Useful Terms, Concepts, People, Classes, etc
Biology, SynBio, Acronyms, Orgs, People, Training/Classes
I found that I was defining a lot of terms repeatedly in my Blog entries. As a programmer, I was feeling the DRY heaves, so I decided to abstract them to here. Many of these were collected from my weekly journal.
Its a bit rambly and meant for my and my kids consumption. I’m sharing it here for those who stumble across it. Its under constant, iterative refinement. At some point, I’ll even alphabatize it.
"BioTriangle" Image Courtesy of Eric Lander's class: Intro To Bio
Biology
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The Central Dogma
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Genomics
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Genetics
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BioChemistry
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Molecular Biology
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Systems Biology: understanding and experimentng upon systems like gut biomes, SCOBYs, forests.
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- Physical: butterfly nets, interviewing traditional healers
- Virtual: Bioinformatics, virtual evolution
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Biotechnology: The exploitation of biological processes for industrial and other purposes, especially the genetic manipulation of microorganisms for the production of antibiotics, hormones, etc.
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Bioinformatics: discovery and feedback from engineering
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Genetic Engineering
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Stoichometric vs Catalytic Therapeutic
Synthetic Biology
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Synthetic Biology An enhanced version of Genetic Engineering, with more emphasis on agile, iterative Design-Build-Test cycles pioneered by the software industry, encoded in DevOps culture. Also SynBio.
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Biosimulation: Simulating expected behavior in virtual, cellular or intracellular environments (e.g. Tesla Dojo, or MIT Evolution Gym). Existing examples:
- Intracellular: Virtual Cell, BIOCHAM, BioNetGen, Cellular Dynamic Simulator (CDS), Smoldyn, and COPAS
- Cellular: Multiscale Systems Immunology Project (MSI), EPISIM, LINDSAY, SimuLife, FLAME, Simmune, C-ImmSim, CellSys, and Compucell3D.
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Biomanufacturing: producing the end products at scale (fermenters, other bioreactors)
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“In Silico”. I use this to mean virtual or digital, no actual silicon chips directly involved, unless noted otherwise. I will typically use ”Lab on a Chip” when I mean actual silicon is involved.
Acronyms
- CRISPR
- CRISPR/CAS 9
- CRISPR/CAS 7/11
- NGS (Next Generation Sequencing): they are delicate and produce tons of data
Orgs and Incubators
- Broad Institue Boston. Eric Lander.
- Innovative Genomics Institute Berkeley. Jennifer Doudna.
- Imperial College Synthetic Biology Hub. Hub includes:
- Synbicite, [London DNA Foundry](URL IS BAD).
People
- Jennifer Doudna: Berkeley, CRISPR
- George Church: Harvard and MIT
- Tom Knight: MIT, Ginkgo
- Eric Lander: MIT, Broad Institute, Human Genome Project
- Michael Levin: Tufts. Xenobots. Program cells at anatomical, not genetic, level. Cell Cybernetics. Morphogenisis.
Training and Programs
These are courses and programs for non-students. They are offered via EdX, Coursera, MITx, etc.
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ML Engineering For Production (MLOps Specialization). This is Andrew Ng’s newer material, from his DeepLearning.ai. Ideally, it will be cross digital cloud vendor compatible, as their ML infrastructures will almost certainly converge.