Grasshopper Docs

Community documentation for Grasshopper add-ons & plugins

Alba

ADDON. Version 0.111. Released on Unknown. Provides 49 components. Created by Ryan Hoover. Features 0 video tutorials.
Alba is a suite of tools in Rhino/Grasshopper that allows a user to visualize molecular biology and to perform genetic engineering in silico. These tools help to open the discipline of synthetic biology to creative artists, designers, and architects, allowing them to bring the insight of their respective disciplines into this powerful and rapidly-developing field.
Digest
Library
Ligate
Protein
Transcription/Translation
Utilities
Visualize

Library

BioBrick Categories of Parts (BB Categories)
Provides a list of part categories for inputinto the BB Library
BioBrick Prefix and Suffix Adder (Pre~Suf)
Contains a cluster of Grasshopper components
BioBricks Library (BB Library)
library of all the parts in the BioBricks registry.
BioBricks Prefix Standard (BB Pre)
simply the sequence of the standard BioBricks prefix used to enable ligation with compatible sticky ends
BioBricks Prefix ATG (BB Pre ATG)
simply the sequence of the standard BioBricks prefix used, with sequences starting with ATG, to enable ligation with compatible sticky ends
BioBricks Suffix (BB Suf)
simply the sequence of the standard BioBricks suffix used to enable ligation with compatible sticky ends
E0240 GFP with RBS, and Terminator (GFP RET)
RBS: B0032 +
GFP Reporter: E0040 +
Terminators: B0010 & B0012
GFP with Promoter, RBS, and Terminator (GFP PRET)
Tet Promotor R0040 +
RBS: B0034 +
GFP Reporter: E0040 +
Terminators: B0010 & B0012
Plasmid Backbones DNA (Backbones)
Provides the DNA for teh 4 commonly use BioBrick backbones.
Plasmid Insert (Insert)
Insert a gene into a plasmid backbone, optionall add in the BB prefix and suffix. Index reamins at beginning of gene; the prefix is at the end of the sequence.
Promoter DNA (Promoters)
Provides a list of the 10 most commomnly used BioBrick promoters, and outputs the DNA of the selected part.
Protein Coding DNA (Coding)
Provides a list of the 10 most commomnly used BioBrick protein codeing sequences, and outputs the DNA of the selected part.
Resistance to Chloramphenicol (CamR)
DNA sequence to produce Chloramphenicol resistance
Resistance to Kanamycine (KanR)
DNA sequence to produce Kanamycine resistance
Resistance to Tetracycline (TetR)
DNA sequence to produce Tetracycline resistance. On BioBrick plasmid backbone pSB1T3 this gene is on the primary strand.
Resitance to Amp (AmpR)
DNA sequence to produce Ampicillin resistance
RFP with RBS, and Terminator (RFP RET)
RBS: B0034 +
RFP Reporter: E1010 +
Terminators: B0010 & B0012
Ribosome Binding Site DNA (RBS)
Provides a list of the 10 most commomnly used BioBrick RBS, and outputs the DNA of the selected part.
Teminator DNA (Terminators)
Provides a list of the 10 most commomnly used BioBrick terminators, and outputs the DNA of the selected part.
YFP with RBS, and Terminator (YFP RET)
RBS: B0034 +
YFP Reporter: E0030 +
Terminators: B0010 & B0012

Utilities

Complementary Strand (Comp)
creates a complementary strand based in the input sequence
DNA Clean
gets rid of anything that is not a, A,T,G, or C and capitalizes all characters
DNA Find (Find)
Finds a sequence within a sequence and return the domain of its location.
Primer Design (Primer Des)
to find a primer with good melt temp and GC content and avoiding bad hairpins
Random DNA (Ran DNA)
create a ramndom string of GTAC
Reverse DNA (Rev)
reverses the sequence of DNA
Reverse Subdomain (Rev Sub)
reverses the position and direction of a subdomain

Transcription/Translation

E. coli Optimization (E.coli Opt)
create an optimized RNA sequence for E coli to produce the input AA chain.
Simple Transcription (Tx)
simple conversion DNA to RNA changing T to U
Simple Translation (Tl)
converts RNA into Amino Acids
Transcription Promoter to Terminator (Transcription)
Transcribes DNA to RNA starting just after the promoter site and ending just prior to the termitator site
Transcription σ
Converts DNA to RNA based on -35 and -10 sites
Translation
Translates RNA to amino acid chain with options for finding the proper reading frame

Visualize

Amino Acid Visualizer (AA Viz)
Creates and displays an offset complementary strand
DNA Subdomain Visualizer (DNA Sub Viz)
Visualizes the specified subdomain of a strand
DNA Complementary Strand Visualizer (DNA Comp Viz)
Creates and displays an offset complementary strand
DNA Complementary Subdomain Visualizer (DNA Comp Sub Viz)
Visualizes the specified subdomain of a created offset complementary strand
DNA Visualizer (DNA Viz)
Visualizes the DNA in the Rhino viewport

Protein

PDB Sort (PDB Sort)
sort protein data base file
PDB Open
make the pdb info accessible
PDB Plot
create a visual energy plot of a pdb file
Protein Query
Search the RCSB Protein DataBase for matching Amino Acis sequences and the address of a corresponding .pdb file.
Protein Ribbon
visualizes the structure of a protein

Ligate

A Simple Ligation (Lig)
Concatenates two DNA sequences
Ligate
Ligate tests to see if 2 strands have matching sticky ends. Is sothey are joined together. If both ends connect, plasmid is set to true.
Sticky Ends (Sticky)
identifies the overhanging ends of DNA.

Digest

Enzyme List (Enzymes)
A list of enzymes to choose from that passes the proper index for the Restriction Enzymes output object
Restriction Enzyme Digest (Digest)
Cuts up DNA based on target sits of the input restriction enzyme and outputs double stranded DNA with sticky ends.
Restriction Enzymes Cut Locations (Restrict. Enzymes)
outputs the cut locations of any major restriction enzyme. use the Enzymes List to choose the enzyme you want or enter the index if you know it already

Site design © Robin Rodricks.   Alba and associated data © 2020 Ryan Hoover.  
Rhinoceros and Grasshopper are registered trademarks of Robert McNeel & Associates.  Hosted by GitHub

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