Programming and Systems Biology
Class 11 · Biotechnology
4 ideas in Class 11 Biotechnology, explained in plain words, with games and quizzes to practise.
Code for Biologists
Part of: Code Meets Cell
Linux hosts most tools with PERL at the sequence core, Python 1991 by Rossum runs on unix mac and windows with clear syntax and rich libraries, R by two Roberts stays free open and functional for stats, MATLAB adds a paid workbench, and newcomers GEC from Microsoft and Kera from Kerala with its Samhita library design living systems.
Why it matters. Language-to-job plus platform answers tool questions.
Key words
- PERL
- : Classic sequence-handling language.
- Python
- : Clear general scripting language.
- R
- : Free stats programming language.
- GEC
- : Cell-engineering rule language.
- Samhita
- : Kera biological library.
Try it in two minutes
- Boot Linux first.
- Script with Python.
- Count with R.
Try at home. Assign five tasks to languages.
Systems Biology Idea
Part of: Code Meets Cell
Systems biology builds math models that mimic living systems, the genome project seeded the thought, metabolic and signalling networks model best, reductionists list parts while integration maps object networks with kinetics equations, and health plus therapy uses follow.
Why it matters. Model idea plus parts-versus-whole answers theme questions.
Key words
- System model
- : Math mimic of biology.
- Reductionist
- : Parts-first researcher.
- Integration
- : Linking parts into whole.
- Emergent property
- : Whole-only new behaviour.
- Signalling network
- : Message-path model.
Try it in two minutes
- Model the system.
- Link the parts.
- Solve for health.
Try at home. Contrast listing parts with linking them.
Milestone Years
Part of: Time and Tools
Hodgkin-Huxley modelled axons in 1952, Noble built the heart pacemaker model in 1960, Mesarovic launched systems theory with biology in 1966, Bertalanffy published precursor theory in 1968, functional genomics flooded data from the 1990s, MIT took the whole-cell challenge in 2003, and the wall-less Mycoplasma genitalium model arrived in 2012 beside the Physiome heart project.
Why it matters. Year-person pairs answer timeline questions.
Key words
- Axon model
- : 1952 nerve maths.
- Pacemaker model
- : 1960 heart maths.
- Whole-cell model
- : Full cell simulation.
- Physiome
- : Multi-scale body framework.
- Functional genomics
- : Large-scale gene data era.
Try it in two minutes
- Chain 1952 to 1968.
- Jump to 2003.
- Land in 2012.
Try at home. Place six years on a line.
Data Rules and Tool Matrix
Part of: Time and Tools
Management rests on minimum information plus XML formats plus GO and SBO ontologies with spreadsheets ELN and LIMS as systems, workflows run on KNIME Taverna and Galaxy, MATLAB R and BANJO infer networks while MetNetMaker runs MCA and AUTO BUNKI study splits, and FEM solves PDEs in ANSYS and MATLAB.
Why it matters. Trio plus matrix rows answer tool-picking questions.
Key words
- Minimum information
- : Essential experiment metadata.
- Ontology
- : Term-relation vocabulary.
- LIMS
- : Lab data manager.
- FEM
- : Equation-solving method.
- MCA
- : Network control analysis.
Try it in two minutes
- Name the trio.
- Row the matrix.
- Solve with FEM.
Try at home. Sort six tools into jobs.
What your child will practise
- Code for Biologists: Candy Puzzle (Clue Puzzle)
- Code for Biologists: Candy Quick Fire (Quick Fire)
- Data Rules and Tool Matrix: Desert Puzzle (Clue Puzzle)
- Milestone Years: Jungle Quest (Flip and Match)
- Systems Biology Idea: Ocean Quick Fire (Quick Fire)
- Quiz: Code for Biologists (8 questions)
- Quiz: Data Rules and Tool Matrix (8 questions)
- Quiz: Milestone Years (8 questions)
- Quiz: Systems Biology Idea (8 questions)