@oriro/orirocli 0.1.8 → 0.1.11

package/skills/sag/SKILL.md

@@ -1,91 +1,91 @@
----
-provider: ORIRO.ai
-copyright: Copyright (c) 2026 ORIRO.ai
-watermark: ORIRO
-disable-model-invocation: true
-name: sag
-description: "ElevenLabs text-to-speech with mac-style say UX."
-homepage: https://sag.sh
-metadata:
-  {
-    "oriro":
-      {
-        "emoji": "🔊",
-        "requires": { "bins": ["sag"], "env": ["ELEVENLABS_API_KEY"] },
-        "primaryEnv": "ELEVENLABS_API_KEY",
-        "install":
-          [
-            {
-              "id": "brew",
-              "kind": "brew",
-              "formula": "oriro/tap/sag",
-              "bins": ["sag"],
-              "label": "Install sag (brew)",
-            },
-          ],
-      },
-  }
----
-
-# sag
-
-Use `sag` for ElevenLabs TTS with local playback.
-
-API key (required)
-
-- `ELEVENLABS_API_KEY` (preferred)
-- `SAG_API_KEY` also supported by the CLI
-
-Quick start
-
-- `sag "Hello there"`
-- `sag speak -v "Roger" "Hello"`
-- `sag voices`
-- `sag prompting` (model-specific tips)
-
-Model notes
-
-- Default: `eleven_v3` (expressive)
-- Stable: `eleven_multilingual_v2`
-- Fast: `eleven_flash_v2_5`
-
-Pronunciation + delivery rules
-
-- First fix: respell (e.g. "key-note"), add hyphens, adjust casing.
-- Numbers/units/URLs: `--normalize auto` (or `off` if it harms names).
-- Language bias: `--lang en|de|fr|...` to guide normalization.
-- v3: SSML `<break>` not supported; use `[pause]`, `[short pause]`, `[long pause]`.
-- v2/v2.5: SSML `<break time="1.5s" />` supported; `<phoneme>` not exposed in `sag`.
-
-v3 audio tags (put at the entrance of a line)
-
-- `[whispers]`, `[shouts]`, `[sings]`
-- `[laughs]`, `[starts laughing]`, `[sighs]`, `[exhales]`
-- `[sarcastic]`, `[curious]`, `[excited]`, `[crying]`, `[mischievously]`
-- Example: `sag "[whispers] keep this quiet. [short pause] ok?"`
-
-Voice defaults
-
-- `ELEVENLABS_VOICE_ID` or `SAG_VOICE_ID`
-
-Confirm voice + speaker before long output.
-
-## Chat voice responses
-
-When the user asks for a "voice" reply (e.g., "crazy scientist voice", "explain in voice"), generate audio and send it:
-
-```bash
-# Generate audio file
-sag -v Orirod -o /tmp/voice-reply.mp3 "Your message here"
-
-# Then include in reply:
-# MEDIA:/tmp/voice-reply.mp3
-```
-
-Voice character tips:
-
-- Crazy scientist: Use `[excited]` tags, dramatic pauses `[short pause]`, vary intensity
-- Calm: Use `[whispers]` or slower pacing
-- Dramatic: Use `[sings]` or `[shouts]` sparingly
-
-Default voice for Orirod: `lj2rcrvANS3gaWWnczSX` (or just `-v Orirod`)
+---
+provider: ORIRO.ai
+copyright: Copyright (c) 2026 ORIRO.ai
+watermark: ORIRO
+disable-model-invocation: true
+name: sag
+description: "ElevenLabs text-to-speech with mac-style say UX."
+homepage: https://sag.sh
+metadata:
+  {
+    "oriro":
+      {
+        "emoji": "🔊",
+        "requires": { "bins": ["sag"], "env": ["ELEVENLABS_API_KEY"] },
+        "primaryEnv": "ELEVENLABS_API_KEY",
+        "install":
+          [
+            {
+              "id": "brew",
+              "kind": "brew",
+              "formula": "oriro/tap/sag",
+              "bins": ["sag"],
+              "label": "Install sag (brew)",
+            },
+          ],
+      },
+  }
+---
+
+# sag
+
+Use `sag` for ElevenLabs TTS with local playback.
+
+API key (required)
+
+- `ELEVENLABS_API_KEY` (preferred)
+- `SAG_API_KEY` also supported by the CLI
+
+Quick start
+
+- `sag "Hello there"`
+- `sag speak -v "Roger" "Hello"`
+- `sag voices`
+- `sag prompting` (model-specific tips)
+
+Model notes
+
+- Default: `eleven_v3` (expressive)
+- Stable: `eleven_multilingual_v2`
+- Fast: `eleven_flash_v2_5`
+
+Pronunciation + delivery rules
+
+- First fix: respell (e.g. "key-note"), add hyphens, adjust casing.
+- Numbers/units/URLs: `--normalize auto` (or `off` if it harms names).
+- Language bias: `--lang en|de|fr|...` to guide normalization.
+- v3: SSML `<break>` not supported; use `[pause]`, `[short pause]`, `[long pause]`.
+- v2/v2.5: SSML `<break time="1.5s" />` supported; `<phoneme>` not exposed in `sag`.
+
+v3 audio tags (put at the entrance of a line)
+
+- `[whispers]`, `[shouts]`, `[sings]`
+- `[laughs]`, `[starts laughing]`, `[sighs]`, `[exhales]`
+- `[sarcastic]`, `[curious]`, `[excited]`, `[crying]`, `[mischievously]`
+- Example: `sag "[whispers] keep this quiet. [short pause] ok?"`
+
+Voice defaults
+
+- `ELEVENLABS_VOICE_ID` or `SAG_VOICE_ID`
+
+Confirm voice + speaker before long output.
+
+## Chat voice responses
+
+When the user asks for a "voice" reply (e.g., "crazy scientist voice", "explain in voice"), generate audio and send it:
+
+```bash
+# Generate audio file
+sag -v Orirod -o /tmp/voice-reply.mp3 "Your message here"
+
+# Then include in reply:
+# MEDIA:/tmp/voice-reply.mp3
+```
+
+Voice character tips:
+
+- Crazy scientist: Use `[excited]` tags, dramatic pauses `[short pause]`, vary intensity
+- Calm: Use `[whispers]` or slower pacing
+- Dramatic: Use `[sings]` or `[shouts]` sparingly
+
+Default voice for Orirod: `lj2rcrvANS3gaWWnczSX` (or just `-v Orirod`)

package/skills/science/sci-astronomy/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2026 ORIRO.ai
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+MIT License
+
+Copyright (c) 2026 ORIRO.ai
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/skills/science/sci-astronomy/SKILL.md

@@ -1,80 +1,80 @@
----
-watermark: ORIRO
-disable-model-invocation: true
-name: sci-astronomy
-provider: ORIRO.ai
-copyright: Copyright (c) 2026 ORIRO.ai
-description: >
-  Astronomy and cosmology — solar system, stars, galaxies, cosmology, telescopes,
-  and the scale of the universe. Activate for questions about planets, stars,
-  black holes, the Big Bang, space exploration, or any astronomy topic.
-  Sources: NASA, ESA, MIT OCW Astrophysics, OpenStax Astronomy (CC-BY).
----
-
-# Astronomy
-
-## The solar system
-
-**Eight planets (mnemonic: My Very Excellent Mother Just Served Us Nachos):**
-Mercury, Venus, Earth, Mars (rocky/terrestrial) | Jupiter, Saturn, Uranus, Neptune (gas giants)
-
-**Distances:** Earth-Sun = 1 AU (Astronomical Unit) = 150 million km. Neptune: 30 AU. Nearest star (Proxima Centauri): 4.2 light-years = 268,000 AU.
-**Sizes:** Sun contains 99.86% of solar system's mass. Jupiter: 318 Earth masses. Earth: 1.
-
-**Key features:**
-Sun: G-type main-sequence star. Surface temp: 5,778K. Core temp: 15 million K. Nuclear fusion (hydrogen → helium).
-Mars: Largest volcano (Olympus Mons = 3× Everest), longest canyon (Valles Marineris), thin CO2 atmosphere.
-Jupiter: Largest planet. Great Red Spot (storm larger than Earth). 95 known moons. Europa: subsurface ocean.
-Saturn: Ring system (mostly ice). Density less than water (would float in a large enough ocean).
-
-## Stars
-
-### Stellar classification (Harvard spectral classification)
-
-**OBAFGKM** — Oh Be A Fine Girl/Guy, Kiss Me
-O (hottest, blue-white, >30,000K) → B → A → F → G → K → M (coolest, red, <3,500K)
-Sun is a G-type (yellow-white). Most common: M-type red dwarfs.
-
-### Stellar lifecycle
-
-**Main sequence:** Hydrogen fusion in core. Pressure vs. gravity in equilibrium. ~90% of star's lifetime.
-**Red giant:** Core hydrogen exhausted → outer layers expand. Helium fusion begins.
-**Stellar death:**
-
-- Low/medium mass (like Sun): Red giant → planetary nebula → white dwarf
-- High mass: Red supergiant → supernova → neutron star (or black hole if >~3 solar masses)
-
-**Hertzsprung-Russell diagram:** Plots stars by luminosity vs. temperature. Main sequence is the diagonal band.
-
-## Galaxies and cosmology
-
-### Our galaxy
-
-**Milky Way:** Barred spiral galaxy. ~200-400 billion stars. Diameter ~100,000 light-years.
-Earth is ~27,000 light-years from the galactic center.
-Supermassive black hole at center: Sagittarius A\*, 4 million solar masses.
-
-### Universe scale
-
-Observable universe: ~93 billion light-years diameter. ~2 trillion galaxies.
-**Light-years:** Distance light travels in one year = 9.46 × 10^12 km.
-The most distant observable objects are seen as they were ~13.8 billion years ago.
-
-### Big Bang cosmology
-
-**Age:** ~13.8 billion years.
-**Evidence:** Cosmic microwave background (CMB), Hubble expansion, abundance of light elements.
-**Hubble's Law:** V = H₀ × d (Galaxies receding at speed proportional to distance)
-**Dark matter:** ~27% of universe. Evidence: Galaxy rotation curves. Nature unknown.
-**Dark energy:** ~68% of universe. Driving accelerating expansion. Nature unknown.
-**Ordinary matter:** ~5% of universe.
-
-## Black holes
-
-**Singularity:** Infinite density. Spacetime curvature breaks known physics.
-**Event horizon:** Point of no return. Escape velocity = speed of light.
-**Schwarzschild radius:** r = 2GM/c² (For Earth: ~9mm. For Sun: ~3km.)
-**Supermassive black holes:** Centers of most galaxies. Millions to billions of solar masses.
-**Detection:** Gravitational lensing, orbital effects on nearby stars, accretion disk radiation, gravitational waves (LIGO).
-
-Sources: NASA (nasa.gov — free), ESA (esa.int — free), OpenStax Astronomy 2e (CC-BY, openstax.org), Khan Academy Cosmology and Astronomy (CC-BY-NC-SA), MIT OCW 8.286 Astrophysics
+---
+watermark: ORIRO
+disable-model-invocation: true
+name: sci-astronomy
+provider: ORIRO.ai
+copyright: Copyright (c) 2026 ORIRO.ai
+description: >
+  Astronomy and cosmology — solar system, stars, galaxies, cosmology, telescopes,
+  and the scale of the universe. Activate for questions about planets, stars,
+  black holes, the Big Bang, space exploration, or any astronomy topic.
+  Sources: NASA, ESA, MIT OCW Astrophysics, OpenStax Astronomy (CC-BY).
+---
+
+# Astronomy
+
+## The solar system
+
+**Eight planets (mnemonic: My Very Excellent Mother Just Served Us Nachos):**
+Mercury, Venus, Earth, Mars (rocky/terrestrial) | Jupiter, Saturn, Uranus, Neptune (gas giants)
+
+**Distances:** Earth-Sun = 1 AU (Astronomical Unit) = 150 million km. Neptune: 30 AU. Nearest star (Proxima Centauri): 4.2 light-years = 268,000 AU.
+**Sizes:** Sun contains 99.86% of solar system's mass. Jupiter: 318 Earth masses. Earth: 1.
+
+**Key features:**
+Sun: G-type main-sequence star. Surface temp: 5,778K. Core temp: 15 million K. Nuclear fusion (hydrogen → helium).
+Mars: Largest volcano (Olympus Mons = 3× Everest), longest canyon (Valles Marineris), thin CO2 atmosphere.
+Jupiter: Largest planet. Great Red Spot (storm larger than Earth). 95 known moons. Europa: subsurface ocean.
+Saturn: Ring system (mostly ice). Density less than water (would float in a large enough ocean).
+
+## Stars
+
+### Stellar classification (Harvard spectral classification)
+
+**OBAFGKM** — Oh Be A Fine Girl/Guy, Kiss Me
+O (hottest, blue-white, >30,000K) → B → A → F → G → K → M (coolest, red, <3,500K)
+Sun is a G-type (yellow-white). Most common: M-type red dwarfs.
+
+### Stellar lifecycle
+
+**Main sequence:** Hydrogen fusion in core. Pressure vs. gravity in equilibrium. ~90% of star's lifetime.
+**Red giant:** Core hydrogen exhausted → outer layers expand. Helium fusion begins.
+**Stellar death:**
+
+- Low/medium mass (like Sun): Red giant → planetary nebula → white dwarf
+- High mass: Red supergiant → supernova → neutron star (or black hole if >~3 solar masses)
+
+**Hertzsprung-Russell diagram:** Plots stars by luminosity vs. temperature. Main sequence is the diagonal band.
+
+## Galaxies and cosmology
+
+### Our galaxy
+
+**Milky Way:** Barred spiral galaxy. ~200-400 billion stars. Diameter ~100,000 light-years.
+Earth is ~27,000 light-years from the galactic center.
+Supermassive black hole at center: Sagittarius A\*, 4 million solar masses.
+
+### Universe scale
+
+Observable universe: ~93 billion light-years diameter. ~2 trillion galaxies.
+**Light-years:** Distance light travels in one year = 9.46 × 10^12 km.
+The most distant observable objects are seen as they were ~13.8 billion years ago.
+
+### Big Bang cosmology
+
+**Age:** ~13.8 billion years.
+**Evidence:** Cosmic microwave background (CMB), Hubble expansion, abundance of light elements.
+**Hubble's Law:** V = H₀ × d (Galaxies receding at speed proportional to distance)
+**Dark matter:** ~27% of universe. Evidence: Galaxy rotation curves. Nature unknown.
+**Dark energy:** ~68% of universe. Driving accelerating expansion. Nature unknown.
+**Ordinary matter:** ~5% of universe.
+
+## Black holes
+
+**Singularity:** Infinite density. Spacetime curvature breaks known physics.
+**Event horizon:** Point of no return. Escape velocity = speed of light.
+**Schwarzschild radius:** r = 2GM/c² (For Earth: ~9mm. For Sun: ~3km.)
+**Supermassive black holes:** Centers of most galaxies. Millions to billions of solar masses.
+**Detection:** Gravitational lensing, orbital effects on nearby stars, accretion disk radiation, gravitational waves (LIGO).
+
+Sources: NASA (nasa.gov — free), ESA (esa.int — free), OpenStax Astronomy 2e (CC-BY, openstax.org), Khan Academy Cosmology and Astronomy (CC-BY-NC-SA), MIT OCW 8.286 Astrophysics

package/skills/science/sci-biology/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2026 ORIRO.ai
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+MIT License
+
+Copyright (c) 2026 ORIRO.ai
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/skills/science/sci-biology/SKILL.md

@@ -1,74 +1,74 @@
----
-watermark: ORIRO
-disable-model-invocation: true
-name: sci-biology
-provider: ORIRO.ai
-copyright: Copyright (c) 2026 ORIRO.ai
-description: >
-
-
-  Biology fundamentals — cell biology, genetics, evolution, ecology, physiology, and molecular biology basics.
-
-
-
-
-  Sources: OpenStax textbooks (CC-BY), Khan Academy, MIT OCW, NOAA, IPCC reports.
----
-
-# Biology Fundamentals
-
-## Cell biology
-
-**Cell theory:** All living things are made of cells; cells come from pre-existing cells; cells are the basic unit of life.
-**Prokaryotic vs. eukaryotic:**
-Prokaryotic (bacteria, archaea): No nucleus. Circular DNA. Smaller (~1-10 µm). Faster reproduction.
-Eukaryotic (plants, animals, fungi, protists): Membrane-bound nucleus. Linear DNA. Larger (~10-100 µm).
-
-**Key organelles:**
-Nucleus: Contains DNA. Command center.
-Mitochondria: ATP production through cellular respiration. Have own DNA.
-Ribosomes: Protein synthesis from mRNA instructions.
-ER (Endoplasmic Reticulum): Rough ER = protein processing; Smooth ER = lipid synthesis.
-Golgi apparatus: Package/modify/ship proteins.
-Chloroplasts (plants): Photosynthesis. Have own DNA.
-Lysosomes: Cellular digestion. Break down waste and foreign material.
-
-## DNA and genetics
-
-**DNA structure:** Double helix. Deoxyribose sugar + phosphate backbone + nitrogenous bases.
-Base pairing: A-T, G-C (antiparallel strands).
-**Central dogma:** DNA → RNA → Protein (transcription then translation).
-**Gene:** Sequence of DNA that codes for a functional product (usually protein).
-**Codon:** 3-nucleotide sequence that codes for an amino acid (64 codons, 20 amino acids, genetic code is redundant).
-
-**Mendelian genetics:**
-Dominant allele: Expressed when present (capital letter, e.g., B).
-Recessive allele: Expressed only when homozygous (lowercase, e.g., b).
-Homozygous: Two copies of same allele (BB or bb).
-Heterozygous: One copy of each (Bb) — dominant expressed.
-Punnett square: Predicts offspring probabilities.
-
-## Evolution
-
-**Natural selection:** Variation exists → some variations help survival/reproduction → heritable variations passed to offspring → population changes over generations.
-**Evidence:** Fossil record, comparative anatomy, DNA sequence similarities, direct observation (bacterial antibiotic resistance, beak changes in Galápagos finches).
-**Speciation:** Formation of new species. Geographic isolation → reproductive isolation → genetic divergence.
-
-## Ecology
-
-**Population ecology:** How populations change over time. Birth, death, immigration, emigration.
-Exponential growth (J-curve): Unlimited resources. dN/dt = rN.
-Logistic growth (S-curve): Carrying capacity limits growth. Levels off at K.
-**Community ecology:** Interactions between species. Competition, predation, mutualism, commensalism, parasitism.
-**Ecosystem ecology:** Energy flow and nutrient cycling. Primary productivity, trophic levels.
-Only ~10% of energy transfers between trophic levels (10% rule).
-**Biogeochemical cycles:** Carbon, nitrogen, water, phosphorus. Essential elements cycle through living and non-living components.
-
-## Molecular biology basics
-
-**PCR (Polymerase Chain Reaction):** Amplify specific DNA sequences. Foundation of genetic testing, forensics, COVID testing.
-**CRISPR-Cas9:** Precise DNA editing. Cut specific sequence → repair can insert or delete. Revolutionary for medicine and research.
-**Proteins:** Polymers of amino acids. Function determined by 3D shape. Shape determined by sequence.
-Denaturation: Loss of 3D structure (heat, pH extremes) → loss of function.
-
-Sources: OpenStax Biology 2e (CC-BY), Khan Academy Biology, Campbell Biology (principles), MIT OCW 7.012 Biology
+---
+watermark: ORIRO
+disable-model-invocation: true
+name: sci-biology
+provider: ORIRO.ai
+copyright: Copyright (c) 2026 ORIRO.ai
+description: >
+
+
+  Biology fundamentals — cell biology, genetics, evolution, ecology, physiology, and molecular biology basics.
+
+
+
+
+  Sources: OpenStax textbooks (CC-BY), Khan Academy, MIT OCW, NOAA, IPCC reports.
+---
+
+# Biology Fundamentals
+
+## Cell biology
+
+**Cell theory:** All living things are made of cells; cells come from pre-existing cells; cells are the basic unit of life.
+**Prokaryotic vs. eukaryotic:**
+Prokaryotic (bacteria, archaea): No nucleus. Circular DNA. Smaller (~1-10 µm). Faster reproduction.
+Eukaryotic (plants, animals, fungi, protists): Membrane-bound nucleus. Linear DNA. Larger (~10-100 µm).
+
+**Key organelles:**
+Nucleus: Contains DNA. Command center.
+Mitochondria: ATP production through cellular respiration. Have own DNA.
+Ribosomes: Protein synthesis from mRNA instructions.
+ER (Endoplasmic Reticulum): Rough ER = protein processing; Smooth ER = lipid synthesis.
+Golgi apparatus: Package/modify/ship proteins.
+Chloroplasts (plants): Photosynthesis. Have own DNA.
+Lysosomes: Cellular digestion. Break down waste and foreign material.
+
+## DNA and genetics
+
+**DNA structure:** Double helix. Deoxyribose sugar + phosphate backbone + nitrogenous bases.
+Base pairing: A-T, G-C (antiparallel strands).
+**Central dogma:** DNA → RNA → Protein (transcription then translation).
+**Gene:** Sequence of DNA that codes for a functional product (usually protein).
+**Codon:** 3-nucleotide sequence that codes for an amino acid (64 codons, 20 amino acids, genetic code is redundant).
+
+**Mendelian genetics:**
+Dominant allele: Expressed when present (capital letter, e.g., B).
+Recessive allele: Expressed only when homozygous (lowercase, e.g., b).
+Homozygous: Two copies of same allele (BB or bb).
+Heterozygous: One copy of each (Bb) — dominant expressed.
+Punnett square: Predicts offspring probabilities.
+
+## Evolution
+
+**Natural selection:** Variation exists → some variations help survival/reproduction → heritable variations passed to offspring → population changes over generations.
+**Evidence:** Fossil record, comparative anatomy, DNA sequence similarities, direct observation (bacterial antibiotic resistance, beak changes in Galápagos finches).
+**Speciation:** Formation of new species. Geographic isolation → reproductive isolation → genetic divergence.
+
+## Ecology
+
+**Population ecology:** How populations change over time. Birth, death, immigration, emigration.
+Exponential growth (J-curve): Unlimited resources. dN/dt = rN.
+Logistic growth (S-curve): Carrying capacity limits growth. Levels off at K.
+**Community ecology:** Interactions between species. Competition, predation, mutualism, commensalism, parasitism.
+**Ecosystem ecology:** Energy flow and nutrient cycling. Primary productivity, trophic levels.
+Only ~10% of energy transfers between trophic levels (10% rule).
+**Biogeochemical cycles:** Carbon, nitrogen, water, phosphorus. Essential elements cycle through living and non-living components.
+
+## Molecular biology basics
+
+**PCR (Polymerase Chain Reaction):** Amplify specific DNA sequences. Foundation of genetic testing, forensics, COVID testing.
+**CRISPR-Cas9:** Precise DNA editing. Cut specific sequence → repair can insert or delete. Revolutionary for medicine and research.
+**Proteins:** Polymers of amino acids. Function determined by 3D shape. Shape determined by sequence.
+Denaturation: Loss of 3D structure (heat, pH extremes) → loss of function.
+
+Sources: OpenStax Biology 2e (CC-BY), Khan Academy Biology, Campbell Biology (principles), MIT OCW 7.012 Biology

package/skills/science/sci-chemistry/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2026 ORIRO.ai
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+MIT License
+
+Copyright (c) 2026 ORIRO.ai
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.