RSBP Draft Documentation Standards
This page summarizes the content needed for a well-documented basic part. Section I lists the information needed for all parts [in two categories: (1)essential items, and (2) possible enhancements]. Sections II-...
Contents
RSBP Documentation Requirements for All Parts
ESSENTIAL ITEMS
Main Page (What is it?)
0. Designer and affiliation. (research laboratory, iGEM team or company)
1. Part number. (equivalent to an “Accession number”)
2. Short name. ("nickname")
3. Extended name. (formal title)
4. Origin (biological species or synthetic/designed).
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.
B. 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 given above under items (5) and (6).]
8. DNA sequence (including ends if they lack the proper BioBrick prefix and suffix)
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.]
C. 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.
D. 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.
RSBP Documentation Requirements for Coding Sequences I -- Enzymes
ESSENTIAL ITEMS
Main Page (What is it?)
0. Designer(s)/iGEM team [e.g., Erin Zwack, Sabriya Rosemond /iGEM 2006_Davidson]
1. Part number [e.g., BBa_J31002]
2. Short name [e.g., AadA-bkw]
3. Extended name [e.g., kanamycin resistance backwards (KanB)]
4. Origin (biological species if available). [e.g., pSB1AK3, Escherichia coli]
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. SwissProt primary accession number (if available) [e.g., P0AG05]
7. Enzyme Commision number (if assigned), [e.g., 2.7.7.47]
8. Dependencies: other parts, special materials, chassis, etc. [cf. BBa_J23012 & BBa_J31003]
Design Page (How did you make it?)
9. Raison d’être for constructing the part. Links to related parts from the same project. [Details in addition to those under items (5) and (8).]
10. DNA sequence with proper BioBrick ends (AU of the first codon included).
11. Primers used (if part was created using PCR).
12. Synthesis details (if part was made by DNA synthesis).
13. Special design features: (a) insertion/removal of BioBrick cloning sites, (b) codon optimization, (c) reverse orientation, (d) added tags…
14. Graphical sequence bar with all appropriate feature annotations.
15. One-to-three references to literature on the protein’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, OpenWetWare pages, etc.)
16. Difficulties/pitfalls encountered in the design process. Unworkable designs, necessary revisions etc. If everything worked exactly as planned, say so!
17. 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?)
18. Summary of actual applications to date in originating laboratory.
19. Measurements or tests of part.
20. Uploaded data, figures, etc. can be put on the Registry wiki and linked here.
Hard Information Page (Reference data)
21. Sequence (FASTA format).
22. Exact source of the original sequence(s) used to construct the part. Both GenBank accession number (“VERSION”) and “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).
23. More features (exact details of modified sequences).
POSSIBLE ENHANCEMENTS
(Liven it up, use visual materials!)
Main Page
1. Structure cartoon(s), PDB_IDs
2. Catalyzed reaction, either in words or chemical formulas. This can come from the KEGG database in many instances or from the IUBMB website. [e.g., ATP + streptomycin = pyrophosphate + 3"-adenylylstreptomycin ...]
Experience Page
3. Tables of measurements.
4. Figures depicting functional output.
5. Links to additional databases [e.g., KEGG,…]