Help:Document Parts
- Registry Help Pages:
- TOC
- At-a-Glance
- FAQ
Add a Part to the Registry: Related Registry Help Pages
- 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
Have questions on adding a part to the Registry? Send an email to hq (at) igem . org.
Documenting Parts
Adding a part to the Registry requires some basic information:
| Required | Comments |
|---|---|
| Sequence | Parts require an accurate sequence. A part's sequence can be edited though part tools >> edit sequence and features |
| Short Description | The biological or technical short hand for the part's function. The short description can be edited through the part information page |
| Long Description | Description of your part, and its functions. The long description can be edited through the wiki, tools >> edit this page |
Adding your part to the Registry is a great first step, but there's still more to do!
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.
| Section | Description |
|---|---|
| Usage | What is your part used for? |
| Biology | Describe the biology of your part. |
| Characterization | Characterize and measure your part. |
| References | Be sure to include references for your part and its documentation. |
| Other | Design Notes, Source, Categories, etc. There's additional areas that require documentation. |
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
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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:
| Promoter | RBS | Coding Region | Terminator | Device |
|---|---|---|---|---|
| BBa_K801020 | BBa_K1084104 | BBa_K1172501 | BBa_K731721 | BBa_K863005 |
| BBa_K1216007 | BBa_K1017202 | BBa_K525515 | BBa_K404108 | BBa_K404163 |
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
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
Design Notes
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.
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
If you belong to an iGEM team participating in a current iGEM competition, then there are certain requirements that your project must meet. Generally, this entails submitting at least one part that meets the submission requirements.
There are specific criteria that must be met to be eligible for Medals (Bronze/Silver/Gold) and the Special Awards (Best Basic Part/Best Composite Part/Best Part Collection. Make sure to check the requirements for your competition year. We've provided information for iGEM 2017 below.
- [http://2017.igem.org/Competition/Team_Requirements 2017 Team Requirements]
- [http://2017.igem.org/Judging/Medals 2017 Medal Criteria]
- [http://2017.igem.org/Judging 2017 Judging Handbook]
- [http://2017.igem.org/Judging/Rubric 2017 Judging Rubric]