It can be tricky to follow everything we're talking about when we're on such inherently technical subjects as bioinformatics and modelling the whole body digitally, let alone the methods by which our hardware will manipulate molecules. We can't guarantee that we'll catch every difficult word in this glossary, but we hope it will help. It may be under construction for some time. For definitions we haven't sufficiently covered, you can always try Wikipedia. We also intend to provide a simplified version of our website and documentation when possible.
To search this page, use the keyboard shortcut Ctrl-F in your browser and type the word you want to find, then press Enter. If you are on a phone or other device that doesn't give you that shortcut, you may still have a 'find in page' option in the browser's menu. Eventually we may be able to add a search function to the site which is not browser-dependent.
- A: Adenine, one of the most common nucleotide molecule types used in biological cells.
- AI:Artificial Intelligence. This refers to computer systems or software capable of human-level reasoning or greater in one or more fields or specialisms.
- AIC: Alternative initiation codon, that is, a different codon from the usual expected codon to start mRNA translation to proteins, which may also or instead be used for initiating mRNA translation to proteins.Amino acids: a collection of peptide molecules that form the structural components of proteins. If in a cell but not assembled into proteins, they are likely to be attached to tRNA molecules to facilitate the ribosome’s assembly of a polypeptide chain.
- AR: Augmented Reality (visuals and data overlaid on real surroundings).
- Biocybersecurity: the combination of cybersecurity and biological data and wetware. The need to protect one’s wetware from bugs or attacks via computer code for genetic editing or its vectors.
- Blockchain: a decentralised, distributed peer-to-peer form of database extended by sequential recording and verification of transactions usually verified by some type of cryptographic calculations. (Mentioned in this document to make comparisons against our approach).
- C: Cytosine, one of the most common nucleotide molecule types used in biological cells.
- Cap and tail: The ‘cap’ of an mRNA is a Guanine nucleotide at the 5` end of the mRNA molecule, protected at its 7th atom by a methyl group. The ‘tail’ is a long chain of Adenine nucleotides. When these are removed, the mRNA degrades and is removed from use.Codon: any set of three consecutive nucleotides in an mRNA chain, with which tRNAs can be aligned to assemble polypeptide chains for construction of proteins.
- Cryptocurrency: a digital currency which uses a cryptographically verified blockchain. (Mentioned in this document to make comparisons against our approach).
- Data mining (scraping): Using automated tools to purposely collect large quantities of data from publicly available resources, usually online.
- DHT: Distributed Hash Table (a way to ensure distributed peer to peer data sharing can be kept up to date without relying on any specific centralised entity or server). This refers to a method of multiplying and spreading metadata across multiple devices in a peer to peer network to securely distribute and retrieve data between those devices.
- DNA: Deoxyribonucleic Acid, the biochemical long molecular substance formed of chains of nucleotide molecules which are arranged as letters in a quaternary (base-4) code in the chromosomes of each cellular nucleus and mitochondrion (or in plants, chloroplast) of any living organism. DNA is used by biological cells as a programmatic instruction manual.
- DNA Computing: A module of the GUESS software for calculating how to optimally use DNA to carry out computational operations or to store arbitrary data in the gene editing vector or in the recipient of the gene edits.
- DRM: Digital Rights Management (a mechanism to restrict data sharing by embedding code or other methods to thwart duplication in media).
- Epigenetic Mothballing: a module of the GUESS for the creation of backup nucleoli of the original versions of edited genes, and a process through which to revert a transformation if it is going wrong.
- ER: Endoplasmic Reticulum compartment of the eukaryotic biological cell. Provides a space for proteins to be prepared for transfer to other organelles in the cell or to the Golgi apparatus for export to the extracellular medium.
- Erlang: A general purpose high-level programming language designed to work well with a distributed and fault tolerant runtime environment and immutable data.
- FASTA: A standard format for bioinformatic nucleotide and peptide sequence data.
- G: Guanine, one of the most common nucleotide molecule types used in biological cells.
- GeFi: the Genetic Fidelity graphical user interface of the GUESS software.
- Grey Goo: The nightmare scenario produced by an out of control type of self-replicating nanobot that consumes all it can to make more copies of itself (Drexler 1990).
- GUESS: The GUESS Unified Editing Suite and SDK (Systems Development Kit). It is a recursive acronym and refers to an open source software system for whole-body simulation and gene editing that is being developed at Vulpine Labs Inc.
- HIP_DAME: The Hormones, Immunity, Pathways, Dismantlement and Apoptotic Management of Effects module of the GUESS, which handles many cellular processes not covered by other modules.
- Initiation/Start Codon: A codon which is almost always ‘AUG’ in mRNA, and forms the most likely place on the mRNA chain for ribosomal translation of the mRNA to make proteins, to begin.
- INITIATOR SET: The module of the GUESS system responsible for processing translation from mRNA to protein, and all the variables involved.
- IRES: Internal Ribosomal Entry Site. A position in the mRNA which is folded to allow viral protein translations to be initiated.
- Kozak Context: The sequence of nucleotides before and after an initiation codon or an AIC, which affects likelihood of ribosomal assembly at that codon.
- Laberation: a peer to peer network between users of the GUESS, featuring ways to securely share data on for example, gene edits and vectors to carry them.
- LERM: the module of the GUESS for Lipid Effects and Rafts Modelling, handling cellular membranes, cholesterol and fat storage.
- Microbiome: the module of the GUESS handling the whole microbiome of the body – its entire population of symbiotic bacteria and other microbes.
- Molecures: Molecular cures (combinations of a set of genetic edits and a vector to carry them), a term coined by Al Cammack, circa 2016.
- Motif: a folded structural shape in a long chain molecule. This can have profound impacts on the utility of said molecule.
- mRNA: messenger Ribonucleic Acid, the long chains of nucleotide molecules used by biological cells as a notepad to transfer relevant excerpts of instructions from the DNA in the nucleus to the ribosomes in the cytoplasm and endoplasmic reticular membrane of the cell.
- Mutations: Changes to the genetic code caused by unintended interactions between the DNA and its surroundings or passing charged particles. Compare with deliberate gene editing.
- Neng: Nanoengineering module of the GUESS, for the creation of non-traditional gene editing devices and nanotechnology (involving nanometre-scale molecular constructs).
- Node: individual GUESS system or other server connected to Laberation’s distributed network, from which you download your content. Multiple nodes may be used per transaction.
- Nucleotides: molecules which form repeatable structured chains and consist of a ribose sugar group and a phosphate group. The phosphates form the ‘backbone’ of DNA and RNA.
- Ontologies: The collected resources on the nature and essential properties and relations of all beings.
- ORF: Open Reading Frame. This refers to how the sequential position of the initiation codon sets the alignment of the ribosome and its tRNAs to the rest of the sequence thereafter, setting the ‘reading frame’ which dictates which nucleotides are part of which codons from the ribosome’s perspective.
- PAMM: Prion and Amyloid Management and Mitigation, a module of the GUESS which handles protein folding and the avoidance of problematic misfolds.
- PDB: Protein Data Bank, an online resource of known protein 3D structures.
- PostGreSQL (Postgres): an open source relational database management system with support for SQL.
- R: the R Programming Language, a language well suited to bioinformatics data handling.
- Ribosomes: biological cellular protein factories, which assemble around mRNA initiation codons (or around AICs) and then read each codon in turn until they reach a STOP codon, producing a polypeptide chain as they go, using tRNAs to do so.
- RNA: Ribonucleic acid, long chains of nucleeotide molecules used in various forms by biological cells. These include but are not limited to mRNA, rRNA, snoRNA, tRNA and the RNA guides used in CRISPR.
- rRNA: Ribosomal Ribonucleic acid, used for the construction and specialisation of ribosomes.
- SnoRNA: Small Nucleolar RNA, a short segment of RNA usually associated with nucleolus structures within the cell nucleus.
- Source code: programming code that has not beencompiled yet into its final form to run on any system, and is stillin its original language in which it was written.
- SQL: Structured Query Language, a programming language used for handling relational database management systems and the data within them.
- SRP: Signal Recognition Particle of the Endoplasmic Reticulum translocation process, which recognises the sequence in a nascent protein in the process of being translated, which decides whether that protein is translocated across the ER membrane into the ER, or is just translated then placed into the cytoplasm.
- STOP codon: a codon which under normal conditions (notwithstanding leaky scanning), forces ribosomal translation to cease and the ribosome to disassemble when it reaches this point in the mRNA chain.
- T: Thymine, one of the most common nucleotide molecule types used in biological cells and used in DNA but not RNA.
- Tentpoles: The module of the GUESS responsible for handling the cytoskeleton and similar structures such as the Extracellular Matrix, hair and nails.
- The OGRE: The Optical Genetic Recognition Engine for the GUESS software.
- Transcription:the GUESS module responsible for handling transcription of DNA codeinto mRNA, and replication of DNA for cell division.
- tRNA: Transfer ribonucleic acid, the chains of nucleotide molecules which are folded into a convenient shape for ribosomes to handle and which carry amino acids (peptide molecules) for the construction of polypeptide chains.
- U: Uracil, one of the most common nucleotide molecule types used in biological cells and used in RNA but not DNA.
- UML: Unified Modelling Language. A tool for visualising systems designs prior to software code development.
- uORF: Untranslated Open Reading Frame, where a potential ORF doesn’t align with but may interfere with a coding sequence.
- URL:Uniform Resource Locator, for example a web address consisting of adomain name along with specifiers of exact pages or files in a website.
- UTR: the untranslated region of an mRNA before the initiation codon (5`UTR) and after the STOP codon (3`UTR).
- Vectron: GUESS module responsible for encryption and checksums and other aspects of data security and biosecurity, to ensure biocybersecurity is enforced on all parts of the gene editing process possible.
- VPN: Virtual Private Network, a way to displace your apparent geographic location and IP address on the internet. Commonly used to provide a route for internet traffic that makes the user’s computer appear to be located elsewhere in the world.
- VR: Virtual Reality (immersive replacement of real surroundings with a virtual world)
- XNA: Exogenously created nucleotide-bearing deoxyribonucleic acid. Artificial nucleotides being incorporated into DNA would make XNA.
- 4D: In our context, this means three spatial dimensions and one of time, which can be adjusted to view the model at different positions and angles and to view it at different times in the body’s life with the currently entered/edited genome.
- 5` and 3`: the ends of a nucleotide chain are identified by whether the nucleotides at the ends have the 5th atom or the 3rd atom of their structures the most prominent for attachment of further nucleotides.
