Our team is dedicated to advancing the field of synthetic biology and supporting fellow iGEMers through innovative tools and resources. Below are the key contributions we are proud to offer to the iGEM community and the scientific community at large.

IMPROViSeD

IMPROViSeD is a cutting-edge, robust, scalable, and efficient tool specifically designed to model protein complexes using experimentally derived geometric constraints. Unlike traditional methods that often rely on computational predictions, IMPROViSeD integrates actual experimental data to deliver precise and accurate structural models of protein complexes. This data-driven approach ensures that the models reflect the real-world dynamics of protein interactions, which is crucial for understanding biological mechanisms at a molecular level.

For iGEMers, the power of IMPROViSeD lies in its ability to aid in visualisation and thereby accelerate the development of targeted therapeutics. By elucidating the precise structure of protein complexes, such as those involved in cancer metastasis (as we have), teams can design more effective drugs and therapies that target specific protein-protein interactions with higher precision. The platform's scalability ensures that even large, multi-subunit complexes can be modelled efficiently, making it an invaluable resource for synthetic biology projects that require detailed molecular insights.

Whether it's designing antibodies, inhibitors, or other therapeutic molecules, IMPROViSeD empowers iGEM teams to bridge the gap between structural biology and clinical applications, opening new possibilities for developing next-generation treatments for complex diseases.

BEPT

In today's research landscape, many scientists encounter challenges when utilizing software tools available on platforms like GitHub, often due to unfamiliarity with the command line or difficulty in comprehending documentation. To address this gap, we developed BEPT (Bioinformatics Environment for Protein Tools), an interactive command line interface that simplifies the use of APBS (Adaptive Poisson-Boltzmann Solver) for protein electrostatics studies.

BEPT automates the generation of pdb2pqr commands and allows users to adjust APBS calculation parameters effortlessly. By recreating the functionality of the APBS web server within the terminal, BEPT provides a user-friendly design that helps researchers overcome initial apprehensions about command-line tools. Our contribution aims to make protein electrostatics more accessible, enabling scientists to conduct meaningful research without the barriers often associated with traditional command-line interfaces.

Bept also provides a framework for the iGEM community for building their interactive command line tool in Python.

Define Scope
Outline the tool's goals, core functionalities, and supported techniques (e.g., protein analysis, electrostatics). Bept has a well defined scope for protein electrostatics studies clearly defined in the documentation.
Use Beginner-Friendly Libraries
Leverage python libraries like `click` or `argparse` for CLI and `rich` for interactive output, ensuring ease of use. Grouping commands logically, providing clear help descriptions, and including simple examples helps users understand the tool's capabilities. Bept uses `click`, `rich`, `beaupy`, `textual` and more libraries for interactive interfaces.
Testing and Maintainance
Implement unit tests, integration tests, and continuous integration to ensure the tool's reliability and performance. Regular updates and bug fixes enhance the user experience. Bept has been tested cross-platform on Linux, MacOS and Windows and well maintained on Github.
Documentation
Create detailed documentation with installation instructions, usage examples, and troubleshooting tips to guide users effectively. You can add the documentation online using Read the Docs, GitHub Pages, or other platforms. Bept uses Sphinx and Read the Docs for documentation.
Publishing on Package Managers
Distribute the tool on PyPI, Conda, Homebrew, etc. for easy installation and accessibility. Include versioning and dependencies for seamless integration.

Bept is available on Github, PyPI, Homebrew Tap. Online documentation for Bept is present at Read the Docs.

Inclusivity Tool for Enhanced Accessibility

Understanding the importance of inclusivity in research and education, we have developed a plug-in tool designed to enhance accessibility on our web platform. This tool features options for color customization to aid colorblind individuals, a reading focus option for those with attention disorders, and text customization for improved readability. Additionally, it highlights links and buttons on the webpage to ensure that all users can navigate our resources effectively.

By prioritizing inclusivity, we aim to create an environment where every individual, regardless of their abilities or challenges, can engage with our project and the broader field of synthetic biology. This plug-in tool can be utilised by iGEMers to enhance accessibility and inclusivity on their wikis.

Synthetic Biology Ideathon Framework

To assist upcoming iGEM teams in organizing effective ideathons, we designed a systematic workflow that can be used to make these events both informative and impactful. This framework aims to help future teams expand their reach, engage their audience, and communicate ideas effectively through structured ideation sessions. The workflow emphasizes the importance of clear objectives, well-defined challenges, audience targeting, and providing participants with the right tools, resources, and mentorship to foster creative thinking and problem-solving. By following this process, iGEM teams can host ideathons that inspire innovative ideas and drive meaningful discussions in synthetic biology and related fields.

Define Objectives and Goals
- Purpose: Clearly state the purpose of the ideathon. Is it to generate innovative ideas in synthetic biology, sustainability, education, or social good?
- Goal Setting: Define clear outcomes:
  - A list of innovative ideas.
  - Participant engagement and learning.
  - Awareness and collaboration among participants on real-world issues.
Identify and Segment the Target Audience
- Define Audience Profile:
  - High school or college students, entrepreneurs, early-career professionals, or a mixed group.
  - Consider their background (technical, non-technical) to ensure balanced participation.
- Understand Needs:
  - Conduct pre-event surveys or interact with potential participants to assess their interests and challenges.
  - Target students or professionals interested in solving problems but unsure how to proceed with ideation.
Theme and Challenge Design
- Theme Selection: Choose a relevant and engaging theme aligned with your objectives (e.g., "Innovating with Synthetic Biology," "Sustainable Solutions for the Future"). In our case, it was “using computational and synthetic biology to produce sustainable solutions”.
- Challenges: Define challenges under the theme. Challenges should:
  - Be broad enough to allow creativity but specific enough to address real-world problems.
  - Provide context for participants, offering real-life scenarios where their ideas could be applied.
- Problem Statements: Prepare clear problem statements or ask participants to identify a challenge they want to solve.
Content Design and Preparation
- Workshops and Resources:
  - Pre-event webinars or resources on creative thinking, problem framing, and ideation techniques (e.g., design thinking, mind-mapping).
  - Provide case studies and relevant data related to the ideathon’s theme to guide participants.
  - Industry insights and articles to give participants inspiration and context.
- Mentorship:
  - Recruit mentors with expertise in the ideathon’s theme who can guide participants through brainstorming and idea refinement.
  - Organize one-on-one mentoring sessions or open Q&A formats.
Ideation and Evaluation Process
- Structured Ideation:
  - Guide participants through structured ideation techniques such as:
    - Brainstorming sessions.
    - Design thinking workshops to empathize, define, ideate, prototype, and test solutions.
  - Encourage participants to focus on the viability, feasibility, and impact of their ideas.
- Checkpoints:
  - Set up checkpoints during the event where teams can present progress, get feedback, and refine their ideas.
Judging Criteria and Pitching
- Criteria:
  - Clarity of problem definition.
  - Innovation and creativity.
  - Impact and potential for real-world application.
  - Feasibility of the idea.
  - Presentation and storytelling skills.
- Pitch Preparation:
  - Offer workshops or guides on how to craft effective pitches.
  - Time-limit pitches (e.g., 5 minutes per team), allowing for succinct communication.
- Panel of Judges:
  - Invite industry experts, academics, and relevant professionals to evaluate the pitches based on the criteria.
Tools and Platforms
- Platform for Virtual Events:
  - If virtual, select a platform that supports team collaboration, such as Zoom, Microsoft Teams, or Discord.
  - Use platforms like Miro, Figma, or Google Slides for collaborative brainstorming and presentations.
- Submission System:
  - Designate a platform or form for idea submissions (e.g., Google Forms, Devpost, or an internal submission system).
Post-Ideathon Engagement
- Follow-Up:
  - Provide feedback to participants on their ideas.
  - Share winning ideas and promote further collaboration through newsletters, social media, or community forums.
- Resources for Further Development:
  - Share resources or connect participants to incubators, mentors, or potential funding to turn their ideas into reality.
- Offer Certificates and Prizes:
  - Offer incentives like certificates, mentorship opportunities, internships, or small seed funding for further idea development.
Promotion and Participant Outreach
- Targeted Marketing:
  - Reach out through schools, universities, social media, and relevant industry forums.
  - Tailor your messaging to inspire creativity and focus on the opportunity to contribute to a meaningful cause or challenge.
- Engage Communities:
  - Partner with student clubs, online communities, or industry groups to amplify your reach.

Recommended Timeline

6-8 Weeks Before the Event:
- Define objectives and theme.
- Identify the target audience.
- Start promoting and open registration.
4 Weeks Before the Event:
- Confirm mentors, judges, and speakers.
- Design workshops or webinars.
2 Weeks Before the Event:
- Finalize logistics and share event materials (challenges, schedules, resources).
During the Event:
- Facilitate ideation, provide ongoing mentorship, and hold checkpoints.
- Conduct the final pitching session.
Post-Event:
- Announce winners, share feedback, and promote ongoing engagement.

During our discussions with faculty at MSMF, we identified a key challenge in antibody therapeutics: the need to screen numerous antibodies to determine the most effective one. Our software can model the interfaces between two proteins that are crucial to disease propagation. By understanding the structure of these interfaces, the ultimate goal is to design antibodies that can effectively combat these diseases. We are also working towards enabling our software to predict the structure of an antibody based on the epitope at the protein interface. This advancement would significantly improve the efficiency of antibody screening by greatly reducing development time.

Our team's contributions are designed to enhance collaboration, accessibility, and innovation within the iGEM community and the broader field of synthetic biology. By providing essential tools like IMPROViSeD and BEPT, along with our inclusivity plug-in and the framework for the Synthetic Biology Ideathon, we aim to empower iGEMers and the research community at large.