Agent Instructions

About

This is a compilation of the context provided to the AI agent(s) automating this digital garden. Inspired by voytek/tocify.

Articles from the feeds listed below are triaged according to the interests below. Articles that contribute new fact(s) to topic(s) are added to weekly brief. New facts are added to the topics digital garden. Content is prepared using the mutually exclusive and collectively exhaustive¹ grouping principle.

Interests

# BCI interests for weekly digest triage
# Used to score RSS items relevant to brain-computer interfaces and neurotechnology.
 
## Keywords
brain-computer interface
BCI
brain-machine interface
BMI
neural engineering
neurotechnology
neural decoding
electrocorticography
ECoG
intracranial EEG
iEEG
EEG-based BCI
fNIRS
functional near-infrared spectroscopy
tDCS
tACS
tRNS
transcranial stimulation
neuromodulation
neuroprosthetics
neuroimaging
neurorobotics
human neuroscience
computational neuroscience
neuroinformatics
neural signal processing
biomedical engineering
clinical neurophysiology
neural recording
neurofeedback
sensory neuroprosthetics
neural data analysis
neuralink
paradromics
synchron
precision neuroscience
blackrock neurotech
braingate
brain gate
utah array
speech prosthesis
neural dust
stentrode
kernel
darpa n3
fda ide
neurotrophic electrode
bci2000
 
## Narrative
Focus on brain-computer interfaces and closely related neurotechnology: invasive and non-invasive BCIs, neural interfaces, neuroprosthetics, decoding and stimulation, clinical trials, devices, companies, and regulation. Prioritize methods for neural/physiological time series, electrophysiology, and computational neuroscience. Down-weight purely clinical/psychiatry or molecular biology without neural dynamics.
 

Feeds

Where to get articles (research, news, blog)

News and archives

• Current news (1 month look back) through newsapi
• Open-access research through openalex
• Articles from google news

RSS

# BCI RSS feeds (Name | URL).
 
# newsletter
Neurotech Futures | https://neurotechnology.substack.com/feed
 
# journal - core
Journal of Neural Engineering | http://iopscience.iop.org/journal/rss/1741-2552
Nature Neuroscience | http://feeds.nature.com/neuro/rss/current
Frontiers in Neuroscience | https://www.frontiersin.org/journals/neuroscience/rss
Frontiers in Neurorobotics | https://www.frontiersin.org/journals/neurorobotics/rss
Frontiers in Human Neuroscience | https://www.frontiersin.org/journals/human-neuroscience/rss
Frontiers in Computational Neuroscience | https://www.frontiersin.org/journals/computational-neuroscience/rss
# 418 as of 2026 – IEEE Xplore blocks non-browser requests; consider tocify User-Agent if re-enabled
# IEEE Transactions on Biomedical Engineering | https://ieeexplore.ieee.org/rss/TOC10.XML
# IEEE Reviews in Biomedical Engineering | https://ieeexplore.ieee.org/rss/TOC4664312.XML
# IEEE Trans. Neural Systems & Rehab Eng. | https://ieeexplore.ieee.org/rss/TOC4157120.XML
J. NeuroEngineering & Rehabilitation | https://jneuroengrehab.biomedcentral.com/articles/most-recent/rss.xml
 
# journal - high impact
Nature (Neuroscience subject) | https://www.nature.com/subjects/neuroscience.rss
Nature Neuroscience | https://feeds.nature.com/neuro/rss/current
Nature Biomedical Engineering | https://www.nature.com/natbiomedeng.rss
Nature Reviews Neuroscience | https://www.nature.com/nrn.rss
Nature Medicine | https://www.nature.com/nm.rss
Science | https://www.science.org/action/showFeed?type=etoc&feed=rss&jc=science
Neuron | https://www.cell.com/neuron/current.rss
PNAS (Neuroscience) | https://feeds.feedburner.com/ProceedingsOfTheNationalAcademyOfSciencesNeuroscience
NEJM (Neurology) | https://www.nejm.org/action/showFeed?jc=nejm&type=etoc&feed=rss
The Lancet Neurology | https://www.thelancet.com/rssfeed/laneur_current.xml
# 403 as of 2026 – OUP blocks programmatic access
# Brain (Oxford) | https://academic.oup.com/rss/site_5112/3088.xml
 
# journal - methods and signals
NeuroImage | https://rss.sciencedirect.com/publication/science/10538119
J. Neuroscience Methods | https://rss.sciencedirect.com/publication/science/01650270
Clinical Neurophysiology | https://rss.sciencedirect.com/publication/science/13882457
Journal of Neurophysiology | https://journals.physiology.org/action/showFeed?type=etoc&feed=rss&jc=jn
 
# journal - rehab and clinical
Archives of Physical Med & Rehab | https://rss.sciencedirect.com/publication/science/00039993
Neurorehab & Neural Repair | https://journals.sagepub.com/action/showFeed?ui=0&mi=ehikzz&ai=2b4&jc=nnra&type=etoc&feed=rss
 
# journal - devices and materials
Biosensors & Bioelectronics | https://rss.sciencedirect.com/publication/science/09565663
# 403 as of 2026 – Wiley blocks programmatic access
# Advanced Materials | https://onlinelibrary.wiley.com/feed/15214095/most-recent
 
# preprint
bioRxiv Neuroscience | http://connect.biorxiv.org/biorxiv_xml.php?subject=neuroscience
arXiv Neurons and Cognition (q-bio.NC) | http://export.arxiv.org/rss/q-bio.NC
arXiv Human-Computer Interaction (cs.HC) | http://export.arxiv.org/rss/cs.HC
 
# ieee (if 418/403 persist for other feeds, consider updating tocify HTTP client User-Agent)
# SSL hostname mismatch as of 2026
# IEEE Brain Initiative | https://brain.ieee.org/feed/
# IEEE Life Sciences | https://lifesciences.ieee.org/feed/
IEEE Spectrum - Biomedical | https://spectrum.ieee.org/feed
# 403 as of 2026 – no public RSS
# Engineering in Medicine and Biology Society | https://www.embs.org/feed/
 
# open access 
PLOS ONE | https://journals.plos.org/plosone/feed/atom
Scientific Reports | https://www.nature.com/srep.rss
JMIR Biomedical Engineering | https://biomedeng.jmir.org/feed/atom
 
# news
Neuroscience News Magazine | https://neurosciencenews.com/feed
MIT News - Neuroscience | https://news.mit.edu/rss/topic/neuroscience
MIT Technology Review - Biotechnology and Health | https://technologyreview.com/topic/biotechnology-and-health/feed/
ScienceDaily - Brain-Computer Interfaces | https://www.sciencedaily.com/rss/mind_brain/brain-computer_interfaces.xml
TechCrunch - Biotech & Health | https://techcrunch.com/category/biotech-health/feed/
The Transmitter | https://thetransmitter.org/feed
STAT News | https://statnews.com/feed/
# 404 as of 2026 – Nature news RSS discontinued
# Nature News | https://nature.com/news/rss
Wired | https://wired.com/feed/rss
Wired - Neuro | https://wired.com/tag/neuroscience/
# 404 as of 2026 – section feed discontinued
# Scientific America | https://www.scientificamerican.com/neuroscience/feed/
# 404/redirect as of 2026 – FDA RSS endpoint moved or removed
# FDA PR | https://www.fda.gov/about-fda/contact-fda/stay-informed/rss-feeds/press-releases/rss.xml
 
# company updates
Neuralink | https://neuralink.com/updates/
Paradromics | https://www.paradromics.com/news
Synchron | https://synchron.com/news

Prompts

Weekly triage

You are triaging research and industry links for a weekly BCI/neurotechnology briefing.
 
Use the Minto Pyramid Principle:
1. Start with the most important conclusions.
2. Group supporting points into coherent themes.
3. Keep each item factual, concise, and decision-useful.
 
Inputs:
- Keywords: {{KEYWORDS}}
- Narrative focus: {{NARRATIVE}}
- Tracked companies: {{COMPANIES}}
- Candidate items (JSON): {{ITEMS}}
 
Task:
- Evaluate only the candidate items provided in {{ITEMS}}.
- Do not invent, merge, or rewrite item identities.
- Keep original id/link/source/published_utc aligned to the same input item.
- Prioritize technical substance over hype.
 
Scoring:
- Use a normalized score in [0.0, 1.0].
- Higher score = more relevant and decision-useful for near-term execution.
- Apply time-decay prioritization across a 36-month horizon:
  - Tier 1 (0-12 months): prioritize first.
  - Tier 2 (12-24 months): include when implementation path is credible.
  - Tier 3 (24-36 months): include sparingly as watchlist context.
 
Neural-noise calibration (apply within the score):
- Favor: stronger keyword match; BCI, neural interfaces, neuroprosthetics, and related devices/trials; methods for neural/physiological time series; electrophysiology and neural decoding; BCI companies, trials, and regulation.
- Down-weight: fMRI-only or behavioral papers without electrophysiology or computational neuroscience; clinical/drug/psychiatry-only content without neural data or computational modeling.
- Heavily down-weight: microbiology, immunology, cancer, or molecular biology without neural dynamics.
 
For each selected item, provide:
- why it matters now (concise)
- one to three concrete takeaways (embedded concisely in why)
- confidence signal via source quality + implementation evidence (concise in why)
- implied tier via tags (e.g., "tier-1", "tier-2", "tier-3")
 
Output requirements:
- Return valid JSON matching the provided schema.
- ranked[].id must reference an input item id exactly.
- ranked[].score must be between 0.0 and 1.0.
- ranked[].tags should be 1-3 short tags (e.g., EEG, ECoG, BCI, methods, clinical) plus the tier tag.
- ranked[].why should be a single concise paragraph.
- Rank highest score first.
- Do not invent or alter item identities.
 
Keywords:
{{KEYWORDS}}
 
Narrative focus:
{{NARRATIVE}}
 
Tracked companies:
{{COMPANIES}}
 
Candidate items (JSON):
{{ITEMS}}

Gardener prompt (weekly)

You are curating a **global digital garden** of evergreen topic pages.
 
Below are (1) this week's weekly brief, and (2) existing topic files. Propose **create** or **update** actions.
 
Return only the JSON object; we will create or update topic files from it. Do not write to any file path.
 
Rules:
- **create**: New topic when the brief introduces a distinct theme. Use lowercase-hyphen slug. Include title, body_markdown, sources, links_to, tags.
  - When the brief mentions a **tracked company** (see list below), prefer creating a topic page for that company if one does not exist.
  - `body_markdown` must be a **fact bullet list** (`- Fact...`), not prose paragraphs. Write the actual fact bullets drawn from the brief, not a description of what to add.
- **update**: Only when the brief adds genuinely new knowledge to an existing topic. Provide slug, append_sources, optionally summary_addendum, summary_addendum_sources, and tags.
  - `summary_addendum` must be a **fact bullet list** (`- Fact...`) when present. Write the actual fact bullets, not a description of what to add.
- Each bullet in `summary_addendum` must map to exactly one source URL in `summary_addendum_sources` (same order, same length).
- Use source attribution with markdown footnotes, e.g. `[^1]` and `[^1]: https://example.com`.
- If no new knowledge is present, do not emit an update action.
 
Tracked companies (strong candidates for new topic pages when mentioned in the brief):
{tracked_companies}
 
This week's brief (category: {topic}):
{brief_content}
 
Existing topic files (slug and preview):
{existing_topics}
 
Return **only** a single JSON object. Schema:
{{"topic_actions": [{{ "action": "create" | "update", "slug": "<slug>", "title": "<title>", "body_markdown": "<markdown>", "sources": ["url"], "links_to": ["slug"], "append_sources": ["url"], "summary_addendum": "<markdown>", "summary_addendum_sources": ["url"], "tags": ["tag"] }}]}}
Bullet examples for markdown fields:
- body_markdown: "- Fact one.\\n- Fact two."
- summary_addendum: "- New finding one.\\n- New finding two."
Omit topic_actions or use [] if nothing to do.

Round-up prompt (monthly)

You are helping an expert analyst prepare a monthly roundup for their newsletter.
 
**Use the Minto Pyramid Principle: structure the roundup to lead with the main conclusions and storylines, then organize supporting information hierarchically.**
 
Return only the **markdown body** of the roundup (no YAML frontmatter). We will add frontmatter and save the file.
Your response must be the **final roundup article**—ready to publish. Do not output a plan, outline, or description of what you will write.
Do not use meta-language (e.g. "I will…", "This section will…"). Write the roundup itself: concrete conclusions and storylines drawn only from the weekly briefs.
 
Generate a monthly roundup from the following weekly briefs. Use only these briefs as your source.
 
Date range: {start_date} to {end_date}
Month: {month_name}
 
Weekly briefs:
{brief_refs}
 
Format the roundup as follows:
1. Title: "# {topic_upper} Monthly Roundup — {month_name}"
2. Date range subtitle
3. "## Introduction" — 1–2 full paragraphs summarizing the month's key storylines (actual summary prose, not one-line placeholders).
4. "## Suggested Titles" — 3–5 concrete newsletter title options (real phrases, not a description of what titles could be).
5. Sections by theme (Papers and Prototypes, Clinical and Regulatory, Companies and Funding, Emerging Themes). Each section: a summary statement then real items from the briefs (title, source/date, link, summary)—not bullet plans like "Include items on X and Y."
 
Keep content comprehensive but polished.
 

Report prompt (yearly)

 
You are helping an expert analyst prepare an annual review for their newsletter.
 
**Use the Minto Pyramid Principle: structure the review to lead with the main conclusions and storylines of the year, then organize supporting information hierarchically.**
 
Return only the **markdown body** of the review (no YAML frontmatter). We will add frontmatter and save the file.
Your response must be the **final annual review article**—ready to publish. Do not output a plan, outline, or description of what you will write.
Do not use meta-language (e.g. "I will…", "This section will…"). Write the review itself: concrete conclusions, events, and storylines drawn only from the monthly roundups.
 
Generate an annual review for the year {year}. Use only the following monthly roundups as your source. Do not invent content.
 
Monthly roundups (in chronological order):
{roundup_refs}
 
Format the review as follows:
1. Title: e.g. "# {topic_upper} Annual Review — {year}" and a date range subtitle
2. "## Introduction" — 2–4 full paragraphs with the year's main conclusions and storylines (no placeholders).
3. "## Timelines" — Chronological narrative or month-by-month highlights with real events from the roundups.
4. "## Trends" — Thematic arcs across the year with real content; use subheadings if helpful—not a list of "we could cover X, Y."
5. Optional: "## Suggested Titles" — 3–5 concrete newsletter title options (real phrases, not a description).
 
Keep content comprehensive but polished. Use only information from the attached roundups.
 

timeline ← → companies

Footnotes

1. Thanks Aristotle and Barbara Minto ↩