NuNet: Bioinformatics simulations with Decentralized Computing // Enabling cheap and reliable simulations on decentralized hardware for Bioinformatics via frameworks. Bioinformatics is essential for management of data in modern biology and medicine.

[GENERAL] Name and surname of main applicant

Ilija Radeljic

[GENERAL] Email address of main applicant

ilija.radeljic@nunet.io

Additional applicants

Avimanyu Bandyopadhyay, PhD candidate

Lead Researcher and systems scientist

Kabir Veitas, PhD

CEO and lead architect

[GENERAL] Please specify how many months you expect your project to last (from 2-12 months)

10

[GENERAL] Please indicate if your proposal has been auto-translated into English from another language.

No

[GENERAL] Does your project have any dependencies on other organizations, technical or otherwise?

Yes

[GENERAL] If YES, please describe what the dependency is and why you believe it is essential for your project’s delivery. If NO, please write “No dependencies.” .

For the development we shall use only open source frameworks as follows: 

• Data science platform (Anaconda)
• Multicellular modeling framework (Cellmodeler)

These technical dependencies do not require permissions to use outside Open Source licensing and are taken into account in our feasibility study. Therefore, integrating these dependencies will not cause any delays.

https://www.anaconda.com/

https://github.com/cellmodeller/CellModeller

[GENERAL] Will your project’s output/s be fully open source?

Yes

[GENERAL] If NO, please describe which outputs are not going to be open source. If YES, please write “Project will be fully open source.”

Project will be fully open source in line with our licensing policy.

[METADATA] Category of Proposal

Data tools

[METADATA] SDG rating

SDG Goals

• 9 - Build resilient infrastructure, promote inclusive and sustainable industrialization and foster innovation
• 10 - Reduce inequality within and among countries

SDG Subgoals

• 9.1 - Develop quality, reliable, sustainable and resilient infrastructure, including regional and transborder infrastructure, to support economic development and human well-being, with a focus on affordable and equitable access for all
• 9.5 - Enhance scientific research, upgrade the technological capabilities of industrial sectors in all countries, in particular developing countries, including, by 2030, encouraging innovation and substantially increasing the number of research and development workers per 1 million people and public and private research and development spending

[IMPACT] Please describe your proposed solution.

Problem:

The recent rise in AI and ML has resulted in the lack of affordable and available GPU and CPU computing power on the market for bioinformatics/medical/physics research. In addition, smaller institutions or private researchers might struggle to find available and affordable computing resources for their research.

Unique solution:

NuNet is a decentralized, open source, p2p computing network utilizing latent computing resources of the world and will enable bioinformatics/medical/physics simulations to run via its network. Via this project, NuNet will enable running compute workflows on the network that require dependencies to popular data science and modeling frameworks (e.g. Anaconda and CellModeller). For example, 35 million users are utilizing the Anaconda framework for their work.

Empowering Decentralized Research on the Cardano Blockchain

Cancer research through blockchains underscores the importance of leveraging blockchain technology for innovative research applications. The focus here is on the Cardano blockchain, a truly decentralized platform that is revolutionizing the way research is conducted. With its robust smart contract capabilities, Cardano is paving the way for a new era of decentralized science (DeSci), particularly in fields such as bioinformatics and other STEM and non-STEM disciplines.

Cardano's decentralized infrastructure and robust smart contract capabilities make it an ideal platform for conducting complex research processes. For instance, multiple research teams can simultaneously update their compute models, enhancing the efficiency and effectiveness of the research process. 

Enabling medical/bioinformatics/physics simulations by utilizing Cardano blockchain as a transaction and settlement layer may greatly increase real world usage of Cardano ecosystem within DeSci, STEM and research community.

An interesting comparison between Traditional science & research (TradSci) and Decentralized Science (DeSci) is visualized in the tweet below:

Basically the flow of info/$$ in TradFi involves a big public/government institution as a middleman. In the DeSci the flow of info/$$ is directly between the public and researchers. Enabling simulations for this on decentralized hardware empowers all research to be done independent of the influence of big government, public or private institutions.

https://www.cryptoaltruism.org/blog/infographic-decentralized-science-vs-traditional-science

Benefits for the Cardano ecosystem:

The research is a continuation and expansion of the already completed Fund8 proposal. It will enable data science, DeSci, STEM and research use cases – specifically bioinformatics/medical/physics simulations – in the web2 and web3 space that need GPU computing power to source it via NuNet. The value for the compute provided will be exchanged via NTX token which is a Cardano Native Token.

Each transaction will be executed as a Smart Contract on the Cardano blockchain which will directly increase the volume of tx, volume of CNT as well as provide unique use cases utilizing bioinformatics/medical/physics frameworks to be built on top of it for the Cardano ecosystem.

[IMPACT] How does your proposed solution address the challenge and what benefits will this bring to the Cardano ecosystem?

The proposal addresses the following directions of the challenge:

• Business solutions - Software products, data management, process management, data management solutions (CRM, ERP etc), privacy products.

Introduction:

The NuNet platform, as outlined in the proposal, currently offers an infrastructure for machine learning computations. However, the potential of this platform can be significantly expanded by integrating an additional option of data platform (Anaconda) containers. This would allow the platform to cater to a wider range of use-cases, including business solutions for both STEM and non-STEM research, thereby making it a more versatile tool for decentralized science and research.

Impact on the Cardano Ecosystem:

The integration of data science platform (Anaconda) containers into the NuNet platform can have a transformative impact on the Cardano ecosystem. By broadening the scope of computational possibilities, the platform can attract a diverse range of researchers from traditional science communities worldwide. This influx of users would not only increase the number of transactions but also strengthen the Cardano community by bringing in new perspectives and ideas.

The proposed solution addresses a key challenge in the Cardano ecosystem: the need for a more versatile computational platform that can cater to a wide range of research needs. By offering a solution that can handle both machine learning and non-machine learning computations, the platform can become a one-stop solution for researchers, thereby solving this issue.

Benefits:

1. Increased User Base: By catering to a broader range of research needs, the platform can attract a larger user base. This would include researchers from various fields who are looking for a decentralized platform for their computational needs.

2. Strengthening the Ecosystem: The influx of new users and the increased number of transactions would strengthen the Cardano ecosystem. It would also foster a more diverse community, which can lead to innovative ideas and solutions.

3. Versatility: The integration of Anaconda containers would make the platform more versatile, allowing it to handle a wide range of computations. This would make it a more attractive option for researchers.

4. Decentralized Science and Research: By providing a platform that can handle a wide range of research computations, the proposed solution would further the cause of decentralized science and research. This would democratize access to computational resources and foster collaboration among researchers.

In terms of quantifying the impact, it's realistic to expect a significant increase in the number of users and transactions within a reasonable timeframe after the project completes. The exact numbers would depend on various factors, including the marketing efforts and the adoption rate among researchers. However, given the unique value proposition of the platform, it's reasonable to expect a positive response from the research community.

[IMPACT] How do you intend to measure the success of your project?

Introduction:

The success of integrating data science platform (Anaconda) containers into the NuNet platform can be measured through a combination of quantitative and qualitative metrics. These metrics will provide insights into the impact of the project on the Cardano ecosystem's productivity and growth, both in the short and long term.

Quantitative Metrics:

1. User Adoption: Monitor the number of users (as a number of unique DIDs or DApp integrations) who start using the platform for their research needs. This can be further broken down into the number of STEM and non-STEM researchers (private persons or organizations using NuNet solutions).

2. Transaction Volume: Track the number of transactions on the platform. An increase in transaction volume would indicate a higher usage of the platform.

3. Successful Deployments: Count the number of successful deployments of research tools, such as the CellModeller framework with 480 citations for multi-cellular modeling. This would provide a direct measure of the platform's utility for research purposes.

Qualitative Metrics:

1. User Feedback: Collect feedback from users about their experience with the platform. This could include their opinions on the ease of use, the versatility of the platform, and the benefits of decentralization.

2. Community Engagement: Monitor the level of engagement within the Cardano community. This could include discussions about the platform on forums, social media, and other platforms.

3. Research Outcomes: Track the outcomes of the research conducted using the platform. This could include the number of research papers published, the impact of the research, and the innovative solutions developed.

The integration of the data science platform (Anaconda containers) into the NuNet platform is expected to have a positive impact on Cardano's productivity and growth. In the short term, it can attract a larger user base and increase the number of transactions. In the long term, it can foster a more diverse and innovative community, leading to the development of novel solutions and advancements in various fields of research.

These measures are realistic as they are based on the unique value proposition of the platform and its potential to cater to a wide range of research needs. The successful testing of the CLI version of the CellModeller framework on the NuNet platform further supports the feasibility of these measures.

Some of the direct benefits to the Cardano ecosystem are:

• Number of projects using cheaper GPU resources for AI/ML tasks
• Computing resources used in the processes are to be compensated in NTX, which is a Cardano Native Token
• Each exchange of value will be done as a Smart Contract on Cardano
• Currently over 2000+ people are in NuNet Discord testing the various builds of the NuNet platform

Some of the indirect benefits to the Cardano ecosystem are:

• Cardano becomes the settlement layer for decentralized Open Source computing frameworks used in training AI/ML models
• Other solutions can be built on top of the framework, greatly expanding the potential business models
• With the right onramp/offramp solutions Web2 users can utilize compute power without even realizing the Web3 layer underneath. NuNet is interested in joint work with the experts in this field.

[IMPACT] Please describe your plans to share the outputs and results of your project?

Spreading Outputs Over a Timescale

Our project plan includes clear milestones and deliverables, which will be shared publicly as they are completed. This incremental release of outputs will ensure a continuous stream of updates for the community.

This approach lets us provide updates on a regular basis, and offers users the chance to provide feedback that we can use to guide subsequent development.

Sharing Outputs, Impacts, and Opportunities

We intend to leverage various communication channels to share our project's outputs, impacts, and opportunities:

1. GitLab: The primary hub for our technical work, hosting our codebase, documentation, and issue tracking. This will be the main point of reference for the details of our project.
2. Social Platforms: We plan to regularly post updates on our progress on platforms like Twitter, LinkedIn, and Reddit. This will include major milestones, bug fixes, and insights from our development work.
3. Technical Discussions: We will continue to hold weekly technical discussion where we discuss the technical aspects of our work. This provides a forum for live Q&A and discussion with our community.
4. Blogs: A regular blogs to summarize the progress we have made, highlighting key achievements and outlining the next steps in our project.

Testing and further research

As an open-source project, our outputs will be freely accessible for further research and development. We encourage the community's involvement in testing our solutions to enhance their real-world performance.

Community Testing: We'll invite our users to participate in alpha and beta testing phases, where they can help identify bugs and suggest improvements. We'll use GitLab's issue tracking for managing feedback and provide guidelines for issue reporting and feature suggestions.

Internally, we'll use project insights and community feedback to guide our future work, optimize performance, and prioritize new features. Our aim is to foster a collaborative development ecosystem that is robust, relevant, and of high quality.

[CAPABILITY/ FEASIBILITY] What is your capability to deliver your project with high levels of trust and accountability?

Illustration of Capacity:

Our organization comes with a history of successfully bringing intricate technology projects to fruition. The pillars of our success lie in our deep-rooted technical understanding, stringent project management practices, and an unwavering focus on transparency and responsibility.

At NuNet we have employed a PhD candidate who is performing this kind of research in particular - GPU based Bioinformatics and is the lead on this proposal. The draft publication of his work is publicly available here:

https://peerj.com/preprints/26920/

NuNet is committed to Open Source Software development from the inception. Therefore, all our development and progress is available for public scrutiny at all times as well as open collaboration with the community. We actively invite and work with the community in regards to contribution, usage, work and testing of the platform codebase.

Link: https://gitlab.com/nunet

NuNet licencing policy:

https://docs.nunet.io/nunet-licensing-policy/

Openness and Responsibility:

We have established a robust framework to ensure openness and responsibility in the execution of the project and the management of finances:

1. Elaborate Budgeting: We present an exhaustive budget layout at the start of the project that details the fund allocation across various tasks. This leaves no room for ambiguity regarding the utilization of funds.

2. Periodic Reporting: Regular updates regarding the project and financial statements will be shared, offering complete transparency into the progression of the project and the use of funds.

3. External Auditing: We are open to audits conducted by independent third parties at regular intervals. This ensures responsibility and openness in our financial management.

4. Escrow Mechanisms: To further reassure proper use of funds, we can utilize an escrow service. This arrangement ensures that the project funds are held by a third party and released according to pre-set milestones. This provides an extra layer of assurance for the funds.

5. Payment Based on Milestones: Our payment structure is built around specific, agreed-upon milestones. This ensures that funds are released as we achieve these milestones. The completion of each milestone can be verified, ensuring you pay only for verifiable progress.

These measures reflect our commitment to openness, responsibility, and proper management of funds. We believe that these factors, along with our technical capabilities, make us an ideal choice to successfully execute this project.

We understand that not all steps we have implemented are valid for the Catalyst proposal but it demonstrates the internal working procedures we have in place.

Catalyst Experience

NuNet also has received the funding for proposals in Fund7 and Fund8. One proposal is successfully closed and the other is close to completion with one technical obstacle left to be solved. Overall, the funds were spent as intended on the development which can be monitored on Gitlab with daily commits since the award.

https://gitlab.com/groups/nunet/-/milestones/19#tab-issues

https://gitlab.com/groups/nunet/-/milestones/20#tab-issues

Financial Stability

As a 28+ strong team, we have independent funding to develop the core platform with a cash runway for at least 1-1.5 years. Cardano Catalyst proposals are used to extend the functionality and add features to the platform in order to enrich the possible use cases.

The financial report is publicly available and can be reviewed here:

https://medium.com/nunet/nunet-financial-report-2022-and-outlook-for-2023-405d38397629

[CAPABILITY/ FEASIBILITY] What are the main goals for the project and how will you validate if your approach is feasible?

Introduction:

The primary goal of this project is to enhance the NuNet platform's capabilities by integrating data science platform (Anaconda containers), thereby expanding its use-cases to include both STEM and non-STEM research. This section outlines the specific objectives of the project and the methods for validating their achievement.

Main Goals:

1. Technical Integration: The first objective is to successfully integrate Anaconda containers into the NuNet platform. This will be validated by testing the platform's ability to handle a range of computational tasks, beyond machine learning, using Anaconda containers.

2. User Adoption: The second objective is to increase the user base of the platform. This will be measured quantitatively by tracking the number of new users and qualitatively by collecting user feedback.

3. Transaction Volume: The third objective is to increase the number of transactions on the platform. This will be measured by tracking the transaction volume before and after the integration of Anaconda containers.

4. Community Engagement: The fourth objective is to foster a more diverse and engaged Cardano community. This will be measured qualitatively by monitoring discussions about the platform on community forums and social media.

5. Research Outcomes: The final objective is to facilitate innovative research outcomes. This will be measured qualitatively by tracking the research conducted using the platform and its impact.

Validation of Feasibility:

The feasibility of the approach will be validated through a combination of technical testing and user feedback. The successful testing of the CellModeller CLI on NuNet’s GPU platform provides a strong indication of the technical feasibility of the approach. Further validation will be obtained by deploying other research tools using Anaconda containers and assessing their performance.

User feedback will provide valuable insights into the usability and utility of the platform. By collecting feedback from users, we can assess whether the platform meets their research needs and identify areas for improvement.

In conclusion, the goals of the project are aligned with the needs of the Cardano ecosystem and the broader research community. The validation methods outlined above will ensure that these goals are achieved and that the project delivers a significant impact.

[CAPABILITY/ FEASIBILITY] Please provide a detailed breakdown of your project’s milestones and each of the main tasks or activities to reach the milestone plus the expected timeline for the delivery.

Introduction:

The project of integrating data science platform (Anaconda) into the NuNet platform will be executed in a phased manner, with each phase marked by a specific milestone. The following is a detailed breakdown of the project's milestones, the main tasks or activities to reach each milestone, and the expected timeline for delivery.

Milestone 1: Project Commencement and detailed architecture blueprints

• Main Tasks / Activities: Forming the squad, building communication platforms, conducting weekly brainstorming sessions for comprehensive understanding of the Cardano universe and its latest computational offerings, identifying the prerequisites for integrating data science platform, drafting a comprehensive project blueprint, and conducting a practicability study based on the specified prerequisites and available resources.
• Expected Delivery Time: 2.5-5 Weeks

Milestone 2: Technical Integration of Anaconda Containers for DeSci

• Main Tasks / Activities:
• Implement the integration as per detailed blueprint developed in Milestone 1
• Test the platform's ability to handle computational tasks using Anaconda containers.
• Acceptance Criteria: 
• Successful integration of Anaconda containers and the platform's ability to handle a range of computational tasks.
• Expected Delivery Time: 5.5-15 Weeks

Milestone 3: Marketing and community development strategy

• Main Tasks / Activities
• Develop a marketing and community strategy to attract new users and developers.
• Develop community testing and feedback adoption strategy;
• Expected Delivery Time: 2-4 Weeks

Milestone 4: Implementation of marketing and community development and testing strategy

• Main Tasks / Activities
• Monitor the number of new users and collect user and community developers feedback;
• Solve community provided bug reports and implement additional features as deemed required;
• Monitor the number of transactions on the platform.
• Implement strategies to encourage more transactions, such as user incentives or improved features.
• Engage with the Cardano community through forums, social media, and other platforms.
• Monitor discussions about the platform and respond to queries and feedback.
• Expected Delivery Time: 10 Weeks

Milestone 5: Dissemination and identified additional documentation

• Main Tasks / Activities: 
• Gathering and analyzing data from the deployed system and writing additional documentation based on gathered data and the entire project experience.
• Additional marketing and communication activities as needed;
• Expected Delivery Time: 3-6 Weeks

The project will be managed using a combination of agile and waterfall project management approaches. The technical integration will follow a waterfall approach, with each task being completed before the next one begins. The user adoption, transaction volume, community engagement, and research outcomes will follow an agile approach, with tasks being executed concurrently and adjustments being made based on feedback and data.

The projected cost to achieve each milestone will depend on various factors, including the resources required, the complexity of the tasks, and the market conditions. However, a detailed budget plan will be developed and shared with the stakeholders to ensure transparency and accountability.

[CAPABILITY/ FEASIBILITY] Please describe the deliverables, outputs and intended outcomes of each milestone.

Introduction:

Each milestone in the project of integrating Anaconda containers into the NuNet platform will result in specific deliverables and outputs, leading to intended outcomes that contribute to the overall project goals. Here's a detailed description of what to expect from each milestone.

Milestone 1: Project Commencement and detailed architecture blueprints

• Deliverables:
• Project blueprint, general architecture and applied research, practicability analysis, project roadmap, defining risk management strategy and resource allocation plan.
• Outcomes:
• Detailed documents of all strategies, including a timeline, resource distribution, and dependencies.

Milestone 2: Technical Integration of Anaconda Containers for DeSci

• Deliverables:
• The primary deliverable for this milestone is the NuNet platform with integrated Anaconda containers. The output will be a technical report detailing the integration process, challenges encountered, and solutions implemented.

• Outcomes:
• The successful integration of Anaconda containers will enhance the platform's capabilities, allowing it to handle a wider range of computational tasks. This will position the platform as a viable alternative to other platforms like Ethereum, which have become increasingly centralized.

Milestone 3: Marketing and community development strategy

• Deliverables: 
• A marketing strategy 
• A strategy to encourage more transactions.
• Engagement strategies and community feedback reports.

• Outcomes:
• The project has a robust and thought-out way to attract Cardano, NuNet and DeSci communities into a joint collaboration space;
• Continuous monitoring and improvement via the community interaction

Milestone 4: Implementation of marketing and community development and testing strategy

• Deliverables: 
• User feedback reports, bug requests, number of opened issues based on them and closed issues;

• Outcomes:
• Strengthened Cardano community through increased user adoption, increased number of transactions on the platform, and valuable insights into user needs for future development.
• Higher usage of the platform with a research perspective, indicated by an increase in transaction volume, contributing to the strength and vitality of the Cardano ecosystem.
• A more diverse and innovative Cardano community through increased engagement, and valuable feedback for future platform development.

Milestone 5: Dissemination and identified additional documentation

• Deliverables: 
• Gathering and analyzing data from the deployed system and writing additional documentation based on the gathered real usage data and the entire project experience.
• A report detailing the research conducted using the platform and its impact
• Outcomes: 
• Continuous improvement of the system based on user feedback and changing needs, a system that remains relevant, efficient, and effective over time. Broad community involvement in usage and further development.
• Demonstration of the platform's utility for research purposes through successful research outcomes, inspiring other researchers to use the platform, and further increasing its user base and transaction volume

Each milestone’s progress will be tracked through the completion of the stated expected results and the achievement of the anticipated impact. Regular project update meetings and reports will provide visibility into the project's progress, and any issues or delays will be addressed through the project's risk management process. The overall project management methodology will be agile, with regular sprint planning, daily stand-up meetings, and retrospective meetings. Key performance indicators will be defined to track the progress and success of the project. The team will regularly communicate with stakeholders and the Cardano community to keep them updated on the progress and gather feedback.

[RESOURCES & VALUE FOR MONEY] Please provide a detailed budget breakdown of the proposed work and resources.

Each project is examined in great detail which can be seen in the proposed budgeting sheet. This results in pre-feasibility and feasibility studies which minimize the risk of budget overruns.

Project management in NuNet is on a high level with employed techniques such as Agile, Scrum, CCPM and others resulting in a good daily overview of the project progress.

The project is complex and involves research and development uncertainties however, NuNet is a well funded deep tech startup and in case of budget overruns will continue to develop until delivered due to this being a critical part of the overall NuNet development plan. This is evidenced by the funding received in Cardano Catalyst Fund 7 and 8 where NuNet has continued the work despite the substantial unexpected technical roadblocks and time impact.

[RESOURCES & VALUE FOR MONEY] How does the cost of the project represent value for money for the Cardano ecosystem?

The costs of the project are based on the average salary levels of engineers currently employed by NuNet. Since the team is fully distributed and remote, it is challenging to have a suitable median cost that covers the range of countries (India, Pakistan, Ethiopia, Brasil, Egypt, UAE, UK, Italy and others).

We believe that the costs are reasonable and reflect the seniority and knowledge of various positions involved in the delivering of the proposal.

In line of full openness, in the budget table can be seen the very granular distribution of costs, all the way to the hours of each position for each milestone.

In addition, fully remote workers can compete for jobs in Western countries driving the individual compensation levels much higher than in their native countries.

[IMPORTANT NOTE] The Applicant agreed to Fund10 rules and also that data in the Submission Form and other data provided by the project team during the course of the project will be publicly available.

I Accept