Help:Document Parts

Revision as of 21:28, 6 August 2015 by Vinoo (Talk | contribs)

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
Ready to add your part? Go to the Add a Part page.
Have questions on adding a part to the Registry? Send an email to hq (at) igem . org.

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Adding Parts

Adding a part to the Registry requires minimal 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 information page
Long Description Description of your part, and its functions. The long description can be edited through the wiki, tools >> edit this page


Documenting Parts

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.


Usage

Explain what you used the part for in your project, and what other uses it might serve.

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 detail the biological origin and purpose of your part.

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. This section will show that your part works (or doesn't work!) as expected.

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.

Promoter RBS Coding Region Terminator Device
BBa_K801020 BBa_K1084104 BBa_K1172501 BBa_K731721 BBa_K863005


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 specific conditions/parameters of your experiment
  • 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.


Judging