User:Scmohr/Part Evaluation
This page is intended to develop a method to score the documentation of a part -- with the ultimate goal of automating the scoring process.
RSBP Documentation: Itemization, Explanations and Help for All Parts
Scott C. Mohr version 1.0 (6/26/08)
N.B. This version is limited to basic parts (a single encoded function). Subsequent versions will be developed for composite parts, devices and systems.
This page itemizes all the information required to document any part in the Registry. Each item has a headlined name with an explanation that (a) defines it, (b) tells why and how it will be used, and (c) gives instructions and makes suggestions to help the depositor enter the information for that item. Items marked with an asterisk (*) must be completed for the part to be accepted by the Registry.
Protein coding sequences (CDS’s) / Enzymes; Repressors and Activators; Reporters; Uncategorized
Ribosome binding sites (RBS’s)
Terminators
Regulatory regions
RNA
DNA
Conjugation
ESSENTIAL ITEMS FOR ALL PARTS
Main Page (What is it?)
0. Designer/iGEM team.
1. Part number. (alternatively “Accession number”)
2. Short name.
3. Extended name. (alternatively “Title”)
4. Origin (biological species if available).
5. A short abstract that tells (a) what the part does (function), (b) how it works (mechanism) and (c) why you made it (purpose).
6. Dependencies: other parts, special materials, chassis, etc.
Design Page (How did you make it?)
7. Raison d’être for constructing the part. Links to related parts from the same project. [Details in addition to those under items (5) and (6).]
8. DNA sequence with proper BioBrick ends.
9. Primers used (if part was created using PCR).
10. Synthesis details (if part was created by DNA synthesis).
11. Special design features: (a) insertion/removal of BioBrick cloning sites, (b) codon optimization, (c) reverse orientation, (d) added tags…
13. Graphical sequence bar with all appropriate feature annotations.
14. One-to-three (possibly more for composite parts, devices and systems) references to literature on the part’s biological function and uses in synthetic biology. Frequently there is a key reference reporting on the first use or design of a modified version of the protein (see entries under “Reporters”). If no published references are available, cite other sources used (such as online, open-access textbooks, Open Wetware pages, etc.)
15. Difficulties/pitfalls encountered in the design process. Unworkable designs, necessary revisions etc. If everything worked exactly as planned, say so!
16. List all applicable patents and materials transfer agreements (MTAs). [Give link to disclaimer page on IP & iGEM issues.]
Experience Page (How well does it work?)
17. Summary of actual applications to date in originating laboratory.
18. Measurements or tests of part. Include efficiency.
19. Uploaded data, figures etc. can be put on the Registry wiki and linked here.
Hard Information Page (Reference data)
20. Sequence (FASTA format).
21. Exact source of the original sequence(s) used to construct the part. GenBank accession number (“VERSION”) and/or “GI” (aka “gi”) number if available. Otherwise any available published sequence or other source of information, including experimental sequence reads (which can be put on the Registry wiki and linked here).
22. More features (exact details of modified sequences).
POSSIBLE ENHANCEMENTS
(Liven it up, use visual materials!)
Main Page
1. Structure cartoon(s). PDB_IDs.
2. Figures relating to the function and/or physical characteristics of the part. (Include forward and reverse efficiencies if known.)
Experience Page
3. Tables of measurements.
4. Figures depicting functional output.
5. Links to additional databases.