Difference between revisions of "User:Scmohr/Part Evaluation"
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This page is intended to develop a method to score the documentation of a part -- with the ultimate goal of automating the scoring process.
 
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
+
=RSBP Documentation: Itemization, Explanations and Help for All Parts=
 
Scott C. Mohr
 
Scott C. Mohr
 
version 1.0
 
version 1.0
 
(6/26/08)
 
(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.
+
'''N.B. This version is limited to basic parts (''i.e.,'' those with a single encoded function).  Subsequent versions will be expanded to include composite parts, devices and systems.'''
  
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This itemizes all the information required to document any part in the Registry.  Each item has an underlined 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.
+
The first section of this page summarizes the documentation required for '''''all''''' parts.  The sections that follow itemize all the '''additional''' information required to document a specific type of BASIC part in the Registry.  Each section of documentation (corresponding to one of the four pages that comprise the documentation for  a part) 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.  The following list summarizes the categories used by the Registry to classify basic parts.  Note that the protein category is further divided into four sub-categories that have slightly different documentation requirements.  
  
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Each item begins on a new page and is labeled with the part categories to which it applies:
+
*Protein coding sequences (CDS’s)
 +
**Enzymes
 +
**Repressors and Activators
 +
**Reporters
 +
**Uncategorized CDSs
 +
*Ribosome binding sites (RBS’s)
 +
*Terminators
 +
*Regulatory regions
 +
*RNA
 +
*DNA
 +
*Conjugation
  
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Protein coding sequences (CDS’s) / Enzymes; Repressors and Activators; Reporters; Uncategorized
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==ESSENTIAL ITEMS FOR '''ALL''' PARTS==
  
−
Ribosome binding sSites (RBS’s)
+
===Main Page (What is it?)===
  
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Terminators
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0. Designer/iGEM team.<SPAN style= 'color:red'>*</span>
  
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Regulatory regions
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1. Part number.  (alternatively “Accession number”)<SPAN style= 'color:red'>*</span>
 +
 +
2. Short name.<SPAN style= 'color:red'>*</span> 
  
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RNA
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3. Extended name. (alternatively an informative title)<SPAN style= 'color:red'>*</span>
  
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DNA
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4. Origin (biological species if available, otherwise name the source: "supplied by __________" or "designed, based on ____________").<SPAN style= 'color:red'>*</span>
  
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Conjugation
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5. A short abstract that tells (a) what the part does (function), (b) how it works (mechanism) and (c) why you made it (purpose).<SPAN style= 'color:red'>*</span>
 +
 
 +
6. Dependencies: other parts, special materials, chassis, etc. (if applicable)
 +
 
 +
===Design Page (How did you make it?)===
 +
 
 +
7. Raison d’être for constructing the part.<SPAN style= 'color:red'>*</span>  Links to related parts from the same project. [Details in addition to those under items (5) and (6).]
 +
 
 +
8. DNA sequence ''without'' the BioBrick ends.<SPAN style= 'color:red'>*</span>
 +
 
 +
9. Primers used (if part was created using PCR<SPAN style= 'color:red'>*</span>).
 +
 
 +
10. Synthesis details (if part was created by DNA synthesis<SPAN style= 'color:red'>*</span>).
 +
 
 +
11. Special design features: (a) insertion/removal of BioBrick cloning sites, (b) codon optimization, (c) reverse orientation, (d) added tags…<SPAN style= 'color:red'>*</span>
 +
 
 +
13. Graphical sequence bar with all appropriate feature annotations.
 +
 
 +
14. One-to-three references to literature<SPAN style= 'color:red'>*</span> 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!<SPAN style= 'color:red'>*</span>
 +
 
 +
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.<SPAN style= 'color:red'>*</span>
 +
 
 +
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).<SPAN style= 'color:red'>*</span>
 +
 
 +
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).<SPAN style= 'color:red'>*</span>
 +
 
 +
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.

Latest revision as of 20:38, 26 June 2008

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 (i.e., those with a single encoded function). Subsequent versions will be expanded to include composite parts, devices and systems.

The first section of this page summarizes the documentation required for all parts. The sections that follow itemize all the additional information required to document a specific type of BASIC part in the Registry. Each section of documentation (corresponding to one of the four pages that comprise the documentation for a part) 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. The following list summarizes the categories used by the Registry to classify basic parts. Note that the protein category is further divided into four sub-categories that have slightly different documentation requirements.

  • Protein coding sequences (CDS’s)
    • Enzymes
    • Repressors and Activators
    • Reporters
    • Uncategorized CDSs
  • 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 an informative title)*

4. Origin (biological species if available, otherwise name the source: "supplied by __________" or "designed, based on ____________").*

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. (if applicable)

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 without the 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 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.