Help:Document Parts

Revision as of 14:25, 5 October 2018 by LindsayMo (Talk | contribs) (→‎Usage: ARK-shRNA-1 was used to silence arginine kinase gene of phylotreta striolata)

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.


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.


Part:BBa_K2878006 (1) Eukaryotic organisms including insects possess this RNAi mechanism for sequence-specific gene silencing that is triggered by the introduction of double-stranded RNA (dsRNA). Once introduced into the cell, the dsRNA is cleaved into small interfering RNA (siRNA) by an enzyme called Dicer, producing multiple siRNAs. One strand of each siRNA is loaded into Argonaute, an endonuclease, to form an RNA-induced Silencing Complex (RISC), and guiding the RISC to the target mRNA, resulting in the effective cleavage and subsequent degradation of the target mRNA. RNAi mechanism can be triggered by introducing either dsRNA, siRNA or shRNA. In our project, ARK-shRNA-1 was used to silence arginine kinase gene of phylotreta striolata. Arginine kinase participates in arginine metabolism, transferring phosphorus group from ATP to arginine. When gene for Arginine kinase is silenced, phylotreta striolata is killed.

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:
BBa K801020 Categories.png


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 2018 below.

  • [http://2018.igem.org/Competition/Team_Requirements 2018 Team Requirements]
  • [http://2018.igem.org/Judging/Medals 2018 Medal Criteria]
  • [http://2018.igem.org/Judging 2018 Judging Handbook]
  • [http://2018.igem.org/Judging/Rubric 2018 Judging Rubric]