Registry of Standard Biological Parts/Organization

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possible changes, everything here is subject for discussion

Change the front page. Include expanded section for parts and devices. These changes are motivated by the purposes and users of the registry. We are expecting that the three purposes are (i) navigation (ii) organization / structure of collection (iii) dog and pony shows, and that the user groups are (i) casual surfers (ii) naive parts users (iii) super users and developers.

  1. Features Categories
    • Randy has asked for a list of common features for the Registry, please edit with impunity since many needed features are missing or unclear.
    • Are things like RBS's, terminators, and promoters features, or are they parts? Or are they both?
    1. DNA-level
      1. -35
      2. -10
      3. operator (or protein binding)
      4. repetitive element
      5. mutation
        1. silent
        2. not silent
      6. deletion
      7. insertion
      8. CDS (or is a CDS the part and an ORF the feature?)
      9. primer binding site
      10. replication origin
    2. RNA-level
      1. stem loop (and terminator is the part?)
      2. polyA
      3. transcription start site
      4. transcription stop site
    3. Protein-level: do we want to specify kinds protein domains as well?
      1. DNA binding domain
      2. Oligomerization domain
      3. Catalytic domain
      4. Signal sequence
      5. Tag
      6. Linker
  2. Parts Categories
    1. DNA/RNA: parts whose functions are encoded as nucleic acid polymers
      1. for example, a ribosome binding site
      2. for example, a transcription promoter
    2. DNA/RNA Processing: parts whose functions act on nucleic acid polymers
      1. for example, RNaseIII
    3. Proteins: parts whose functions are encoded as amino acid polymers
      1. for example, green fluorescent protein
    4. Protein Processing: parts whose functions act on amino acid polymers
      1. for example, tobacco etch virus protease
    5. Chassis: parts that contribute to the host cell
      1. for example, alpha subunit of E. coli RNA polymerase
    6. Biochemistry: parts whose functions act on biochemicals, small molecules, and metabolic intermediates
      1. for example, phosphoglucose isomerase
    7. <blank>: a future class of parts
    8. Other: any remaining parts
    9. Hell: parts from the original BB_alpha release.
      1. for example, BBa_R0052
  3. Devices Categories
    1. Generators: devices that generate some thing (for example, a protein)
      1. for example, a PoPS->Protein generator device made up of a RBS:CDS:TERMINATOR
    2. Controllers: devices that control some thing
      1. for example, ...
    3. Senders: devices that sense an some thing (for example, an environmental signal)
      1. for example, a PoPS->diffusible molecule device.
    4. Receivers: devices that sense an some thing (for example, an environmental signal)
      1. for example, a diffusible molecule->PoPS device.
    5. Actuators: devices that do or act on some thing (for example, a device that produces motility)
      1. for example, a PoPS->Invade Cell device, perhaps made up of a RBS:INVASIN CDS:TERMINATOR
    6. Reporters: devices that produce a readily detectable signal (for example, a fluorescent protein)
      1. for example, a PoPS->Light device, perhaps made up of a RBS:GFP CDS:TERMINATOR
    7. Bioprocessors: devices that accept one or more chemicals as input and produce one or more chemicals as output
      1. for example, a device that accepts pyruvate and G3P as inputs, accepts control of dxs, idi, and ispA expression of input, and produces GPP as output
    8. Information Processing: devices that send/receive and act on signals.
      1. for example, a PDL inverter
    9. Others: any remaining devices
      1. for example,
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