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.
The Grasshopper Interface
Grasshopper is a plug-in for the 3D CAD program, Rhino. It is a visual scripting interface that allows for parametric modeling, interfacing with external data sources, and user-generated add-ons like Alba. Components are simply wired together eliminated the need for memorizing specific coding syntax. Alba utilizes this visual interface to perform DNA assemblies and expressions, and then uses the 3D space of Rhino to visualize the results.
Operations done in Alba can be visualized in the Rhino window. DNA sequences are shown in linear or circular (plasmid) formats and as single or double strands. User can zoom in to the see the specific sequence or out to see location of genes. In image, a complete circular DNA plasmid is shown with each of the defined parts highlighted in a different color.
Restriction Enzyme Digestion and Ligation
Alba has a complete library of restriction enzymes. The digest tools show the sites targeted by the selected restriction enzymes, and the resultant “sticky ends” created by the cut. Ligation tools can then be used to assemble strands with compatible sticky ends.
Transcription and Translation
The transcription tools convert the DNA to RNA, with the option of using the same cues of promoters and terminators typically used in nature. The Translation tools convert the RNA to amino acids, again with the option to use natural cues, here the ribosome binding site. Zooming in on the assembled plasmid, we see the DNA sequence and how each three-nucleotide codon is translated into an amino acid.
The amino acids sequence generated by the transcription and translation tool can then be searched in the Protein Database at RCSB.org via Alba's Protein Query tool. The resultant .pdb files can then be opened and the secondary and tertiary structures of the protein are determined and visualized with the Protein Ribbon tool.
A more defined rendering can be generated by baking the geometry from Grasshopper into Rhino and setting material properties for rendering.
About the name "Alba"
This plug-in is named after, Alba, the “GFP Bunny” of Eduardo Kac’s pioneering work of art. It is the hope the she will remind users to continually reflect on the end results of their work. In this digital space where life is abstracted into code, it takes a considerable effort to imagine the results of our work and the related social, ethical, and environmental concerns. Alba, the living rabbit, embodies these factors.
This Grasshopper tool set is not affiliated with Eduardo Kac, nor specifically endorsed by the artists. It is the hope of the developer, Ryan Hoover, that this resource is consistent with Kac’s views that artists and others should address the pressing issues generated by rapidly-developing biotechnology through thoughtful and creative applications of these technologies. Any shortcomings in this regard, or technical flaws in the software, are the fault of the developer. Users are invited to modify and improve the tool set (each element is an editable User Object), to communicate with Hoover and fellow users, and to continue the development of these tools in an open collaborative manner.
Alba is available to download for free. Contributions to the project are welcome, however. This can take the form of monetary donations, helping with debugging, and extending these tools. Everything is written as an unlocked "User Object" so the entire plug-in is open for you to edit, improve, and share back.