I live my life in circles that grow wide And endlessly unroll, I may not reach the last, but on I glide Strong pinioned toward my goal. About the old tower, dark against the sky, The beat of my wings hums, I circle about God, sweep far and high On through milleniums. Am I a bird that skims the clouds along, Or am I a wild storm, or a great song?
Rainer Maria Rilke, The Book of a Monk's Life
Evidence-first engineering knowledge system
A structured reference book for biological engineering. This guide covers the mechanisms, architectures, components, methods, and design–build–test–learn workflows. It is generated by AI combing the (mostly) human literature, and curating the db into something useful. There is an API service available for programmatic access. This is meant to serve as an inspiration source or workbook for engineering complex biological systems.
Toolkit Model
The collection is best read as two hierarchies beneath workflows: mechanisms and techniques. Within mechanisms, the hierarchy runs from mechanism to architecture to component. Within techniques, the hierarchy runs from technique to method.
Mechanism Branch
Layer 1
Mechanisms
Top-level concepts: biophysical action modes such as heterodimerization, photocleavage, or RNA binding.
A stimulus triggers a structural change that exposes a previously hidden functional element. Current coverage includes 23 architectures and 25 components. Representative components include AsLOV2, Avena sativa LOV2 domain variants, and Avena sativa phototropin LOV2 domain.
23 architectures · 25 components
A stimulus triggers targeted degradation of a protein via the proteasome or other pathways. Current coverage includes 18 architectures and 10 components. Representative components include Arabidopsis CRY2, LOV2 domain-based optogenetic tool, and LOVdeg tag.
18 architectures · 10 components
A protein binds DNA in a stimulus-dependent manner to regulate gene expression. Current coverage includes 2 architectures and 1 component. Representative components include AsLOV2-Jα.
2 architectures · 1 components
Two different proteins are brought together by a stimulus, enabling recruitment or complex formation. Current coverage includes 70 architectures and 30 components. Representative components include Aer PAS domain, Arabidopsis thaliana cryptochrome 2, and CIB1 N-terminal CRY2-binding region.
70 architectures · 30 components
A protein is recruited to a membrane surface (e.g. plasma membrane) by a stimulus. Current coverage includes 13 architectures and 3 components. Representative components include light activated nuclear shuttle (LANS) domain, light-inducible nuclear localization signal, and light-inducible nuclear localization signals.
13 architectures · 3 components
A protein self-associates into multimers upon stimulation, enabling clustering or activation. Current coverage includes 27 architectures and 9 components. Representative components include Arabidopsis CRY2, Arabidopsis CRY2 photosensory domain, and BcLOV4 photoreceptor.
27 architectures · 9 components
Light breaks a covalent bond, irreversibly releasing a caged peptide or domain. Current coverage includes 22 architectures and 14 components. Representative components include 2A sequence, HeFSpCas9, and LHCII N-terminal domain.
22 architectures · 14 components
A protein or RNA element binds RNA to control translation or stability. Current coverage includes 9 architectures and 3 components. Representative components include RNA aptamer, caged guide RNA, and hypoxanthine switch.
9 architectures · 3 components
Post-transcriptional regulation of mRNA translation rate or efficiency. Current coverage includes 16 architectures and 9 components. Representative components include 2A sequence, LOVdeg tag, and human opsins.
16 architectures · 9 components
Layer 2
Architectures
Arrangements that realize or deploy mechanisms, including switches, construct patterns, and delivery strategies.
Layer 3
Components
Low-level parts and sequence-defined elements used inside architectures, including protein domains and RNA elements.
Technique Branch
Layer 1
Approaches
High-level engineering practices such as computational design, directed evolution, sequence verification, and functional assay.
In silico design of protein sequences, structures, or circuits using algorithms or machine learning. Current coverage includes 80 concrete methods.
80 methods
Iterative mutagenesis and selection to evolve improved biological parts. Current coverage includes 5 concrete methods.
5 methods
Measuring the activity or performance of an engineered part in a biological context. Current coverage includes 160 concrete methods.
160 methods
Experimental selection from a library to enrich for variants with desired properties. Current coverage includes 26 concrete methods.
26 methods
Confirming construct identity by Sanger or next-generation sequencing. Current coverage includes 8 concrete methods.
8 methods
Determining 3D structure via X-ray crystallography, cryo-EM, or NMR. Current coverage includes 26 concrete methods.
26 methods
Layer 2
Methods
Concrete methods used to design, build, verify, or characterize engineered systems.
Families remain a useful supporting lens for browsing related lineages like LOV, BLUF, phytochromes, or display platforms, but they are not the top conceptual hierarchy.
Workflow Layer
Workflows sit above both branches. They combine mechanisms and techniques to obtain, optimize, verify, characterize, deliver, and evaluate engineered systems.