better-dsh 0.2.4 → 0.2.5

package/docs/80_upstream-docs-and-skills/hermes-dev-skill/src/docs/user-guide/skills/optional/productivity/productivity-telephony.md

@@ -0,0 +1,435 @@
+---
+title: "Telephony — Provision Twilio numbers, SMS/MMS, and AI outbound calls"
+sidebar_label: "Telephony"
+description: "Provision Twilio numbers, SMS/MMS, and AI outbound calls"
+---
+
+{/* This page is auto-generated from the skill's SKILL.md by website/scripts/generate-skill-docs.py. Edit the source SKILL.md, not this page. */}
+
+# Telephony
+
+Provision Twilio numbers, SMS/MMS, and AI outbound calls.
+
+## Skill metadata
+
+| | |
+|---|---|
+| Source | Optional — install with `hermes skills install official/productivity/telephony` |
+| Path | `optional-skills/productivity\telephony` |
+| Version | `1.0.0` |
+| Author | Nous Research |
+| License | MIT |
+| Platforms | linux, macos, windows |
+| Tags | `telephony`, `phone`, `sms`, `mms`, `voice`, `twilio`, `bland.ai`, `vapi`, `calling`, `texting` |
+| Related skills | [`maps`](/docs/user-guide/skills/bundled/productivity/productivity-maps), [`google-workspace`](/docs/user-guide/skills/bundled/productivity/productivity-google-workspace), [`agentmail`](/docs/user-guide/skills/optional/email/email-agentmail) |
+
+## Reference: full SKILL.md
+
+:::info
+The following is the complete skill definition that Hermes loads when this skill is triggered. This is what the agent sees as instructions when the skill is active.
+:::
+
+# Telephony — Numbers, Calls, and Texts without Core Tool Changes
+
+This optional skill gives Hermes practical phone capabilities while keeping telephony out of the core tool list.
+
+It ships with a helper script, `scripts/telephony.py`, that can:
+- save provider credentials into `${HERMES_HOME:-~/.hermes}/.env`
+- search for and buy a Twilio phone number
+- remember that owned number for later sessions
+- send SMS / MMS from the owned number
+- poll inbound SMS for that number with no webhook server required
+- make direct Twilio calls using TwiML `<Say>` or `<Play>`
+- import the owned Twilio number into Vapi
+- place outbound AI calls through Bland.ai or Vapi
+
+## What this solves
+
+This skill is meant to cover the practical phone tasks users actually want:
+- outbound calls
+- texting
+- owning a reusable agent number
+- checking messages that arrive to that number later
+- preserving that number and related IDs between sessions
+- future-friendly telephony identity for inbound SMS polling and other automations
+
+It does **not** turn Hermes into a real-time inbound phone gateway. Inbound SMS is handled by polling the Twilio REST API. That is enough for many workflows, including notifications and some one-time-code retrieval, without adding core webhook infrastructure.
+
+## Safety rules — mandatory
+
+1. Always confirm before placing a call or sending a text.
+2. Never dial emergency numbers.
+3. Never use telephony for harassment, spam, impersonation, or anything illegal.
+4. Treat third-party phone numbers as sensitive operational data:
+   - do not save them to Hermes memory
+   - do not include them in skill docs, summaries, or follow-up notes unless the user explicitly wants that
+5. It is fine to persist the **agent-owned Twilio number** because that is part of the user's configuration.
+6. VoIP numbers are **not guaranteed** to work for all third-party 2FA flows. Use with caution and set user expectations clearly.
+
+## Decision tree — which service to use?
+
+Use this logic instead of hardcoded provider routing:
+
+### 1) "I want Hermes to own a real phone number"
+Use **Twilio**.
+
+Why:
+- easiest path to buying and keeping a number
+- best SMS / MMS support
+- simplest inbound SMS polling story
+- cleanest future path to inbound webhooks or call handling
+
+Use cases:
+- receive texts later
+- send deployment alerts / cron notifications
+- maintain a reusable phone identity for the agent
+- experiment with phone-based auth flows later
+
+### 2) "I only need the easiest outbound AI phone call right now"
+Use **Bland.ai**.
+
+Why:
+- quickest setup
+- one API key
+- no need to first buy/import a number yourself
+
+Tradeoff:
+- less flexible
+- voice quality is decent, but not the best
+
+### 3) "I want the best conversational AI voice quality"
+Use **Twilio + Vapi**.
+
+Why:
+- Twilio gives you the owned number
+- Vapi gives you better conversational AI call quality and more voice/model flexibility
+
+Recommended flow:
+1. Buy/save a Twilio number
+2. Import it into Vapi
+3. Save the returned `VAPI_PHONE_NUMBER_ID`
+4. Use `ai-call --provider vapi`
+
+### 4) "I want to call with a custom prerecorded voice message"
+Use **Twilio direct call** with a public audio URL.
+
+Why:
+- easiest way to play a custom MP3
+- pairs well with Hermes `text_to_speech` plus a public file host or tunnel
+
+## Files and persistent state
+
+The skill persists telephony state in two places:
+
+### `${HERMES_HOME:-~/.hermes}/.env`
+Used for long-lived provider credentials and owned-number IDs, for example:
+- `TWILIO_ACCOUNT_SID`
+- `TWILIO_AUTH_TOKEN`
+- `TWILIO_PHONE_NUMBER`
+- `TWILIO_PHONE_NUMBER_SID`
+- `BLAND_API_KEY`
+- `VAPI_API_KEY`
+- `VAPI_PHONE_NUMBER_ID`
+- `PHONE_PROVIDER` (AI call provider: bland or vapi)
+
+### `~/.hermes/telephony_state.json`
+Used for skill-only state that should survive across sessions, for example:
+- remembered default Twilio number / SID
+- remembered Vapi phone number ID
+- last inbound message SID/date for inbox polling checkpoints
+
+This means:
+- the next time the skill is loaded, `diagnose` can tell you what number is already configured
+- `twilio-inbox --since-last --mark-seen` can continue from the previous checkpoint
+
+## Locate the helper script
+
+After installing this skill, locate the script like this:
+
+```bash
+SCRIPT="$(find ~/.hermes/skills -path '*/telephony/scripts/telephony.py' -print -quit)"
+```
+
+If `SCRIPT` is empty, the skill is not installed yet.
+
+## Install
+
+This is an official optional skill, so install it from the Skills Hub:
+
+```bash
+hermes skills search telephony
+hermes skills install official/productivity/telephony
+```
+
+## Provider setup
+
+### Twilio — owned number, SMS/MMS, direct calls, inbound SMS polling
+
+Sign up at:
+- https://www.twilio.com/try-twilio
+
+Then save credentials into Hermes:
+
+```bash
+python "$SCRIPT" save-twilio ACXXXXXXXXXXXXXXXXXXXXXXXXXXXX your_auth_token_here
+```
+
+Search for available numbers:
+
+```bash
+python "$SCRIPT" twilio-search --country US --area-code 702 --limit 5
+```
+
+Buy and remember a number:
+
+```bash
+python "$SCRIPT" twilio-buy "+17025551234" --save-env
+```
+
+List owned numbers:
+
+```bash
+python "$SCRIPT" twilio-owned
+```
+
+Set one of them as the default later:
+
+```bash
+python "$SCRIPT" twilio-set-default "+17025551234" --save-env
+# or
+python "$SCRIPT" twilio-set-default PNXXXXXXXXXXXXXXXXXXXXXXXXXXXX --save-env
+```
+
+### Bland.ai — easiest outbound AI calling
+
+Sign up at:
+- https://app.bland.ai
+
+Save config:
+
+```bash
+python "$SCRIPT" save-bland your_bland_api_key --voice mason
+```
+
+### Vapi — better conversational voice quality
+
+Sign up at:
+- https://dashboard.vapi.ai
+
+Save the API key first:
+
+```bash
+python "$SCRIPT" save-vapi your_vapi_api_key
+```
+
+Import your owned Twilio number into Vapi and persist the returned phone number ID:
+
+```bash
+python "$SCRIPT" vapi-import-twilio --save-env
+```
+
+If you already know the Vapi phone number ID, save it directly:
+
+```bash
+python "$SCRIPT" save-vapi your_vapi_api_key --phone-number-id vapi_phone_number_id_here
+```
+
+## Diagnose current state
+
+At any time, inspect what the skill already knows:
+
+```bash
+python "$SCRIPT" diagnose
+```
+
+Use this first when resuming work in a later session.
+
+## Common workflows
+
+### A. Buy an agent number and keep using it later
+
+1. Save Twilio credentials:
+```bash
+python "$SCRIPT" save-twilio AC... auth_token_here
+```
+
+2. Search for a number:
+```bash
+python "$SCRIPT" twilio-search --country US --area-code 702 --limit 10
+```
+
+3. Buy it and save it into `${HERMES_HOME:-~/.hermes}/.env` + state:
+```bash
+python "$SCRIPT" twilio-buy "+17025551234" --save-env
+```
+
+4. Next session, run:
+```bash
+python "$SCRIPT" diagnose
+```
+This shows the remembered default number and inbox checkpoint state.
+
+### B. Send a text from the agent number
+
+```bash
+python "$SCRIPT" twilio-send-sms "+15551230000" "Your deployment completed successfully."
+```
+
+With media:
+
+```bash
+python "$SCRIPT" twilio-send-sms "+15551230000" "Here is the chart." --media-url "https://example.com/chart.png"
+```
+
+### C. Check inbound texts later with no webhook server
+
+Poll the inbox for the default Twilio number:
+
+```bash
+python "$SCRIPT" twilio-inbox --limit 20
+```
+
+Only show messages that arrived after the last checkpoint, and advance the checkpoint when you're done reading:
+
+```bash
+python "$SCRIPT" twilio-inbox --since-last --mark-seen
+```
+
+This is the main answer to “how do I access messages the number receives next time the skill is loaded?”
+
+### D. Make a direct Twilio call with built-in TTS
+
+```bash
+python "$SCRIPT" twilio-call "+15551230000" --message "Hello! This is Hermes calling with your status update." --voice Polly.Joanna
+```
+
+### E. Call with a prerecorded / custom voice message
+
+This is the main path for reusing Hermes's existing `text_to_speech` support.
+
+Use this when:
+- you want the call to use Hermes's configured TTS voice rather than Twilio `<Say>`
+- you want a one-way voice delivery (briefing, alert, joke, reminder, status update)
+- you do **not** need a live conversational phone call
+
+Generate or host audio separately, then:
+
+```bash
+python "$SCRIPT" twilio-call "+155****0000" --audio-url "https://example.com/briefing.mp3"
+```
+
+Recommended Hermes TTS -> Twilio Play workflow:
+
+1. Generate the audio with Hermes `text_to_speech`.
+2. Make the resulting MP3 publicly reachable.
+3. Place the Twilio call with `--audio-url`.
+
+Example agent flow:
+- Ask Hermes to create the message audio with `text_to_speech`
+- If needed, expose the file with a temporary static host / tunnel / object storage URL
+- Use `twilio-call --audio-url ...` to deliver it by phone
+
+Good hosting options for the MP3:
+- a temporary public object/storage URL
+- a short-lived tunnel to a local static file server
+- any existing HTTPS URL the phone provider can fetch directly
+
+Important note:
+- Hermes TTS is great for prerecorded outbound messages
+- Bland/Vapi are better for **live conversational AI calls** because they handle the real-time telephony audio stack themselves
+- Hermes STT/TTS alone is not being used here as a full duplex phone conversation engine; that would require a much heavier streaming/webhook integration than this skill is trying to introduce
+
+### F. Navigate a phone tree / IVR with Twilio direct calling
+
+If you need to press digits after the call connects, use `--send-digits`.
+Twilio interprets `w` as a short wait.
+
+```bash
+python "$SCRIPT" twilio-call "+18005551234" --message "Connecting to billing now." --send-digits "ww1w2w3"
+```
+
+This is useful for reaching a specific menu branch before handing off to a human or delivering a short status message.
+
+### G. Outbound AI phone call with Bland.ai
+
+```bash
+python "$SCRIPT" ai-call "+15551230000" "Call the dental office, ask for a cleaning appointment on Tuesday afternoon, and if they do not have Tuesday availability, ask for Wednesday or Thursday instead." --provider bland --voice mason --max-duration 3
+```
+
+Check status:
+
+```bash
+python "$SCRIPT" ai-status <call_id> --provider bland
+```
+
+Ask Bland analysis questions after completion:
+
+```bash
+python "$SCRIPT" ai-status <call_id> --provider bland --analyze "Was the appointment confirmed?,What date and time?,Any special instructions?"
+```
+
+### H. Outbound AI phone call with Vapi on your owned number
+
+1. Import your Twilio number into Vapi:
+```bash
+python "$SCRIPT" vapi-import-twilio --save-env
+```
+
+2. Place the call:
+```bash
+python "$SCRIPT" ai-call "+15551230000" "You are calling to make a dinner reservation for two at 7:30 PM. If that is unavailable, ask for the nearest time between 6:30 and 8:30 PM." --provider vapi --max-duration 4
+```
+
+3. Check result:
+```bash
+python "$SCRIPT" ai-status <call_id> --provider vapi
+```
+
+## Suggested agent procedure
+
+When the user asks for a call or text:
+
+1. Determine which path fits the request via the decision tree.
+2. Run `diagnose` if configuration state is unclear.
+3. Gather the full task details.
+4. Confirm with the user before dialing or texting.
+5. Use the correct command.
+6. Poll for results if needed.
+7. Summarize the outcome without persisting third-party numbers to Hermes memory.
+
+## What this skill still does not do
+
+- real-time inbound call answering
+- webhook-based live SMS push into the agent loop
+- guaranteed support for arbitrary third-party 2FA providers
+
+Those would require more infrastructure than a pure optional skill.
+
+## Pitfalls
+
+- Twilio trial accounts and regional rules can restrict who you can call/text.
+- Some services reject VoIP numbers for 2FA.
+- `twilio-inbox` polls the REST API; it is not instant push delivery.
+- Vapi outbound calling still depends on having a valid imported number.
+- Bland is easiest, but not always the best-sounding.
+- Do not store arbitrary third-party phone numbers in Hermes memory.
+
+## Verification checklist
+
+After setup, you should be able to do all of the following with just this skill:
+
+1. `diagnose` shows provider readiness and remembered state
+2. search and buy a Twilio number
+3. persist that number to `${HERMES_HOME:-~/.hermes}/.env`
+4. send an SMS from the owned number
+5. poll inbound texts for the owned number later
+6. place a direct Twilio call
+7. place an AI call via Bland or Vapi
+
+## References
+
+- Twilio phone numbers: https://www.twilio.com/docs/phone-numbers/api
+- Twilio messaging: https://www.twilio.com/docs/messaging/api/message-resource
+- Twilio voice: https://www.twilio.com/docs/voice/api/call-resource
+- Vapi docs: https://docs.vapi.ai/
+- Bland.ai: https://app.bland.ai/

package/docs/80_upstream-docs-and-skills/hermes-dev-skill/src/docs/user-guide/skills/optional/research/research-bioinformatics.md

@@ -0,0 +1,254 @@
+---
+title: "Bioinformatics — Gateway to 400+ genomics and computational biology skills"
+sidebar_label: "Bioinformatics"
+description: "Gateway to 400+ genomics and computational biology skills"
+---
+
+{/* This page is auto-generated from the skill's SKILL.md by website/scripts/generate-skill-docs.py. Edit the source SKILL.md, not this page. */}
+
+# Bioinformatics
+
+Gateway to 400+ genomics and computational biology skills.
+
+## Skill metadata
+
+| | |
+|---|---|
+| Source | Optional — install with `hermes skills install official/research/bioinformatics` |
+| Path | `optional-skills/research\bioinformatics` |
+| Version | `1.0.0` |
+| Author | Teknium (teknium1), Hermes Agent |
+| License | MIT |
+| Platforms | linux, macos |
+| Tags | `bioinformatics`, `genomics`, `sequencing`, `biology`, `research`, `science` |
+
+## Reference: full SKILL.md
+
+:::info
+The following is the complete skill definition that Hermes loads when this skill is triggered. This is what the agent sees as instructions when the skill is active.
+:::
+
+# Bioinformatics Skills Gateway
+
+Use when asked about bioinformatics, genomics, sequencing, variant calling, gene expression, single-cell analysis, protein structure, pharmacogenomics, metagenomics, phylogenetics, or any computational biology task.
+
+This skill is a gateway to two open-source bioinformatics skill libraries. Instead of bundling hundreds of domain-specific skills, it indexes them and fetches what you need on demand.
+
+## Sources
+
+◆ **bioSkills** — 385 reference skills (code patterns, parameter guides, decision trees)
+  Repo: https://github.com/GPTomics/bioSkills
+  Format: SKILL.md per topic with code examples. Python/R/CLI.
+
+◆ **ClawBio** — 33 runnable pipeline skills (executable scripts, reproducibility bundles)
+  Repo: https://github.com/ClawBio/ClawBio
+  Format: Python scripts with demos. Each analysis exports report.md + commands.sh + environment.yml.
+
+## How to fetch and use a skill
+
+1. Identify the domain and skill name from the index below.
+2. Clone the relevant repo (shallow clone to save time):
+   ```bash
+   # bioSkills (reference material)
+   git clone --depth 1 https://github.com/GPTomics/bioSkills.git /tmp/bioSkills
+
+   # ClawBio (runnable pipelines)
+   git clone --depth 1 https://github.com/ClawBio/ClawBio.git /tmp/ClawBio
+   ```
+3. Read the specific skill:
+   ```bash
+   # bioSkills — each skill is at: <category>/<skill-name>/SKILL.md
+   cat /tmp/bioSkills/variant-calling/gatk-variant-calling/SKILL.md
+
+   # ClawBio — each skill is at: skills/<skill-name>/
+   cat /tmp/ClawBio/skills/pharmgx-reporter/README.md
+   ```
+4. Follow the fetched skill as reference material. These are NOT Hermes-format skills — treat them as expert domain guides. They contain correct parameters, proper tool flags, and validated pipelines.
+
+## Skill Index by Domain
+
+### Sequence Fundamentals
+bioSkills:
+  sequence-io/ — read-sequences, write-sequences, format-conversion, batch-processing, compressed-files, fastq-quality, filter-sequences, paired-end-fastq, sequence-statistics
+  sequence-manipulation/ — seq-objects, reverse-complement, transcription-translation, motif-search, codon-usage, sequence-properties, sequence-slicing
+ClawBio:
+  seq-wrangler — Sequence QC, alignment, and BAM processing (wraps FastQC, BWA, SAMtools)
+
+### Read QC & Alignment
+bioSkills:
+  read-qc/ — quality-reports, fastp-workflow, adapter-trimming, quality-filtering, umi-processing, contamination-screening, rnaseq-qc
+  read-alignment/ — bwa-alignment, star-alignment, hisat2-alignment, bowtie2-alignment
+  alignment-files/ — sam-bam-basics, alignment-sorting, alignment-filtering, bam-statistics, duplicate-handling, pileup-generation
+
+### Variant Calling & Annotation
+bioSkills:
+  variant-calling/ — gatk-variant-calling, deepvariant, variant-calling (bcftools), joint-calling, structural-variant-calling, filtering-best-practices, variant-annotation, variant-normalization, vcf-basics, vcf-manipulation, vcf-statistics, consensus-sequences, clinical-interpretation
+ClawBio:
+  vcf-annotator — VEP + ClinVar + gnomAD annotation with ancestry-aware context
+  variant-annotation — Variant annotation pipeline
+
+### Differential Expression (Bulk RNA-seq)
+bioSkills:
+  differential-expression/ — deseq2-basics, edger-basics, batch-correction, de-results, de-visualization, timeseries-de
+  rna-quantification/ — alignment-free-quant (Salmon/kallisto), featurecounts-counting, tximport-workflow, count-matrix-qc
+  expression-matrix/ — counts-ingest, gene-id-mapping, metadata-joins, sparse-handling
+ClawBio:
+  rnaseq-de — Full DE pipeline with QC, normalization, and visualization
+  diff-visualizer — Rich visualization and reporting for DE results
+
+### Single-Cell RNA-seq
+bioSkills:
+  single-cell/ — preprocessing, clustering, batch-integration, cell-annotation, cell-communication, doublet-detection, markers-annotation, trajectory-inference, multimodal-integration, perturb-seq, scatac-analysis, lineage-tracing, metabolite-communication, data-io
+ClawBio:
+  scrna-orchestrator — Full Scanpy pipeline (QC, clustering, markers, annotation)
+  scrna-embedding — scVI-based latent embedding and batch integration
+
+### Spatial Transcriptomics
+bioSkills:
+  spatial-transcriptomics/ — spatial-data-io, spatial-preprocessing, spatial-domains, spatial-deconvolution, spatial-communication, spatial-neighbors, spatial-statistics, spatial-visualization, spatial-multiomics, spatial-proteomics, image-analysis
+
+### Epigenomics
+bioSkills:
+  chip-seq/ — peak-calling, differential-binding, motif-analysis, peak-annotation, chipseq-qc, chipseq-visualization, super-enhancers
+  atac-seq/ — atac-peak-calling, atac-qc, differential-accessibility, footprinting, motif-deviation, nucleosome-positioning
+  methylation-analysis/ — bismark-alignment, methylation-calling, dmr-detection, methylkit-analysis
+  hi-c-analysis/ — hic-data-io, tad-detection, loop-calling, compartment-analysis, contact-pairs, matrix-operations, hic-visualization, hic-differential
+ClawBio:
+  methylation-clock — Epigenetic age estimation
+
+### Pharmacogenomics & Clinical
+bioSkills:
+  clinical-databases/ — clinvar-lookup, gnomad-frequencies, dbsnp-queries, pharmacogenomics, polygenic-risk, hla-typing, variant-prioritization, somatic-signatures, tumor-mutational-burden, myvariant-queries
+ClawBio:
+  pharmgx-reporter — PGx report from 23andMe/AncestryDNA (12 genes, 31 SNPs, 51 drugs)
+  drug-photo — Photo of medication → personalized PGx dosage card (via vision)
+  clinpgx — ClinPGx API for gene-drug data and CPIC guidelines
+  gwas-lookup — Federated variant lookup across 9 genomic databases
+  gwas-prs — Polygenic risk scores from consumer genetic data
+  nutrigx_advisor — Personalized nutrition from consumer genetic data
+
+### Population Genetics & GWAS
+bioSkills:
+  population-genetics/ — association-testing (PLINK GWAS), plink-basics, population-structure, linkage-disequilibrium, scikit-allel-analysis, selection-statistics
+  causal-genomics/ — mendelian-randomization, fine-mapping, colocalization-analysis, mediation-analysis, pleiotropy-detection
+  phasing-imputation/ — haplotype-phasing, genotype-imputation, imputation-qc, reference-panels
+ClawBio:
+  claw-ancestry-pca — Ancestry PCA against SGDP reference panel
+
+### Metagenomics & Microbiome
+bioSkills:
+  metagenomics/ — kraken-classification, metaphlan-profiling, abundance-estimation, functional-profiling, amr-detection, strain-tracking, metagenome-visualization
+  microbiome/ — amplicon-processing, diversity-analysis, differential-abundance, taxonomy-assignment, functional-prediction, qiime2-workflow
+ClawBio:
+  claw-metagenomics — Shotgun metagenomics profiling (taxonomy, resistome, functional pathways)
+
+### Genome Assembly & Annotation
+bioSkills:
+  genome-assembly/ — hifi-assembly, long-read-assembly, short-read-assembly, metagenome-assembly, assembly-polishing, assembly-qc, scaffolding, contamination-detection
+  genome-annotation/ — eukaryotic-gene-prediction, prokaryotic-annotation, functional-annotation, ncrna-annotation, repeat-annotation, annotation-transfer
+  long-read-sequencing/ — basecalling, long-read-alignment, long-read-qc, clair3-variants, structural-variants, medaka-polishing, nanopore-methylation, isoseq-analysis
+
+### Structural Biology & Chemoinformatics
+bioSkills:
+  structural-biology/ — alphafold-predictions, modern-structure-prediction, structure-io, structure-navigation, structure-modification, geometric-analysis
+  chemoinformatics/ — molecular-io, molecular-descriptors, similarity-searching, substructure-search, virtual-screening, admet-prediction, reaction-enumeration
+ClawBio:
+  struct-predictor — Local AlphaFold/Boltz/Chai structure prediction with comparison
+
+### Proteomics
+bioSkills:
+  proteomics/ — data-import, peptide-identification, protein-inference, quantification, differential-abundance, dia-analysis, ptm-analysis, proteomics-qc, spectral-libraries
+ClawBio:
+  proteomics-de — Proteomics differential expression
+
+### Pathway Analysis & Gene Networks
+bioSkills:
+  pathway-analysis/ — go-enrichment, gsea, kegg-pathways, reactome-pathways, wikipathways, enrichment-visualization
+  gene-regulatory-networks/ — scenic-regulons, coexpression-networks, differential-networks, multiomics-grn, perturbation-simulation
+
+### Immunoinformatics
+bioSkills:
+  immunoinformatics/ — mhc-binding-prediction, epitope-prediction, neoantigen-prediction, immunogenicity-scoring, tcr-epitope-binding
+  tcr-bcr-analysis/ — mixcr-analysis, scirpy-analysis, immcantation-analysis, repertoire-visualization, vdjtools-analysis
+
+### CRISPR & Genome Engineering
+bioSkills:
+  crispr-screens/ — mageck-analysis, jacks-analysis, hit-calling, screen-qc, library-design, crispresso-editing, base-editing-analysis, batch-correction
+  genome-engineering/ — grna-design, off-target-prediction, hdr-template-design, base-editing-design, prime-editing-design
+
+### Workflow Management
+bioSkills:
+  workflow-management/ — snakemake-workflows, nextflow-pipelines, cwl-workflows, wdl-workflows
+ClawBio:
+  repro-enforcer — Export any analysis as reproducibility bundle (Conda env + Singularity + checksums)
+  galaxy-bridge — Access 8,000+ Galaxy tools from usegalaxy.org
+
+### Specialized Domains
+bioSkills:
+  alternative-splicing/ — splicing-quantification, differential-splicing, isoform-switching, sashimi-plots, single-cell-splicing, splicing-qc
+  ecological-genomics/ — edna-metabarcoding, landscape-genomics, conservation-genetics, biodiversity-metrics, community-ecology, species-delimitation
+  epidemiological-genomics/ — pathogen-typing, variant-surveillance, phylodynamics, transmission-inference, amr-surveillance
+  liquid-biopsy/ — cfdna-preprocessing, ctdna-mutation-detection, fragment-analysis, tumor-fraction-estimation, methylation-based-detection, longitudinal-monitoring
+  epitranscriptomics/ — m6a-peak-calling, m6a-differential, m6anet-analysis, merip-preprocessing, modification-visualization
+  metabolomics/ — xcms-preprocessing, metabolite-annotation, normalization-qc, statistical-analysis, pathway-mapping, lipidomics, targeted-analysis, msdial-preprocessing
+  flow-cytometry/ — fcs-handling, gating-analysis, compensation-transformation, clustering-phenotyping, differential-analysis, cytometry-qc, doublet-detection, bead-normalization
+  systems-biology/ — flux-balance-analysis, metabolic-reconstruction, gene-essentiality, context-specific-models, model-curation
+  rna-structure/ — secondary-structure-prediction, ncrna-search, structure-probing
+
+### Data Visualization & Reporting
+bioSkills:
+  data-visualization/ — ggplot2-fundamentals, heatmaps-clustering, volcano-customization, circos-plots, genome-browser-tracks, interactive-visualization, multipanel-figures, network-visualization, upset-plots, color-palettes, specialized-omics-plots, genome-tracks
+  reporting/ — rmarkdown-reports, quarto-reports, jupyter-reports, automated-qc-reports, figure-export
+ClawBio:
+  profile-report — Analysis profile reporting
+  data-extractor — Extract numerical data from scientific figure images (via vision)
+  lit-synthesizer — PubMed/bioRxiv search, summarization, citation graphs
+  pubmed-summariser — Gene/disease PubMed search with structured briefing
+
+### Database Access
+bioSkills:
+  database-access/ — entrez-search, entrez-fetch, entrez-link, blast-searches, local-blast, sra-data, geo-data, uniprot-access, batch-downloads, interaction-databases, sequence-similarity
+ClawBio:
+  ukb-navigator — Semantic search across 12,000+ UK Biobank fields
+  clinical-trial-finder — Clinical trial discovery
+
+### Experimental Design
+bioSkills:
+  experimental-design/ — power-analysis, sample-size, batch-design, multiple-testing
+
+### Machine Learning for Omics
+bioSkills:
+  machine-learning/ — omics-classifiers, biomarker-discovery, survival-analysis, model-validation, prediction-explanation, atlas-mapping
+ClawBio:
+  claw-semantic-sim — Semantic similarity index for disease literature (PubMedBERT)
+  omics-target-evidence-mapper — Aggregate target-level evidence across omics sources
+
+## Environment Setup
+
+These skills assume a bioinformatics workstation. Common dependencies:
+
+```bash
+# Python
+pip install biopython pysam cyvcf2 pybedtools pyBigWig scikit-allel anndata scanpy mygene
+
+# R/Bioconductor
+Rscript -e 'BiocManager::install(c("DESeq2","edgeR","Seurat","clusterProfiler","methylKit"))'
+
+# CLI tools (Ubuntu/Debian)
+sudo apt install samtools bcftools ncbi-blast+ minimap2 bedtools
+
+# CLI tools (macOS)
+brew install samtools bcftools blast minimap2 bedtools
+
+# Or via Conda (recommended for reproducibility)
+conda install -c bioconda samtools bcftools blast minimap2 bedtools fastp kraken2
+```
+
+## Pitfalls
+
+- The fetched skills are NOT in Hermes SKILL.md format. They use their own structure (bioSkills: code pattern cookbooks; ClawBio: README + Python scripts). Read them as expert reference material.
+- bioSkills are reference guides — they show correct parameters and code patterns but aren't executable pipelines.
+- ClawBio skills are executable — many have `--demo` flags and can be run directly.
+- Both repos assume bioinformatics tools are installed. Check prerequisites before running pipelines.
+- For ClawBio, run `pip install -r requirements.txt` in the cloned repo first.
+- Genomic data files can be very large. Be mindful of disk space when downloading reference genomes, SRA datasets, or building indices.