Latest revision as of 21:35, 3 August 2023

• Add a Basic Part - A tutorial on how to add a basic part
• Add a Composite Part - A tutorial on how to add a composite part
• Scars - Information on assembly scars, and how to specify them for a composite part
• Synthesis - Things to keep in mind if you're adding and documenting a part you've synthesized
• Assembly Compatibility - Make sure your part is compatible with an assembly standard
• Twins - Parts are twins if they have the same sequence
• Document Parts - Recommendations on how to document your parts
• Make a Contribution - Improve existing parts

Documenting Parts

Adding a part to the Registry requires some basic information:

Adding your part to the Registry is a great first step, but there's still more to do!

Part Pages

• The Main Page acts as the hub for a part. It should contain information necessary to use a part: information, measurements, and characterization so that users know what the part is and how it works. All users can contribute to this page.
• The Design page contains information on how the part was designed (design process) and also includes its sequence and features box by default.
• The Experience page has information from users about the part. This may come in the form of a simple "this works/doesn't work," or an in-depth review. If you've used a part, be sure to share your experience. If you intend to use a part, you should check to see if others have had any experience with it.
• The Information page has editable elements for the part that classify and organize it within the Registry's database; this includes the short description, part type, categories, parameters, etc. Members belonging to the part's author's group are able to edit these elements.
• The Part Tools menu has various software tools that integrate with the part you're viewing.

Documenting and characterizing your part is vital to its continued use by Registry users. Users will have a clearer understanding of how your part works, and what to expect when using your part in their project. A well documented part offers a foundation for users to experiment and test your part, and build upon your documentation and characterization work. You will find that your well documented part will be used in new composite parts, new systems, and new team projects.

We've provided a few guidelines on how you may want to approach documenting your parts. The guidelines include examples from current Registry parts that are considered well documented.

Usage

Explain what you used the part for in your project, and what other uses it might serve. Take a look at how the authors of BBa_K863006, an E. coli laccase, addressed Usage.

In the last few years a lot of attention has been drawn to laccases due to their ability to oxidize both phenolic and nonphenolic lignin related compounds as well as highly recalcitrant environmental pollutants. This makes them very useful for applications concerning several biotechnological processes. This includes the detoxification of industrial effluents, for example from the paper and pulp, textile and petrochemical industries. Laccases are also valuable as a tool as a tool for medical diagnostics and as a bioremediation agent to clean up herbicides, pesticides and certain explosives in soil. Furthermore these enzymes are also used as catalysts for the manufacture of anti-cancer drugs and even as ingredients in cosmetics[1]. Their capacity to remove xenobiotic substances and produce polymeric products makes them a useful tool for bioremediation purposes. In our project laccases are used as cleaning agents for a water purification system.

Why is this important?

• Users understand why this part was important to your project
• Users can identify if the part may be useful for future projects
• Offers an opportunity to show how novel/innovative this part may be to the Registry and the synthetic biology community

Biology

You may be using your part differently than its biological purpose, so it is important to also detail the biological origin and purpose of your part. Take a look at how the authors of BBa_K863006, an E. coli laccase, addressed Biology.

Laccases are copper-containing polyphenol oxidase enzymes (EC 1.10.3.2) that can be found in many plants, insects, microorganisms and mainly in fungi. These enzymes fulfill several functions in different metabolic pathways. Laccases are able to oxidize a broad range of substrates due to the contained copper-cluster, by reducing oxygen to water. The active site of the enzyme includes a four-copper-ion-cluster, which can be distinguished by spectroscopic analyses. This cluster consists of one blue copper-ion (type 1), one type 2 and two type 3 copper-ions. Because of the blue copper-ion, the laccases belong to the big family of the blue copper proteins. This specific blue copper ion is essential for the enzyme mediated radical oxidation of the phenolic groups. In this reaction the electron from the oxidation is transferred to the other three copper ions. These ions form a trinuclearic cluster, which transfers electrons to the terminal electron acceptor oxygen. By receiving four electrons the molecular oxygen is finally reduced to water.

Why is this important?

• Shows the origin of this part
• It explains the biological context and overall mechanism of the part

Characterization

The bulk of your documentation will likely be characterizing and measuring your part.

Why is this important?

• It will show users that your part works (or doesn't work!) as expected
• Your part will be experimentally validated, and better understood by users
• Others can reproduce your results and build upon them

There isn't any one way to measure or characterize your parts, and you will find that certain parts will need to be experimentally validated differently than others; an inducible promoter will be characterized and measured differently than a metal binding protein. If you're unsure how to get started, you may want to take a look at similar parts in the Registry. See a few examples below:

However, there are elements that should be consistent across all of the characterization for your parts. Always:

• Explain the aim/hypothesis you will be testing
• Detail the conditions/parameters of your experiment, and reference your methods
• Represent your data as clearly as possible
• Include your controls!
• Label your images and graphs
• Summarize the results of your experiment

Design Page

As you work on your project you will find that you've spent a large amount of time on the design of your parts and devices. As you approach your project with a Design->Build->Test cycle, it will be important to document the design considerations you've taken and the reasons for them. On the part's Design Page, detail any design considerations you may have taken for the part. This includes mutations to remove restriction sites, codon optimization, etc.

References

Be sure to include any literature references for your part. This includes references that you have used while documenting your part (be sure to cite properly), as well as any references that you think would be useful as additional reading for users.

Other

Source

On the part's Design Page, you should briefly state the organism of origin and the sample source for your part. It may have been contributed from another lab, you may have PCRed it from an organism, or you may have synthesized it.

Parameters & Categories

You can add categories and parameters for your parts. Categories allow for a part to become content in automatically generated part tables, which is important in the organization of your part within the Registry, and the Catalog of Parts and Devices.

For example, the yeast promoter, BBa_K801020, has the categories:

By adding these categories, BBa_K801020 will appear on part tables for promoters and yeast parts. Since this promoter is induced by ethanol, the author could go further and add the category //regulation/positive

Categories can be added by selecting the information page for the part.

Judging

As part of the iGEM competition, there may be certain medal or award criteria that relate to parts on the Registry. Please note, that any examples in Registry help documentation do not necessarily reflect what the judges expect for a medal or award criteria. Make sure to read through the medal/award criteria on a given iGEM year's website to understand what the judges are looking for.

Remember, all part medal/award criteria will require that you document what you've done on the specified part's page. It is always up to your team to convey your work and convince the judges through your presentation, poster, and part pages, that you meet these criteria.