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This is the full specification for the Raven input file. Files that do not conform to this standard will result in upload errors

Each row represents a part, vector, destination vector, or plasmid. None of the columns need to be unique, but the collection of all columns in one row must be unique and if all columns are blank, the row is ignored.

1. Library

   This field is used upon input to indicate if a part in the file is in the library and can be considered for re-use. If any character is in this column for a given row, it will be considered in the library for reuse. It is important that only parts that can be reused are marked in this section or else the outputs will be incorrect.

2. Name

   This is the field used to name the part.

3. Sequence

   In all cases this fields is optional, but without this field, complete primer designs will not be generated. Primer designs are not optimized, but are valid based for the selected assembly method.

4. Left Overhang & Right Overhang

   These fields mark the overhangs of the parts generated. These overhangs are variables and not sequences. Library part reuse of is based on overhang when calculating the assembly plan. Plasmids, and destination vectors are all allowed to have overhangs.

   The MoClo assembly algorithms only recognize overhangs with the numbers 1 -> 128 for reuse. They also recognize overhangs with the '*' character as reverse compliments of the standard 128 possible MoClo overhangs (i.e. '1*' is the reverse overhang of overhang '1').

   The BioBricks assembly algorithms only recognize 'EX' for the left overhang and 'SP' for the right overhang. Upon input, this field is completely optional, but most outputs contain parts and vectors with overhangs, as this is necessary for assembly.

   CPEC, SLIC, Gibson and GoldenGate algorithms do not use the overhang fields as the constructs are designed to be scarless.

5. Type

   This field is used to create assembly plan pictures using Pigeon-generated SBOLv-compliant glyphs.

   All plasmids must have the key string 'plasmid' in this field.

   Vectors need the key string 'vector' and destination vectors must be marked 'destination vector'.

   NOTE: The difference between 'vector' and 'destination vector' is important. A 'vector' is a linear fragment that represents the vector backbone. A 'destination vector' is a vector with an insert, making it circular. This fragment is generally a lacZ cassette in Raven. Although the 'destination vector' is a circular, replicating plasmid, it should not be indicated as a 'plasmid' in Raven. MoClo and Golden Gate assemblies produce 'destination vectors' which can be re-used as part of the library.

   All other entries are valid, and assumed to be basic part types. Part types not recognized by pigeon are assigned the wild-card glyph in Pigeon images.

   The following key strings are recognized for pigeon images for basic parts:

   Type	Shorthand
   promoter	p
   RBS	r
   gene	g
   terminator	t
   reporter	rep
   resistance	res
   invertase site	ins
   spacer	s
   origin	o
   fusion	fus

   Parts with type 'fusion' denote fusion proteins and the Name column is split with the '-' character to get all the fusion names. Parts with type 'resistance' denote a resistance cassette. Take note that restriction-based assembly cloning methods rely on cloning vectors that also have anti-biotic resistance within them.

6. Resistance

   This field is used to denote the antibiotic resistance of a vector or destination vector.

7. Level

   This field is used only for vectors and destination vectors. Destination vectors with level and overhangs are re-used in an assembly plan if possible. Levels start at '0'.

8. Vector

   The vector field is used to indicate the vector backbones in which a construct lies. Complete plasmids will be re-used in assembly plans if it reduces cost. This field is also used to denote the vector backbone used by destination vectors. Destination vectors are always made of a vector backbone and the lacZ fragment as insert. For MoClo and Golden Gate assembly, which use destination vectors, the construction of destination vectors is not explicitly described in the assembly instructions, but for new destination vectors, primers are designed to amplify the lacZ fragment for insertion into the vector backbone after a SpeI digestion and ligation. To PCR this fragment with different flanking recognition sites, primers will need to be re-designed.

   NOTE: The vector specified in this column is used to indicate which vector backbone a plasmid in the library currently has. For target parts that do not yet exist in the library, this field is ignored. Vector assignments for intermediates and final clones are all specified in the design tab in the user interface.

9. Composition

   This field starts in the column below the headers and extends infinitely based on the size of the composition of the target construct. All target constructs must have a composition size of two or greater and only these constructs will be recognized as targets.

   This field must be formatted in one of the following conventions:

   • 'partName|LeftOverhang|RightOverhang|Direction'
   • 'partName|Direction'
   • 'partName'

   The part name is mandatory. LeftOverhang and RightOverhang are optional. Direction is how a user can specify the strand or 'direction' of a part within a device. All parts are assumed to be forward (on the leading strand) in the absence of specification. The two acceptable directions are '+' and '-'. If a part in a device has Direction equal to '-' it is on the lagging strand.

The input file only recognizes four types of entries. Entries that do not fall into these categories will not be input correctly and/or cause invalid answers. Here are the acceptable entry types: