Research operations without losing the thread.

Hermes Research OS is a private workflow layer for literature review, bioinformatics learning, writing, academic administration, schedule control, and automation oversight. This public page shows only high-level status, project maps, and operating intent.

View project maps See workflow areas Use today

Research

Zotero, Obsidian, and Local Hermes support paper intake, source notes, reading sessions, project intake, and idea capture.

  • Project intake drafts
  • Source notes
  • Focused reading sessions

Bioinformatics Learning

A structured learning track connects wet-lab expertise with Python, R, statistics, NGS workflows, and reproducible analysis.

  • Example-first curriculum
  • Crawl-assisted term inventory
  • GitHub and Reddit tool radar
  • Math and statistics drills
  • Daily progress reviews
  • Term-driven concept map

Daily Planning

VPS Hermes, n8n, Google Calendar, and Google Tasks handle recurring briefs and review flows.

  • Morning plan
  • Restart check-in
  • Evening shutdown

Slack Handoff

Local Hermes and VPS Hermes coordinate through a controlled handoff channel with thread-only replies and mirror guard rules.

  • Handoff ID tracking
  • No verbatim echoing
  • Summary is context, not reply text
  • Slack channel readiness check
  • Automation log diagnostic

Use today

Start with a brief Check the operating status first, then choose one action instead of opening every tool.
Pick research mode When the goal is research or learning, use the research next-action flow so concrete study sessions beat generic dashboard tasks.
Run a 25-minute session Bioinformatics study starts from one core term, related terms, a data object, one math/stat line, and one validation risk.
Record or hand off Local work becomes a progress note. Calendar, task, or recurring automation candidates move through the controlled handoff route with thread-only responses.
Reply in thread

Use when the answer belongs to the current Slack discussion and no background automation is needed.

Example: confirm receipt, answer one question, or ask for one missing detail.
Create VPS handoff

Use when a local research result should become a Calendar, Task, Gmail, or n8n action.

Example: send title, date, deadline, owner, and expected action; do not send the whole source.
Summarize as context

Use when the summary helps interpretation but should not be copied as the actual reply.

Example: mark Summary as context and ask for a status update, not a restatement.

Operating loop

Capture Incoming papers, emails, ideas, and seminar notes are captured before they become tasks.
Classify Local Hermes separates research notes, learning sessions, writing work, administration, English practice, and automation issues.
Handoff VPS Hermes handles scheduled workflows, approvals, calendar checks, and task synchronization.
Review Changes are logged internally before new automation or public deployment is considered. If Slack logging fails, run the automation log diagnostic before retrying.

Reference deconstruction

The site structure borrows three public patterns: a portfolio guide index, a bioinformatics wiki term index, and a case-study review board for complex analysis workflows.

Applied component model

Instead of a marketing landing page, this page works like a compact operating manual.

System typePrivate research and automation OS
AudienceResearch operator, collaborators, and future assistants
Primary goalShow tool roles and handoff routes at a glance
Safety rulePublic status only; private execution details stay internal

Start matrix

A quick decision table replaces a long explanation.

Need Start here Next surface
Read or summarize a paper Zotero and Local Hermes Obsidian Source Note
Turn an email into a task Gmail and n8n filter Slack approval, then Tasks
Plan the day Calendar and Tasks VPS Hermes daily brief
Study bioinformatics Bioinformatics Session Research Next Action and progress note

Borrowed from technical field guides

  • Use a mental model first, before listing tools.
  • Offer a quick-start path for different user intents.
  • Keep long details behind references, logs, or private notes.
  • Show safety boundaries next to capabilities.
  • Turn each major workflow into a short guide card.

Borrowed from scientific wiki pages

  • Use structured metadata so the page is scannable.
  • Separate concept, tools, workflow, and suggested next pages.
  • Treat a broad term index as a curriculum map, not as a single article to copy.
  • Convert source pages into term relationships, short exercises, and validation notes.
  • Use comparison tables when many tools perform similar roles.
  • Keep source material distinct from interpretation.

Guide index

A Blake-style guide index turns the system into routes. Each guide starts with one action, one source of truth, and one safety boundary.

Literature guide

Move from Zotero metadata and PDFs into one Obsidian Source Note, then decide whether the paper becomes a project, background source, or archive item.

start: paper intake

Bioinformatics guide

Start from one term, one data object, one validation risk, and one tiny example. Do not install a tool until its input, output, and report are understood.

start: term session

Writing guide

Draft in Markdown, polish in Notion when useful, and keep citation-critical material tied back to Zotero and source notes.

start: outline

Admin guide

Extract sender, deadline, amount, date, location, attachment, and required action before creating a task or calendar item.

start: structured fields

Automation guide

Let n8n handle repeated triggers, VPS Hermes handle scheduled checks, and Slack handle approval. Local Hermes should not run always-on automation.

start: approval path

Handoff guide

Use the handoff channel when desktop context needs server automation. Reply in thread, avoid copied prompts, and log meaningful changes.

start: handoff id

Term wiki surface

An IncoDOM-style wiki surface keeps learning scannable: hot terms, recent study additions, and suggested next concepts stay separate from full notes.

Hot terms

  • NGSFASTQ, quality score, alignment, coverage, variant calling.
  • RNA-seqCount matrix, normalization, differential expression, FDR.
  • Single-cellAnnData, Seurat object, clustering, marker genes, batch effect.
  • AI biologyEmbedding, foundation model, denoising, validation split.

Suggested next pages

  • After FASTQRead quality, adapter trimming, MultiQC report, mapping rate.
  • After FDRp-value, multiple testing, volcano plot, effect size.
  • After PCABatch effect, metadata, outlier review, variance explained.
  • After dockingBinding site, scoring function, control ligand, validation risk.

Recent additions pattern

  • SourceRecord where the term came from before expanding it.
  • ExerciseAttach one toy example or one small public dataset.
  • RiskName the most likely misunderstanding or false confidence point.
  • NextCreate one follow-up term, not a broad new curriculum branch.

Case study review board

A Vibe Genomics-style case board makes ambitious workflows reviewable without turning them into unsafe protocols or private-data demos.

1. GoalState the biological or operational question in one sentence before choosing tools.
2. Data objectName the file, table, matrix, or report that carries the evidence.
3. Analysis routeMap the smallest safe workflow from input to output, including one fallback route.
4. ValidationShow threshold, denominator, expected control, and what would falsify the result.
5. Review outputStore the result as a note, task, or project brief with private details kept off the public page.

Bioinformatics concept map

The learning system now uses a term-first map: every session connects one core term to data objects, analysis workflow, math/statistics, wet-lab interpretation, and AI modeling.

Priority index

Terms are ranked by how often they appear in real bioinformatics work and how much confusion they remove.

P0 Core languageFASTQ, BAM, VCF, count matrix, metadata, normalization, p-value, FDR, PCA.
P1 Workflow termsRead quality, coverage, mapping, reference genome, quantification, differential expression, variant calling.
P2 Expansion termsScanpy, AnnData, ASV, OTU, AlphaFold, docking, MD simulation, RDKit, pathway and network analysis.
P3 Frontier termsAlphaGenome, AlphaMissense, embeddings, loss functions, denoising, protein language models, generative models, and AI workflow review.

Term-to-workflow chain

Each study note should be small enough to finish, but connected enough to become reusable research memory.

Core termPick one term, such as coverage, normalization, count matrix, or denoising.
Related termsAttach two to five terms that normally travel with it.
Data objectIdentify the file, table, plot, or matrix where the term appears.
Math/stat linkState the intuition, not a formula dump.
Wet-lab or AI linkExplain how the term changes experimental judgment or model validation.

Vibe Genomics as a case study

Vibe Genomics is treated as a workflow example, not as a protocol to reproduce. The useful structure is goal, raw data, secondary analysis, variant calling, validation, privacy, cost, and report.

Validation ladder

Every bioinformatics result is read with its threshold and denominator. A score such as GQ, FDR, coverage, or accuracy is only useful when the selected subset and validation source are visible.

IncoDOM-wide term graph

The learning map uses the wider IncoDOM index across NGS, RNA-seq, single-cell, microbiome, structure, statistics, and AI terms. Docking is only one example inside the structure track.

Source synthesis rule

IncoDOM provides term signals, Reddit provides study-order signals, Biohackers provides frontier risk signals, and Vibe Genomics provides the report pattern. None of these are copied as-is.

Crawl-assisted term inventory

The local curriculum keeps a generated inventory of IncoDOM terms and clusters them into P0/P1/P2/P3 study priority. A refresh tool updates the list before new study sessions are planned.

GitHub and Reddit tool radar

Popular repositories and recurring community advice are converted into a read-first tool map. High stars do not mean immediate installation; every tool is tied to file objects, reports, and validation risks first.

Learning source lanes

Learning materials are grouped into sequencing basics, qPCR/statistics, math for machine learning, structure and docking, imaging analysis, and LNP/AI modeling. Each session uses one short source segment, then verifies context before citation.

Safe learning boundary

Public datasets, toy examples, and already-approved local materials come first. Personal genome interpretation, clinical claims, raw protocol execution, and private data exposure remain outside the public surface.

Slack channel readiness

When a Hermes bot does not answer or local logging fails, a read-only readiness check distinguishes required handoff membership from optional direct-posting channels.

Reproducibility barrier

Study notes separate hard blockers from soft blockers. Missing reference data, wrong tool versions, low memory, unclear sample IDs, and retry notes become part of the learning artifact.

Project connection maps

Each map shows the public-safe structure of a workflow: where information starts, which Hermes or n8n layer handles it, and where review or knowledge storage happens.

Daily planning and task control

Recurring schedule and task review without exposing private calendar details.

Always-on
Calendar + TasksEvents, due dates, task lists, and current day context.
n8n + VPS HermesScheduled checks, brief generation, and approval routing.
Slack reviewMorning plan, restart check-in, and shutdown prompt.
Owner
VPS Hermes
Boundary
No personal event data on this page.

Literature intake

Research papers move from collection into structured notes and review-ready summaries.

Local-first
Zotero + PDFsPaper metadata, attachments, citations, and reading source files.
Local HermesReads, classifies, drafts source notes, and prepares extraction tasks.
Obsidian + NotionLong-term Markdown notes and optional polished working summaries.
Owner
Local Hermes
Boundary
Original files stay private and user-controlled.

Important mail to actionable task

Email signals become concise review requests before any task is created.

Approval
GmailSender, subject, deadlines, dates, location, and core message fields.
n8n filterExtracts structure and routes likely action items to Hermes.
Hermes + SlackImportance judgment, short summary, approve or ignore.
Owner
n8n + VPS Hermes
Boundary
Secrets and webhook paths stay internal.

Research project operating system

Project ideas, experiments, writing, and admin work stay organized across tools.

Knowledge
Ideas + recordsLab context, seminar notes, literature leads, and admin requests.
Local HermesClassifies into research, writing, admin, English, or automation tracks.
Obsidian coreProject notes, source notes, decisions, logs, and next actions.
Owner
Local Hermes
Boundary
External submissions need user confirmation.

Bioinformatics learning loop

Books and examples are converted into practical analysis skills and daily progress.

Learning
Terms + tool radarCore terms, selected source segments, toy data, GitHub/Reddit tool signals, and wet-lab questions.
Bioinformatics SessionTurns one term into a 25-minute coding, statistics, interpretation, and validation exercise.
Research Next ActionKeeps the next study task visible before daily progress summaries and polished notes.
Owner
Local Hermes, reviewed by VPS flow
Boundary
Personal learning detail remains private.

Validation and reproducibility loop

Public or toy analyses become stronger when each result includes its threshold, denominator, validation source, and retry notes.

Quality
Metric + thresholdGQ, FDR, coverage, accuracy, or another score with a visible cutoff.
Denominator + validationShow what was counted, what was missed, and what external or toy reference checked it.
Barrier + retry logSeparate hard blockers from soft blockers and turn failed attempts into next-session checks.
Owner
Local Hermes
Boundary
No personal genome, clinical claim, or private dataset on the public surface.

Local-to-VPS handoff

Desktop research work can request always-on automation without sharing local internals or turning request text into a copied reply.

Bridge
Local HermesPrepares a scoped request with target, expected response, context, and a mirror guard.
Slack handoffThread-only handoff with receipt confirmation; the summary is context, not reply text.
VPS Hermes + n8nRuns approved background automation and posts status updates instead of echoing prompts.
Owner
Local and VPS Hermes
Boundary
No direct server changes without approval; no duplicated top-level replies.

System overview

InputsEmail, calendar, tasks, papers, PDFs, notes, browser pages, and ideas.
Automationn8n handles repeatable triggers, approvals, and scheduled checks.
AgentsVPS Hermes stays online. Local Hermes handles desktop research context.
KnowledgeObsidian is the long-term Markdown source. Notion is for polished working views.
ReviewSlack is the control surface for confirmations, logs, and human decisions.
Public boundary

This page must not expose tokens, webhook secrets, private file paths, internal execution links, or personal schedule details.

Internal source of truth

Operational details live in private notes, internal chat logs, and the automation runtime. This page is only a public doorway.