Latest revision as of 17:40, 10 July 2008

Guide to Registry Documentation

This guide explains how to read and interpret the information available about a part in the Registry. It is intended to provide comprehensive assistance to new users and may clarify points for some veteran users as well.

Overview

Each part* in the Registry has two components: (a) physical DNA carried by a plasmid* vector* stored at -80 degrees Celsius, and (b) documentation on the parts.igem.org server. For some parts, only documentation is available. To use such a part you must either synthesize the DNA or reconstruct the part from the given design information.

In what follows, each item used to document parts will be defined and its use(s) explained. The items are presented in the order that they appear on the part pages.

MAIN PAGE

Part Number

This is a "unique identifier" (as that term is used in computer science). It labels the part and all information connected with it. Example: BBa_J45004. This part encodes an enzyme used to construct a pleasant (!) odor-generating system in E. coli. The prefix BBa denotes a BioBrick part from the alpha release of BioBrick* standard biological parts and the J designates the part category. For details see: Part Names. The numbers indicate the specific part.

Part Icon

The Registry uses a set of icons to represent parts and standardize the schematic diagrams used to describe devices and systems. Example: represents a protein-coding sequence. The icon set remains incomplete and under development. Check with Part Names to find currently used icons.

Status Box

At the upper right-hand corner of the Main Page you will see a green box with two lines. The upper line indicates whether or not DNA corresponding to that part is available from the Registry, and the lower line reports the current experience with the part as reported on the Experience Page.

Designer/iGEM Team

The name of one person responsible for the submission of the part and its documentation, together with the name of the affiliated iGEM team or research laboratory as appropriate. Example: __________________

Date of Submission

This is an automatically generated field and refers to time at the Registry. Example: 2006-06-07 (i.e., year/month/day)

Full name

A descriptive name that avoids specialized abbreviations so that it can be quickly understood by anyone with a basic knowledge of molecular biology. Example: "Transcriptional activator protein luxR." Generally these names can be found in specialized databases like [http://www.uniprot.org/UniProt UniProt]. Such databases also list synonymous names and common abbreviations (see next item).

Short name

Abbreviated names (or nicknames) become the norm in laboratory work, but often different groups make up different nicknames for the same object. The Registry attempts to avoid the confusion this may cause by using consistent short names. Wherever possible we select these on the basis of the currently accepted standard in the relevant research field. Thus, for proteins we use the preferred names given in UniProt. Example: "BSMT1" (for BBa_J45004). Because the gene names for many proteins are well-established and used consistently, they become handy nicknames for their protein products. Example: "LuxR" (for the transcription regulator BBa_C0062). Obviously, when a part is created de novo, the designer gets to coin its nickname.

Summary description

A short statement that tells (a) what the part does [function], (b) how it works [mechanism], and why it was created [purpose]. Many descriptions cover additional information about the role of the part either in the original living system or in the project for which it was designed.

Origin

The biological species and the gene name for the original sequence (before any modification). For some synthetic parts (such as variant promoters) this may not be appropriate. Whenever the original sequence is available in GenBank, the "VERSION" and/or "GI" numbers should be given. Absent such database information, any other published sequence data may be cited or experimental sequence reads may be given.

Additional Database Links

For proteins the UniProt (formerly "SwissProt") primary accession number leads to a wealth of well-curated information about the original protein. New users are encouraged to follow this link for several proteins of interest to them. EXAMPLE: LuxR [http://www.uniprot.org/uniprot/P12746 P12746].

Enzyme Commission (EC) numbers are used to classify enzymes according to the reactions that they catalyze. (See Enzyme Background.) These numbers are helpful for searching databases, and also for finding related enzymes. EXAMPLE: BBa_J45008, branched-chain-amino-acid transaminase [http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/6/1/42.html 2.6.1.42].

Kyoto Encyclopedia of Genes and Genomes (KEGG) provides detailed information about enzyme-catalyzed reactions and where they fit in metabolic pathways. EXAMPLE: branched-chain-amino-acid transaminase [http://www.genome.jp/dbget-bin/www_bget?sce+YJR148W sce:YJR148W]

Dependencies

In many cases parts depend upon other parts, special materials (in the growth medium, for example) a particular chassis* or some other feature of the experimental system to work as desired. These requirements are described under the "Dependencies" heading. Whether or not a part is suitable for a particular application may hinge on these details.

Sequence and Features Display

This interactive display gives a variety of types of information depending on the choices clicked in the menu bar. These include sequence information and any modifications (such as removal of BioBricks cloning sites) performed during the part design and creation process. The "Get selected sequence link" produces the FASTA version of the DNA sequence of the part.

DESIGN PAGE

Rationale

A brief description of the method chosen to construct the part and the reasons for the choices made. This should also provide links to other parts created for the same project. These may include those cited under "Dependencies" on the Main Page.

Sequence and Features Display (redux)

This interactive display gives a variety of types of information depending on the choices clicked in the menu bar. These include sequence information and any modifications (such as removal of BioBricks cloning sites) performed during the part design and creation process. The "Get selected sequence link" produces the FASTA version of the DNA sequence of the part.

Part Construction Details

Special design features:
- insertion/removal of BioBrick cloning sites
- codon optimization
- reverse orientation
- added tags…

Synthesis details (if part was made by DNA synthesis).

Primers used (if part was created using PCR).

Difficulties/pitfalls encountered:
- Unworkable designs
- Necessary revisions etc.
- If everything worked exactly as planned, say so!

Intellectual Property Status

A list of all applicable patents and materials transfer agreements (MTAs) relevant to this part. [Give link to disclaimer page on IP & iGEM issues.]

References

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, other sources of information (such as online, open-access textbooks, OpenWetWare pages, etc.) should be cited.

EXPERIENCE PAGE

Actual Applications in Originating Laboratory

The designer(s)/depositor(s) should briefly summarize how the part worked, giving links where possible to other web locations with additional information (e.g., iGEM team pages or Jamboree presentation; published papers; laboratory websites, etc.) . In many cases parts fail to perform adequately or at all. New users may be willing to overhaul such a part, but it is important for the part's limitations to be accurately described.

Measurements

Careful measurements of a part's performance can enable users to adapt it to device and system construction. [cf., BBa_F2620] All measurements or tests on a part should be reported in this field of the experience page.

Additional Data and Figures

Cartoons, figures, tables of data, etc., relevant to a part can be placed in this section. They should be chosen so as to enhance the potential user's understanding of what the part is and how it works.

Actual Applications in Other Laboratories

This type of information is extremely valuable since it can validate the features of the part as described by its designer(s).

HARD INFORMATION PAGE

This page can be omitted. (Information can be made available on other pages.)

PHYSICAL DNA PAGE