsystem
    • Agar Plate Stack Holding Rack
    • Agar Plate Transport Mechanism
    • Lid Lifter Mechanism
    • SBS Deep Well Plate Management
  • Software
    • PAML Integration
    • Klipper Integration - cartesian control
    • OpenCV Integration - discrete colony ID and mapping

Item 3

Our open source automated colony picker is to be used by microbiology and synthetic biology labs that routinely run protocols where imaging, plating, replicating and culturing bugs take up a significant amount of time due to the scale or the yield of the prescribed protocol. Typically, there is an inflection point for some labs where hiring more warm bodies exceeds the cost of automating the process. However, due to the high price of commercial pickers, the cost of acquisition can often exceed the capital expenditure requirements of some labs despite the operational scale advantages of having such machines, not to mention the cost and difficulty in setting up and maintaining such machines. In conversations with some partner labs around the world, this can happen where personnel are hired on a per-project contract basis. Thus, a niche exists wherein the most following conditions apply:

  • There are minimal yet highly skilled personnel operating the lab.
  • The laboratory is located in a remote region of significance where a vast majority of samples have to be processed onsite, e.g. field labs.
  • The costs of acquisition of a commercial colony picking unit vastly exceeds the capital expenditure ability of the laboratory.
  • The laboratory is located in a remote site where setup and maintenance is difficult.
  • The required yield is vastly less than a commercial picking unit yet more than what the lab personnel can do manually.

By using this unit, time spent picking is converted from manpower time to machine time therefore increasing the productivity of the said lab at minimal depreciated cost to the lab itself.

Due to the conditions above, there are a few requirements that need to be satisfied. First, the colony picker should be field maintainable or at least easily transportable without the use of heavy lifting devices. Second, manual user intervention in the picking process must be minimized to realize the maximum advantage of having the machine. Third, all parts of the machine should be easily procurable in most markets.

Item 4

The focus of our round 1 application was on developing some of the subsystems required to realize a complete automated colony picking robot and run through a number of rounds of ideation of the completed robot to identify what additional subsystems are required and how they would integrate with the OpenWorkstation cartesian system.

Majority of the software work done was testing, integrating, and validating OpenCFU with Python bindings for integration into PAML as a separate specialization. As part of the work completed, a boilerplate specialization for the OT-2 as a base was made for later generalization into a generic cartesian gantry system. This would later allow for PAML protocols to natively use the colony picker as a protocol execution component. PAML thus can act as the coordinator of all the movements of the robot. Integration and multi-execution tests are ongoing.

For firmware development, we elected to go with Klipper for the motion control and hardware control of the robot. This is due to the extensibility of Klipper with many 3d printer boards as well as the ability to update the firmware on the fly via the printer.cfg facility. Macros could also be developed for the “plate elevator” to align and calibrate the system for different plate sizes and form factors. For now, work is being done to reverse engineer and reduce the pertinent thermal safeties of the firmware in a safe manner that should not impede robot operation.

Hardware subsystems in round 1 included designing and building the Colony Picking Head Subsystem, the Raspberry Pi-based FluoPi Imaging Subsystem and using OpenCV to identify discrete colonies as well as map the agar surface.

Although not originally included in the round 1 application, we designed, implemented and tested a 3D printed vacuum-based lid lifting mechanism for lifting lids off of the agar plates.

Item 5

Round 1 Contributors continue to participate in the project:

  • The Friendzymes Contributors
    • Jeremy Cahill, USA
    • Isaac Larkin, USA
    • Sarah Ware, USA
    • Isaac Nuñez – FluoPi, Chile
    • Scott Pownall, Canada
    • Homer Sajonia II, Philippines
    • Jacob Segarra, USA
  • Friendzymes Advisor
    • Sebastian Eggert – OpenWorkstation, Germany

New Contributors include the following cohorts:

  • The Friendzymes Contributors
    • Ian Caven, Canada (OSN)
  • Open Insulin
    • Moses Apostol, USA
    • Joshua Harrell, USA
    • Yann Huon (PI), France
  • OpenTrons Engineering
    • Nick Diehl, USA

As members of the Open Insulin project, Moses Apostol, Joshua Harrell, and Yann Huon (PI) share substantial interests with Friendzymes in the development of open colony picking methods. This includes the application of computer vision to imaging tasks with OpenTrons hardware and OpenCFU software. At the nexus of their work with Open Insulin and this colony picker project, Moses and Joshua have laid the groundwork for OT-2 calibration and colony picking pipeline automation, taking as input a colony plate image with the end goal of executing transfer protocols.

Nick Diehl is an Applications Engineer at OpenTrons based in Brooklyn, New York. Nick graduated from Vanderbilt University with a Biomedical Engineering degree in 2018. He joined Opentrons in 2019 to deliver bespoke solutions to OT-2 users around the world.

Ian Caven is a software engineer and active member of Open Science Network’s community lab. He has extensive experience with 3D printing and developing CAD files using open source tools like OpenSCAD. Ian and Scott collaborated to design and print a working lid lifting device. Ian realized the design using OpenSCAD.

Item 6

Friendzymes’ mission is to democratize and globally distribute the means of biotechnological production. The goal of this project remains, as in Round 1, to design and build a low cost cartesian-based open automated colony picking robot using the Raspberry Pi and associated camera system.

Over the course of research, design, and development during Round 1, we successfully created the Colony Picking Head and sterilizing unit and adapted the FluoPi imaging device to integrate with OpenCV for detecting the location of discrete colonies on agar plates.

In this latter phase of our prospective GOSH Collaborative Development Program Phase 2 funding, we aim to extend the work of Round 1 by creating additional subsystems as defined elsewhere in this application and integrating all of the subsystems in a cartesian framework based on OpenWorkstation. We expect we will need a number of iterations in the design, build, test, learn cycle to ensure all components work as we envision.

Item 7

Please find our Gantt chart attached as PNG and PDF below.

Friendzymes_GOSH_Collaborative_Development_Phase_02_Gantt.pdf

Item 8

Please find our Budget (BOM) attached as a spreadsheet below.

Total Budget Request: 17874.78 USD

Friendzymes_GOSH_Collaborative_Development_Phase_02_Budget.xlsx

Item 9

As in Round 1:

  • Friendzymes’ main tool for communication remains our Discord channel.
  • Friendzymes maintains a public GitHub organization, where all project materials will be disseminated.
  • Friendzymes continues as a multi-focal project, with individual team members continuing to organize regularly scheduled team calls and thematic development sessions.
  • Updated links can always be found at https://linktr.ee/friendzymes.

Closing Remarks

Friendzymes would like to thank the Round 1 reviewers for giving this project the opportunity to be realized and the Round 2 reviewers for their consideration of this application.

1 Like

General information

Name of the project

Open-Source Real-Time Amplification Hardware

Track (New Project Track / Established Project Track)

Established Project Track

Contact name

Francisco Javier Quero

Contact email

francisco.quero@cri-paris.org

Proposal

Identified problem or need in OSH Community and lessons learned about this gap in Round 1

As defined in the first phase of this project, the work has focused on developing open-source real-time nucleic acid amplification test (RT-NAAT) devices for its use in cost-effective distributed diagnosis, quantitative detection of genetic elements in environmental samples or for STEAM education.

Although a decade has passed since the first open-source thermocyclers designs, RT-NAAT is still withstanding to arrive into the open-source panorama and hence, also limited its application for disease detection and management especially in low and middle-income countries (LMIC). The few existing designs (f.e, https://www.chaibio.com) still range in the order of thousands of dollars. With a decrease in price and improved accessibility, the significant impact of these technologies is vast and spread around fields such as infectious disease diagnosis, personal diagnostics, environmental or food testing and water purity analysis.

During this first round of the project, we focused on physically meeting in an experimental residence at the Learning Planet Institute (Paris), where we pooled the experience of different researchers in the field of Open-Source hardware for nucleic acid amplification. As a result, after ten days of residence, we successfully developed three functional device prototypes for Real-Time Nucleic Acid Amplification Test (RT-NAAT) that work towards the same goal employing complementary solutions. One of them, the open qLAMP, is ready for scaling the production meanwhile the other two are at the moment being refined into a final production-ready device.

The detailed output of the residence including the results and repositories of the three devices can be found in this link.

Project proposal and upgrades from Round 1

As stated in the previous section, the first round of funding has enabled us to develop three functional prototypes that performed well in laboratory tests. For the next step we plan to focus on medium-scale production and the applicability of the developed equipment in a real-world scenario. Therefore, our proposal for round two is divided into the following categories:

  • We aim to use 45% of the funding (8000$) to establish a production chain to build the first batch of devices and the necessary reaction mixes that later on will be used to test the system in the field. The reactions will be based on a variation of CoronaDetective adapted for real-time nCoV detection.

  • For the rest of the 55% funding (10000$), we propose its use to transport researchers and materials to Mboalab (Yaoundé, Cameroon) as well as its maintenance for one week. As explained later the goal of this residence is triple; Establishing a distributed production network, carrying out user training and device validation and performing user discovery.

User profile and/or market and lessons learned about end-users in Round 1

The applications, and therefore the user profiles, are divided into three categories; Research Education and Diagnosis (RED):

Research: The devices currently on the market to perform RT-NAAT cost above $10,000 (quantitative thermocyclers) or $5,000 (RealTime LAMP incubators). The RT-NAAT devices developed during this project provide a robust alternative with a significantly lower price (30-80€ to produce / 200-400 for the assembled device). Additionally, as the designs are open source, the technology is easy to replicate, without any black-boxes and adaptable for other use cases. Therefore, the local research centres in resource-constrained regions represent a potential market where this project can have a positive change.

Education: As new technologies are coming to light, what used to be cutting-edge technologies are nowadays the basis on which many applications are built, all broadly spread in our daily life. Nucleic acid amplification, a technology previously reserved for university courses, is now being explained in high school classrooms. Unfortunately the budget required to offer the students hands on these technologies is still too high for the vast majority of schools. The decrease in price and the simplicity of use of the designed devices make the entry budget to experiment with nucleic acid amplifications within reach of more and more centers. Therefore, high schools and other educational centers with limited budgets also represent a potential market where this project can have a positive change.

Diagnostics: The state of diagnostics at the global level is centered in highly industrialized areas, both in terms of the employ of diagnostic technologies and their production. Even within the regions of the LMICs themselves, the tests that are performed are centralized in a few laboratories distributed throughout the capitals and large cities, leaving the remote areas out of reach. The systems we have designed are intended to be used in small local clinics, where even stable electricity is not a guarantee. We have also put particular interest not only in establishing production-ready designs but also including local partners in the development process to help us understand the needs of LMICs and to use this technology to build local production and distribution networks. Therefore, small local clinics in remote and resource-limited settings also represent a potential market where this project can have a positive change.

Current state of the project (idea or prototype) with focus on progress done in Round 1

We have successfully gathered in Paris. It has allowed, among other things:

  • Strengthen collaborative relationships through a week of collaborative experimentation.
  • Reverse engineer commercial machines to study the technologies used for RT-NAAT, acquiring knowledge about these devices’ state of the art.
  • Design three functional prototypes of open source solutions for RT-NAAT.
  • Benchmark the different nucleic acid detection prototypes, studying each design’s pros and cons.
  • Discuss and plan how to best implement a decentralized production network of diagnostic hardware and wetware.
  • Discuss how to bring this technology to an impactful application, including the debate on new targets and how to perform a well-designed user discovery process.

The detailed output of the residence including the results and repositories of the three devices can be found in this link.

Each of the resulting designs from the residence has reached the following phases:

Open qLAMP: Version 1.0 is finished and ready for production, having already generated the first Real Time LAMP amplification for fungal infections in chestnut trees and SAR-CoV-2 detection. Prototypes of version 1.1 are being produced. Repository.

WebCam qPCR: The different modules have been successfully tested during the residency, generating impressive results in sensitivity and price. It is one of the most promising solutions but needs to move from the prototyping phase to having a final product ready for production. Wiki.

Chili qLAMP: There is a working prototype and assembly instructions. The machine has excelled in sensitivity among the three solutions. However, it is still necessary to adapt for large-scale production lower production costs and calibrate the sensitivity ranges Repository.

Team Description (Per member: Name, Role, Motivation, Experience). Please, highlight the new members in Round 2.

Cameroon residence trip host

Name: Stephane Fadanka, Beneficial Bio. Role: Host at Mboalab. Study applicability in Cameroon. Experience: Stephane Fadanka is Executive Director at Mboalab and works with Beneficial Bio and Open Bioeconmy Lab to make research tools and protocols more accessible to researchers in Cameroon and abroad through local manufacturing of reagents for molecular biology research and application. Stephane is also a SynBio Africa Emerging Leader in Synthetic Biology and Biosecurity fellow and a fervent advocate of Open Science sharing his experience as an Outreachy mentor and Open Science Ambassador with the Open Life Science Science (OLS-5) program. Stephane is a new member in Phase 2.

Applicability

Name: Harry Akligoh Duplex, Bio Role: Study applicability in Ghana. Experience: Harry leads Duplex Bio, a Limited By Guarantee (LBG) company in Accra, Ghana, that researches, and builds biotechnologies and products for grand challenges like Antimicrobial Resistance in Africa. Through his work with the Open Bioeconomy Lab, he co-founded the Hive Biolab in Kumasi, Ghana to pilot the production of open source enzymes and develop open educational resources to teach young students and researchers in Ghana. He has been a co-organizer of AfricaOSH and helped to democratise DIY Bio and Open Science Hardware in Africa.

Hardware production

Name: Urs Gaudenz, Gaudilabs. Role: WebCam qPCR design, production and application. Experience: Urs is an international reference in open-source laboratory hardware. His designs were the pioneer of the movement, laying the foundations that inspired many of the designs that exist nowadays, a decade later.

Names: Boris Oróstica & Fernan Federici, Lab de Tecnologías Libres Role: Chili qLAMP design, production and application. Latin America enzyme production node. Experience: Fernan Federici leads the Laboratorio de Tecnologías Libres, a reference in South America in decentralised reagents production and OpenSource Hardware. Boris Oróstica is an electrical engineer who works with this lab to design open source solutions that meet the needs of researchers. Boris is the designer of Chili qLAMP, one of the three devices tested during round 1.

Name: Fran Quero, Learning Planet Institute Role: open qLAMP design, production and application. LAMP reactions design and testing. Experience: Fran have being engaged in the creation of numerous DIYBio communities, from a BioMakerspace in Madrid (BioCrea), the initial two igem teams of the city, or one experimental biohacking at tsinghua university (Bio-X-Lab, Shenzhen). Professionally his career is centred on open source distributed diagnostic platforms,currently working at the Learning Planet Institute where he co-coordinates the DNA detective research project.

Reagents production

Name: Nur Akbar Arofatullah, LifePatch & Widya Life Science. Role: South Asia enzyme production node Experience: Akbar is working at the Faculty of Agriculture, Universitas Gadjah Mada, Indonesia as a researcher and lecturer in the field of agricultural microbiology and biotechnology. He is also the co-founder of Lifepatch (lifepatch.id), citizen initiative in art, science and technology. Akbar is interested in the dissemination of Do-It-Yourself (DIY) biology, heis working on the Introduction RT-LAMP for COVID-19 detection, and the local manufacture of the reaction mixes through establishment of a biotech research company PT. Widya Lifescience/Widya Technology Hayati. Akbar is a new member in Phase 2.

Other members of the community

Name: Chinna Devarapu (Ireland) Role: Suggestions on optoelectronics for LAMP hardware Experience: working on a number of DIY hardware devices for biological applications such as LAMP assays. His background is in photonic devices, particularly in nanophotonics which he would like to apply for biological applications.

Project objectives, expected results, and potential limitations for Round 2

Project objectives and expected results

Design of final devices and reaction mixes with insights from Phase 1
Building upon the success of prototyping results of a new Open Source RT-NAAT hardware in Phase 1, we aim to use Phase 2 to consolidate a final production-ready design and assemble the first batch of devices. This process will allow us to have an accurate estimate of production times and cost. As a result, we expect to have a final and well-documented Open Source design with a solution to scale the production

Field trip to Cameroon. Establishing a distributed production network, carrying out device validation and working on user discovery.
Phase 2 will allow a new collaborative time to engage with the OsH community through active collaboration and knowledge sharing. We plan to gather just right before the AfricaOSH conference in Cameroon at MboaLab. The residence will be used as a platform to test the field applicability of our new RT-NAAT hardware in Research, Education and Diagnostics (RED) Additionally, during this time, we will focus on formalising a distributed collaboration network to produce the different materials and assemble the components locally into a final product. Finally, during the residence, we will perform market studies to find potential stakeholders interested in exploring the use of our Open Source Hardware to build business use cases.

The new meetup will be organized one week before AfricaOSH and will take place at MboaLab. Therefore, apart from spending the week experimenting with the RT-NAAT hardware, the residents will be able to help the AfricaOSH organisers prepare for the event after the meetup. Furthermore, as a part of the funding will be used to transport the participants to Cameroon, it will allow the AfricaOSH organisation to offload these costs, allowing them to help other participants to get to the country.

Potential limitations and measures to minimise the impact

Implementation barriers due to the strict regulation of in vitro human diagnostics: Even though the initial amplifications have been carried out with SARS-CoV-2 detection reagents, the scope of this grant is not to bring a fully certified nCov test to market, but to develop a cost-effective open source technology that future entities can use to develop a new certified test. The residence at Cameroon will help to address this goal by allowing us to generate field data that later on can be used by the community to seek for funding to continue with the certification process.

The demand of nCov detection is decreasing: As the pandemic ends, the need for inexpensive tests for SARS-CoV-2 screening decreases. Hence, one of the key activities to be undertaken in Cameroon is a market study to identify other key targets that could have a bigger potential applicability. Preliminary studies during phase one showed Typhoid fever and Malaria as promising targets, but we are also considering non-human health related targets (agricultural, water testing…) as they are much less regulated. We count on additional funding sources and the 5 years experience of the Learning Planet Institute developing new primer sets for LAMP for the primer set-development.

Visa validation and vaccination in time for the trip: Due to the flexible nature of this program, we do not have plenty of time to prepare for the trip to Cameroon. Therefore, the successful arrival of all members to the region will be conditioned by external factors such as visa requirements to enter the country.

Gantt chart (Milestones, tasks, deliverables, responsible, time frames) - A link must be shared - File format: Calc, Excel, PDF, or any Gantt tool

Chart in Notion: Notion – The all-in-one workspace for your notes, tasks, wikis, and databases.

Budget (Bill of materials and other resources) - A link must be shared - File format: Calc, Excel, or PDF

Cost category Details Unitary Cost Quantity Estimated total cost
Travel cost Travel to Mboalab for the 7 days residency
Europe to Yaounde flights 950 2 1900
Asia to Yaounde flights 1600 1 1600
Latin America to Yaounde flights 1600 1 1600
Ghana to Yaounde flights 1000 1 1000
Hosting
Food & accommodation One week of food and accommodation in Yaounde one week 400 7 2800
Transportation inside Cameroon Bus, taxis, gas… To move across the region. 400 400
Additional workshop materials
Fast prototyping materials
(3D printing filament & acrylic) ABS and PLA printing filament for fast prototyping at Mboalab 200 - 300
Lab consumables Supply of pipette tips, tubes, eppendorfs… 300 - 300
Shipment of materials Transportation of materials to Yaounde 200 - 200
Total Mabolab conference 10.000
Hardware & wetware production
Production of first hardware batch PCB production and assembly, case printing… For producing the first batch of devices to be tested and deployed during the trip. 3000 - 3000
Production of first CoronaDetective reactions batch Production of the first batch of lyophilized RealTime-CoronaDetective reactions to be deployed and tested on the field. 5000 - 5000
Total first batch production 8.000

BONUS: Link to the public project repository

The detailed output of the Phase 1 residence including the results and repositories of the three devices can be found in this link.

The repositories/wikis of the different equipment:

P.S edit reason: Typo in the budget when pasted from google calc

2 Likes

Hey, my name is Thomas.

I don’t know if you have seen this paper on 3D Printable Micropipettes but I thought maybe it could be helpful for specifications since it deals with ISO standards in this research area. I was looking for it because I just got a new expensive 3D resin printer and I’m trying to print the rest of my lab.

I just got it and started learning how to use it but if you need any MSLA work done for this project (or other GOSH projects) you can reach me here or email me at thalexander6@gmail.com and see if we can collaborate.