From 2007.igem.org

Latest revision as of 14:54, 12 October 2007

This is a draft of the part documentation guidelines used to evaluate parts Submitted for Acceptance. We want every part to have a paragraph or more of text on the main page, preferably with a diagram (but not necessarily), that clearly answers the questions posed in 2.1, 2.2, and 2.3 of the guidelines.

Part Main page

The main page should offer Registry users a "part-at-a-glance" summary to help decide whether or not a particular part interests them or meets a specific need.

• 1 Part title
• 2 Part Description
  • 2.1 What is it needed for? Function.
  • 2.2 How does it work?
  • 2.3 How do you use it?
• 3 Dependencies on other parts, chemicals, strains, etc. -- (state explicitly)
• 4 Subparts figure for all composite parts." (use icons)
• 5 Diagram showing part features, e.g., predicted RNA secondary structures, a protein 3D structure illustration, a complete biochemical circuit containing the part, etc.
  • 5.1 Inputs and outputs should be clearly labelled for all circuits.

Part Design page

This page functions somewhat like a "Materials and Methods" section and should include enough detail for users to understand how the part was constructed and what its special features are.

• 6 How did you build it? What you would need to know if you wanted to re-create the part? For instance, include as warranted info about:
  • Primers used if DNA was extracted from a natural system using PCR.
  • Mutagenesis performed (e.g., for standards compliance or manipulation of RNA secondary structure)
  • Codon optimization
  • Removal or addition BioBrick cloning sites
  • Synthesis details, if DNA synthesized (method used and vendor -- if purchased)
• 7 Source of original sequence - i.e. where did the sequence provided in Hard Information come from? If from an online database, provide the relevant accession number, otherwise provide pertinent information about the sequencing run.
  • 7.1 Biological species, strain
  • 7.2 Sequence: accession number & database used for sequence, or details about sequencing run.
  • 7.3 What lab did the strain from / or what company supplied it [what is the order number?]
• 8 References (at least 2 – if none, provide links to the other resources used - e.g. online open-access textbook, OWW page, etc.)
• 9 Pitfalls – designs that didn't work, revisions necessary, or an explicit statement that everything worked as planned
• 10 Provide complete attribution to everyone who worked on/is affiliated with the part.
  • 10.1 Attribution - who worked on this part? (whole team, certain members of the team if they divided into subteams,etc.)
  • 10.2 Acknowledgement - who worked on parts that went into this part?
  • 10.3 Sponsorship - who provided funding for the development of this part?

User Experience Page

The creators of the part should provide as much information as possible here so that other users can benefit from their successes (and failures!). This kind of information will weigh heavily in the decision someone else will make about whether or not to use your part.

• 11 Experience - explicitly state how the part worked in your lab; provide any available experimental details generated from testing the part (including uploading data files to the Registry wiki).

Hard Info

This page includes data that belongs permanently with the part and its details should be carefully checked for accuracy.

• 12.1 Sequence
• 12.2 Significant features - If any of the features from the features list is mentioned/talked about in your part description, make sure that it is part of the sequence and features.

Best Documentation Candidates