Version control records identifiable revisions of files and their history, making it possible to inspect an earlier state and determine what changed. A version-control commit records a revision; a version-control branch permits a line of development to proceed alongside another; version-control merging combines changes and exposes conflicts requiring a decision. These operations make collaboration and investigation of software regressions practical.^[ref]

Suppose a numerical simulation produced an unexpected result after a formula changed. Recording the version-control commit with the result identifies the exact source revision, so the old and new formulas can be compared and rerun with the same inputs. Reproducing the full calculation also requires the relevant data, software dependencies and execution settings: file history is one part of that record.

A software container runs one or more operating-system processes with a controlled view of files and other operating system resources. A container image supplies a packaged filesystem and execution configuration; starting it creates running operating-system processes with additional runtime state. A software container typically shares the host operating-system kernel, whereas a virtual machine can run its own operating-system kernel.^[ref]

For example, two analyses can use different versions of the same software dependency without placing both versions in one shared installation. Reusing a container image helps reproduce those dependencies. Results also depend on the input data, configuration, mounted files and compatible host facilities. Packaging the software therefore records part of a reproducible calculation; the scientific assumptions and numerical methods still need their own justification.

Notch signalling is a contact-dependent signalling pathway in which a ligand on one cell activates a receptor on another. Proteolytic processing releases an intracellular receptor fragment that can enter the cell nucleus and participate in transcription control. receptor processing therefore links a local contact to a nuclear response. During vertebrate somitogenesis, coupling through Notch signalling can coordinate neighbouring oscillators without being identical to their intracellular oscillation mechanism. ^[ref]

Signal transduction initiated by Wnt-family ligands. Distinct pathway branches regulate gene expression, cell polarity and cell behaviour; their effects depend on developmental context.

Signal transduction initiated by fibroblast growth factors acting through FGF receptors. A major downstream branch involves MEK and ERK, but receptor activation can engage other pathways.

A BMP-family signalling ligand in Drosophila melanogaster, including an early dorsal embryonic expression domain repressed ventrally by nuclear Dorsal protein.

Extracellular signal-regulated kinase, a kinase downstream of MEK. Phosphorylation and downstream activity must be assayed in the relevant cells when testing inhibitor effects.

A signalling system regulating factors such as YAP. In early mouse embryos it connects cellular position and polarity to lineage-associated transcription.

A fibroblast growth factor important in signalling between early mammalian lineages, including promotion of mouse hypoblast development.

An adaptor protein linking activated receptors to downstream signalling, including a pathway required for normal mouse hypoblast allocation.

MEK is a mitogen-activated protein kinase protein kinase that phosphorylates and activates ERK in the RAS-MAPK signalling pathway. Its dual-specificity chemistry can modify both a threonine and a tyrosine in the activation region of its substrate. MEK therefore connects one protein kinase tier to the next. When testing developmental requirements with an inhibitor, unchanged fate is informative only if inhibition of the downstream pathway has been established. ^[ref]

Developmental signal transduction initiated by Nodal-family ligands, belonging to the broader TGF-beta signalling system.

A family of signalling pathways with context-dependent developmental and cell-state functions. Ligand, receptor and downstream requirements should be distinguished experimentally.

Signalling initiated by leukaemia inhibitory factor, important in some mouse pluripotent-cell culture conditions. A culture dependency is not automatically an embryonic lineage-specification dependency.

Bone morphogenetic protein 4, a signalling ligand with developmental functions including induction of mouse primordial germ cells from competent epiblast.

Mechanistic target of rapamycin complex 1, a nutrient-responsive protein kinase complex. Its activity affects initiation through 4E-BP proteins and other substrates, and also regulates autophagy and growth investment.

A leucine-binding sensor upstream of mTORC1. Its nutrient-dependent interaction with GATOR2 helps couple leucine availability to growth signaling.^[ref]

A regulatory complex in nutrient signaling upstream of Rag GTPases and mTORC1.

It connects selected nutrient-sensing inputs to the machinery controlling growth-associated signalling. Altering the complex can therefore affect the balance between biosynthesis and nutrient availability without directly transporting every nutrient into the cell. ^[ref]

A member of a nutrient-responsive GTP-binding regulatory family involved in positioning mTORC1 at the lysosome.

A signalling protein that influences cell recruitment and positioning, often by inducing directed cell movement through a compatible receptor.