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Biotech and life sciences
lims
laboratory information system
Benchling
System
Techniques · 4
Primitives · 27
lims
Smith-Waterman local alignment
search-sort · medium: Dynamic programming that finds the highest-scoring pair of similar substrings of two sequences under a substitution score and affine gap penalties, in O(nm) time.
›
Tamper-evident audit log
security · medium: An append-only log whose Merkle root, signed per batch, lets anyone verify an entry is present and history was never rewritten, with log-size proofs.
›
Inverted index
storage · medium: Map each term to a sorted, compressed list of the documents containing it; the core of full-text search and other fast set queries.
›
MVCC
storage · medium: Keep timestamped versions of each row so readers see a consistent snapshot without blocking writers; the default concurrency control in modern databases.
›
Digital signatures (Ed25519)
security · low: Small, fast, deterministic public-key signatures that prove who produced a message; the default for tokens, releases and protocols.
›
Barcode symbologies
data-structures · low: Encode/decode 1D and 2D barcodes (Code 128, DataMatrix, QR) with their error correction
Event sourcing
finance · low: Persist state changes as an append-only stream of immutable events per entity; current state is a fold over them, guarded by expected-version appends.
›
Topological sort
graphs · low: Order the vertices of a DAG so every edge points forward; the core of build systems, schedulers and dependency resolution, with cycle detection for free.
›
Hl7v2 message parsing
networking · low: HL7 v2 pipe-delimited segments, escaping, ACKs and MLLP framing for clinical interfaces
Molecular graph representation
physics · low: SMILES parsing, molecular graphs, aromaticity and canonical ordering
Authorization models (RBAC, ABAC, R…
security · low: How to decide who may do what to which object; roles for coarse rules, relationships for sharing, and checks on every object.
›
Reed-Solomon codes
signal-processing · low: Byte-oriented MDS code: n-k parity symbols correct (n-k)/2 unknown symbol errors or n-k known erasures; the workhorse for bursts, QR codes, discs and storage.
›
Entity attribute value schema
storage · low: Schema-flexible EAV / JSON entity storage with typed attribute catalogs and indexes
Optimistic concurrency control
storage · low: Run transactions without locks, record what they read, and validate at commit that nothing changed; fastest when conflicts are rare.
›
Hierarchical state machine
systems · low: Nest states so a substate inherits its parent's reactions and only overrides what differs, with ordered entry and exit actions along the path.
›
SIMD programming
hardware-os · low: Process 4-16 lanes per instruction with AVX2, AVX-512 or NEON via Rust std::arch, with runtime dispatch and a portable fallback.
›
Edit distance
search-sort · low: Levenshtein/Damerau distance by DP, bit-parallel Myers variant
Merkle tree
data-structures · low: Hash tree for verifying and diffing large datasets with logarithmic proofs
Segmented log
distributed · low: Split an append-only log into files named by their first offset, write only the newest, and find any record by binary search plus a sparse index.
›
Trusted timestamping
security · low: RFC 3161 time-stamp tokens: a TSA signs a hash with time, proving data existed then
+ 11 more primitives
System
Techniques · 4
Primitives · 27
lims
Smith-Waterman local alignment
search-sort · medium: Dynamic programming that finds the highest-scoring pair of similar substrings of two sequences under a substitution score and affine gap penalties, in O(nm) time.
›
Tamper-evident audit log
security · medium: An append-only log whose Merkle root, signed per batch, lets anyone verify an entry is present and history was never rewritten, with log-size proofs.
›
Inverted index
storage · medium: Map each term to a sorted, compressed list of the documents containing it; the core of full-text search and other fast set queries.
›
MVCC
storage · medium: Keep timestamped versions of each row so readers see a consistent snapshot without blocking writers; the default concurrency control in modern databases.
›
Digital signatures (Ed25519)
security · low: Small, fast, deterministic public-key signatures that prove who produced a message; the default for tokens, releases and protocols.
›
Barcode symbologies
data-structures · low: Encode/decode 1D and 2D barcodes (Code 128, DataMatrix, QR) with their error correction
Event sourcing
finance · low: Persist state changes as an append-only stream of immutable events per entity; current state is a fold over them, guarded by expected-version appends.
›
Topological sort
graphs · low: Order the vertices of a DAG so every edge points forward; the core of build systems, schedulers and dependency resolution, with cycle detection for free.
›
Hl7v2 message parsing
networking · low: HL7 v2 pipe-delimited segments, escaping, ACKs and MLLP framing for clinical interfaces
Molecular graph representation
physics · low: SMILES parsing, molecular graphs, aromaticity and canonical ordering
Authorization models (RBAC, ABAC, R…
security · low: How to decide who may do what to which object; roles for coarse rules, relationships for sharing, and checks on every object.
›
Reed-Solomon codes
signal-processing · low: Byte-oriented MDS code: n-k parity symbols correct (n-k)/2 unknown symbol errors or n-k known erasures; the workhorse for bursts, QR codes, discs and storage.
›
Entity attribute value schema
storage · low: Schema-flexible EAV / JSON entity storage with typed attribute catalogs and indexes
Optimistic concurrency control
storage · low: Run transactions without locks, record what they read, and validate at commit that nothing changed; fastest when conflicts are rare.
›
Hierarchical state machine
systems · low: Nest states so a substate inherits its parent's reactions and only overrides what differs, with ordered entry and exit actions along the path.
›
SIMD programming
hardware-os · low: Process 4-16 lanes per instruction with AVX2, AVX-512 or NEON via Rust std::arch, with runtime dispatch and a portable fallback.
›
Edit distance
search-sort · low: Levenshtein/Damerau distance by DP, bit-parallel Myers variant
Merkle tree
data-structures · low: Hash tree for verifying and diffing large datasets with logarithmic proofs
Segmented log
distributed · low: Split an append-only log into files named by their first offset, write only the newest, and find any record by binary search plus a sparse index.
›
Trusted timestamping
security · low: RFC 3161 time-stamp tokens: a TSA signs a hash with time, proving data existed then
Bit packing and PFOR
compression · low: Store blocks of integers with exactly b bits each and patch rare outliers separately (PFOR); the fastest integer codec family, billions of values per second.
›
Delta encoding
compression · low: Store differences between consecutive values instead of the values, turning sorted IDs, timestamps and counters into small numbers that pack into few bits.
›
Varint (LEB128)
compression · low: Variable-length integers in 7-bit groups with a continuation bit; small numbers take 1 byte, the wire format of Protobuf, WebAssembly and DWARF.
›
BM25 ranking
search-sort · low: The standard lexical relevance score: IDF-weighted term frequency with saturation (k1) and length normalization (b); default in Lucene, Elasticsearch and SQLite FTS5.
›
Sorted-list intersection
search-sort · low: Intersect sorted id lists by merging, galloping from the short list into the long one, and skipping whole compressed blocks, shortest list first.
›
d-ary heap
data-structures · low: Array heap with d children per node (d = 4 typical): half the binary heap's depth, siblings in one cache line, faster priority queues.
›
BFS and DFS
graphs · low: The two basic graph traversals; BFS gives hop distances and levels, DFS gives discovery/finish order for cycles, components and topological order.
›
Text normalization
machine-learning · low: Rewrite messy text into one canonical form for matchers and models, or into spoken words for speech output (and back), keeping a map to the original offsets.
›
Sparse matrices (CSR)
numerics · low: Compressed sparse row stores only nonzeros as row pointers, column indices and values; SpMV streams them once, so it is memory-bandwidth bound.
›
Top-k selection
search-sort · low: Keep the k best of n items without sorting all n - bounded min-heap for streams, quickselect for arrays, threshold pruning to skip most items.
›
Unicode text tokenization for search
search-sort · low: Turn multilingual text into index terms: segment words (UAX 29 style, CJK bigrams), normalize, case-fold and accent-fold, identically at index and query time.
›
Copy for AI
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