Individual Final Project

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HTGAA 2026: Individual Final Project Documentation

SECTION 1: ABSTRACT Provide a concise, self-contained summary of your project (minimum 150 words). The abstract should allow a reader to understand the purpose, approach, and expected outcomes of the work without referring to other sections.

Your abstract should briefly address the following elements: Significance: What problem or question does the project address, and why is it important? Broad Objective: What is the overall goal of the project? Hypothesis: What prediction or principle is the project testing or demonstrating? Specific Aims: What key steps or milestones will be completed to achieve the objective? Methods: What experimental or technical approaches will be used?

SECTION 1: ABSTRACT

1. Provide an abstract/summary for your project. (minimum 150 words)

  • Self-contained description of the project
  • Should contain a brief outline of:
    • Significance
    • Broad objectives
    • Hypotheses
    • Specific aims
    • Methods to be employed
  • Use lay language (i.e., understandable by the general public) as much as possible

SECTION 2: BACKGROUND

Provide background information and research for your final project. This should describe the current state of knowledge related to your project and should include a critical evaluation of the literature that identifies the gap in knowledge that this project will fill. Explain the larger context of your project area. What are the challenges and obstacles related to your project? What problem(s) are you seeking to address?

Cite at least 2 peer-reviewed research papers. Include any figures or visuals to help assist in explaining the background of your project area.

(min. 2 paragraphs)

SECTION 3: VISION and IMPACT

3a. Introduce the vision and impact of your final project. (min. 1-2 paragraphs) What is the overall vision and goal of your project? How will the world be different if your project is successful? Include figures and visuals as appropriate.

  • Examples of topics to discuss
    • How your project solves a pressing problem in the world
    • Importance of the problem it solves or the critical barrier(s) to progress in the field that the proposed project addresses
    • The ways in which it contributes to the larger society
    • How the proposed project will improve scientific knowledge, technical capability, and/or clinical practice in one or more broad fields
    • How the concepts, methods, technologies, treatments, services, or preventative interventions that drive this field will be changed if the proposed aims are achieved

3b. Describe how your project is innovative (min. 3 sentences)

  • Examples of topics to discuss
    • Novel applications, usage, or development of theoretical concepts, approaches, methodologies, instrumentation, and/or interventions
    • How it challenges current theories, paradigms, or ways in which technology/biological tools are used
  • How your project pushes the boundaries of synthetic biology

3c. Describe the bioethical considerations involved in your project. (min. 2 paragraphs)

  • First paragraph: Include what ethical implications are involved in your project. Try to suggest ethical the principle(s) you may apply (e.g. non-maleficence, justice)?
  • Second paragraph: Describe the measures that should be taken to ensure that your project is ethical (both in how the research is conducted and in its broader implications for society). You may wish to answer the following questions:
    • What action(s) do you propose?
  • What are potential unintended consequences of your proposed actions?
  • What could you have wrong (e.g., incorrect assumptions and uncertainties)?
  • What are alternatives to your proposed actions?

SECTION 4: PROJECT AIMS

Outline three aims of your final project (min. 3 sentences, at least one for each aim)

  1. The first aim should be structured “The first aim of my final project is to [insert an achievable experimental goal that encompasses your project] by utilizing [insert protocols/tools/strategies you will use to achieve your goal]”
    • State or link any methods/experimental protocols/OpenTrons protocols/DNA or protein designs/protein design tools or models/Twist orders you will use
    • You will provide a detailed, step-by-step outline of how you will achieve your goal for the first aim in the experimental design portion of this assignment (i.e., in question 7)
    • Feel free to run your goal by a TA
  2. The second aim should be a medium-term aim that is a follow-up to your first aim and focused on goals beyond this class, building toward your third, visionary aim
    • For example, your second aim may be to successfully execute a set of experimental protocols, solve a specific problem, or develop a specific technology building upon the goals of your first aim.
  3. The third aim should be a visionary, long-term aim
    • Reveal how the larger goal of the project can be impactful
    • Examples: challenging an existing paradigm or clinical practice, addressing a critical barrier to progress in the field, describing how you envision a new technology to change how a certain type of research is conducted

SECTION 5: EXPERIMENTAL DESIGN

Share a detailed experimental plan for your final project. Include a timeline for each part of your experimental plan (i.e., how long you would expect each step in your final project to take). (min. 15 lines/sentences—a numbered list is acceptable)

  • Include specific methods/tools/technologies/biological concepts for each part of the final project and analysis
  • Include any details related to any DNA designs and explain your design choices
  • This section will be used to determine whether the experiments are well designed, feasible, and likely to succeed in testing your hypothesis
  • Often this section is broken into discrete tasks/sub-aims
  • For each experiment and/or analysis, include a description of your expected results
  • If possible, include figure(s) that visually shows a broad workflow of your project or a specific aspect of your experimental plan

SECTION 6: RESULTS

Share the experimental results of your project. Include figures, tables, graphs, etc. to represent your experimental work. What did you measure and what were the results of those measurements? These results can be from lab work, computational methods, etc.

Here is a non-exhaustive list of areas where you can provide results:

  • Performing a PCR reaction using primers relevant to your final project
  • Performing a Gibson assembly relevant to your final project
  • Designing DNA relevant to your final project
  • Creating and performing a cell-free assay related to your final project
  • Creating and running a code to validate an aspect of your final project
  • Developing a model or completing a computational analysis relevant to your project
  • Designing DNA construct(s) that can express at least one gene of interest, ordering it (via Twist), and testing of the expression of the construct(s) (potentially using an OpenTrons robot)

In the event you were unable to run certain experiments, please share your expected results. What kind of data were you hoping to get and why? Show an example data set or plot for reference (this could be from the literature or something you draw or plot).

SECTION 7: DISCUSSION AND FUTURE WORK

7a. Discussion (2 paragraphs minimum). Interpret your results. What worked? What didn’t? What data met your expectations? What did not go as planned and why do you think it didn’t work?

Discuss any other aspects of your project here as well. What were foreseen and/or unforeseen challenges? What strategies did you employ, or will you employ, to overcome these challenges?

7b. Future Work (1 paragraph minimum).

What are the next immediate steps you would like to take? What is your short term future work? What is your medium and long term future work? How do these plans relate to your aims?

SECTION 8: TECHNIQUES, TOOLS, AND TECHNOLOGY

8. We discussed and practiced various techniques related to synthetic biology throughout the semester. Place a check next to the techniques relevant to your project.

  • Foundational Lab Practices
    • Pipetting
    • Lab Safety
    • Bioethical Considerations (must check this box)
  • DNA Skills & Analysis
    • DNA Gel Art
    • DNA Sequencing
    • DNA Editing (e.g., CRISPR)
    • DNA Construct Design
    • Restriction Enzyme Digestion
    • Gel Electrophoresis
  • DNA Purification from Gel
  • Databases (e.g., GenBank, NCBI, Ensembl, UCSC Genome Browser)
  • Laboratory Automation
    • Opentrons
      • Creating Code for Laboratory Automation
      • Using Liquid Handling Robots (e.g., Opentrons)
  • Protein Design
    • Protein Design
      1. Models and Notebooks
      2. Databases
      3. Tools
        • BioProduction
    • Chassis Selection (e.g., DH5α, Bl21-DE3 for expression)
    • Registry of Standard Biological Parts
    • FreeGenes
    • Plasmid Preparation
    • Bacterial Culturing
    • Quality Control / Analysis
    • Bacterial Processing (e.g., Centrifugation, Lysis, DNA Purification)
  • Cell-Free System
    • Cell-Free Reactions
    • Freeze-Dried Cell-Free Systems
    • NEB Express Kits
    • miniPCR Tools
    • - [ ] Gibson Assembly
    • Primer Design or Selection
    • PCR Reactions
    • Gibson Assembly
    • Other Cloning Methods (e.g., Restriction Enzyme Digestion or Gateway Cloning)
    • Creating Twist Order

9. Expand upon two techniques you checked in the previous question by describing how you would utilize those techniques in your final project. (min. 4 sentences

SECTION 9: ADDITIONAL INFORMATION

10a. List all references cited in this assignment (bullet-point list)

10b. Create a supply list and budget for your project (bullet-point list)

  • What supplies, equipment, and budget is needed for your project to work?

SECTION 2: PROJECT AIMS Define three aims for your final project (minimum one sentence per aim).

Aim 1: Experimental Aim (this project): “The first aim of my final project is to [achievable experimental goal] by utilizing [protocols, tools, or strategies].” This aim should describe the core experimental objective you will attempt during this class. List or link any relevant methods or resources you plan to use (e.g., experimental protocols, automation workflows, DNA or protein designs, protein design tools, or Twist orders). You will provide a detailed step-by-step experimental plan for Aim 1 in the Experimental Design section of this assignment.

Aim 2: Development Aim: Describe the next step that would follow a successful Aim 1, extending the work beyond the scope of this course. This aim should represent a realistic progression of the project, such as executing additional experiments, solving a technical limitation, or developing the system or technology further.

Aim 3: Visionary Aim: Describe the long-term vision for the project. Explain how the broader concept could have an impact if fully realized. Examples include: Challenging an existing paradigm or clinical practice. Addressing a major barrier in a field. Enabling a new experimental capability or research approach.

SECTION 3: BACKGROUND Background and Literature Context Provide background research that explains the current state of knowledge and identifies the gap in knowledge or capability that your project addresses.

Briefly summarize two peer-reviewed research citations relevant to your research (minimum four sentences).

Explain how your project is novel or innovative. (Minimum 3 sentences.) Examples of topics to discuss: New applications or uses of existing biological tools or concepts. Development of new approaches, methodologies, or technologies. Ways the project challenges existing paradigms or assumptions. How the work expands the boundaries of synthetic biology.

Explain why your project matters and what impact it could have. (Minimum 5 sentences.) Examples of topics to discuss: The problem addressed: What pressing real-world problem does your project attempt to solve? Importance of the problem: Why is this problem significant, or what critical barrier to progress in the field does it represent? Broader societal contribution: How could the outcomes of your project benefit society beyond the immediate research context? Advancement of knowledge or capability: How might the project improve scientific understanding, technical capability, or clinical practice within one or more fields? Field-level change: If your aims are achieved, how could the concepts, methods, technologies, treatments, services, or preventative approaches used in this field of research change?

Describe the ethical implications associated with your project and identify relevant ethical principles (e.g., non-maleficence, beneficence, justice, or responsibility). (Minimum 2 paragraphs.) First paragraph: Include what ethical implications are involved in your project. Try to suggest ethical the principle(s) you may apply (e.g. non-maleficence, justice)? Second paragraph: Describe the measures that should be taken to ensure that your project is ethical (both in how the research is conducted and in its broader implications for society). You may wish to answer the following questions: What action(s) do you propose? What are potential unintended consequences of your proposed actions? What could you have been wrong (e.g., incorrect assumptions and uncertainties)? What are alternatives to your proposed actions? Note: in an NIH proposal, an ethics statement is used to describe the relevance of this research to public health

SECTION 4: EXPERIMENTAL DESIGN, TECHNIQUES, TOOLS, AND TECHNOLOGY Use Claude AI skills to refine your HTGAA final project experimental design here

Create a detailed experimental plan for your final project. Include a timeline for each part of your experimental plan (i.e., how long you would expect each step in your final project to take). (min. 15 lines/sentences—a numbered list is acceptable) Include specific methods/tools/technologies/biological concepts for each part of the final project and analysis This section will be used to determine whether the experiments are well designed, feasible, and likely to succeed in testing your hypothesis Often this section is broken into discrete tasks/sub-aims For each experiment and/or analysis, include a description of your expected results If possible, include figure(s) that visually shows a broad workflow of your project or a specific aspect of your experimental plan Reminder: All HTGAA projects must include some DNA design! Make sure this form is submitted.

We discussed and practiced various techniques related to synthetic biology throughout the semester. Place a check next to the techniques relevant to your project.

Pipetting Pipetting Lab Safety Bioethical Considerations (must check this box)

DNA Gel Art DNA Sequencing DNA Editing DNA Construct Design Restriction Enzyme Digestion Gel Electrophoresis DNA Purification From Gel Databases (e.g., GenBank, NCBI, Ensembl, and UCSC Genome Browser)

Lab Automation Creating Code for Laboratory Automation Using Liquid Handling Robots (e.g., Opentrons) Designing a Twist Order Creating a plan to use the Autonomous lab at Ginkgo Bioworks

Protein Design Protein Design Use of Boltz or PepMLM Use of Asimov Kernel Use of Benchling Models and Notebooks Databases Bioproduction Bioproduction Chassis Selection (e.g., DH5alpha) Registry of Standard Biological Parts Plasmid Preparation Bacterial Culturing Quality Control/Analysis Bacterial Processing (e.g., Centrifugation, Lysis, DNA Purification)

Cell-Free Systems Cell Free Reactions Freeze-Dried Cell Free Systems miniPCR Tools Protein Purification

Gibson Assembly Primer Design or Selection PCR Reactions Gibson Assembly Other Cloning Methods (e.g., Restriction Enzyme Digestion or Gateway Cloning)

CRISPR CRISPR/Cas9 Designing Prime Editing gRNA

Expand upon two techniques you checked in the previous question by describing how you would utilize those techniques in your final project. (min. 4 sentences)

Identify any How To Grow (Almost) Anything Industry Council companies which are associated with your final project (optional)

Addgene Asimov (Kernel) ATCC Basecamp Research BioFabricate Biome Consortia Bolt Boltz.bio Cultivarium DeepCure Epibone Ginkgo Bioworks Helix Nano Millipore Sigma Mycoworks New England Biolabs Nuclera Opentrons SecureDNA Takeda Pharmaceuticals Thermo Fisher Scientific Transfyr.ai Twist Biosciences Upside Foods Waters Corporation

SECTION 5: Results & Quantitative Expectations

You are required to validate at least one aspect of your final project aims. This is to ensure that you are able to successfully apply a relevant synthetic biology technique to your project. Include figures if you have them—accuracy is critical in figures, tables, and graphs Here is a non-exhaustive list of acceptable validations: Designing DNA relevant to your final project Performing a PCR reaction using primers relevant to your final project Performing a Gibson assembly relevant to your final project Creating and performing a cell-free assay related to your final project Creating and running code to validate an aspect of your final project Developing a model or completing a computational analysis relevant to your project Designing DNA construct(s) that can express at least one gene of interest, ordering it (via Twist), and testing of the expression of the construct(s) (potentially using an Opentrons robot)

What aspect of your final project did you choose to validate? (min. 2 sentences)

Write down a detailed protocol of how you validated this aspect of your final project. (Numbered list or paragraph is fine)

What synthetic biology techniques did you utilize in validating this aspect of your final project? You can refer to the list of techniques in question 8. (min. 4 sentences)

You must present data as part of your final project and include some analysis of that data. The data may be collected experimentally in the lab or generated as simulated data (e.g., using the Asimov Kernel or another simulation method). (min. 2 sentences)

Did you encounter any unexpected challenge(s) when performing your validation? If so, describe the challenge(s) and strategies to overcome it. If not, discuss potential problems, difficulties, limitations, and/or alternative strategies to overcome challenges in your final project. (min. 4 sentences).

SECTION 6: ADDITIONAL INFORMATION

  1. List all references cited in this assignment (bullet-point list)

  2. Create a supply list and budget for your project (bullet-point list)

  • What supplies, equipment, and budget is needed for your project to work?