Research

Estimates time-scaled phylogenies, molecular-clock rates, effective reproduction number R_e, and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict/relaxed clocks; coalescent, Bayesian-Skyline, Skygrid, Birth-Death-Skyline, and sampled-ancestor priors; structured coalescent via MASCOT). Covers root-to-tip clock QC via TempEst, date-randomisation tests, recombination masking via Gubbins/ClonalFrameML before clock inference for recom...

Assigns isolate identity at the right resolution for the question -- ANI/Mash species triage, 7-locus MLST historical comparability, cgMLST/wgMLST outbreak resolution (chewBBACA, BIGSdb, Ridom SeqSphere, EnteroBase HierCC), in-silico serotyping (SISTR/SeqSero2 Salmonella, SerotypeFinder E. coli, Kaptive Klebsiella, SeroBA pneumococcus, spa+SCCmec S. aureus), and lineage callers (TB-Profiler/Mykrobe barcode for MTBC, Pangolin + Nextclade for SARS-CoV-2, PopPUNK GPSC for S. pneumoniae). Use whe...

> [!definition] **Recurrent Constituent Skill** > A recurrent constituent skill is a component of complex cognitive performance executed in the same way regardless of context, governed by automated rules and procedures. It falls under [[cognitive-architecture]], where it is distinguished from non-recurrent skills that require reasoning and problem-solving adaptable to specific contexts. > [!attention] **Boundary** > This concept excludes skills that vary across contexts (non-recurrent constit...

Technical spikes, API feasibility studies, dependency investigations, and performance risk assessments.

When the user wants to find, qualify, and build a list of prospects to reach out to — across B2B SaaS, general B2B, or local small businesses. Also use when the user mentions "prospecting," "build a prospect list," "find prospects," "find leads," "lead gen list," "find SaaS companies that," "find B2B companies," "find local businesses," "ICP-fit accounts," "who should we go after," "outbound list," "target account list," "find clients near me," "businesses without websites," "prospect researc...

When the user wants to optimize post-signup onboarding, user activation, first-run experience, or time-to-value. Also use when the user mentions "onboarding flow," "activation rate," "user activation," "first-run experience," "empty states," "onboarding checklist," "aha moment," "new user experience," "users aren't activating," "nobody completes setup," "low activation rate," "users sign up but don't use the product," "time to value," or "first session experience." Use this whenever users are...

Strip AI-writing tells AND make prose clearer, stronger, and more concise. Use when editing or reviewing text to sound natural and human, or when writing or editing any prose humans will read: documentation, commit messages, pull request descriptions, error messages, UI copy, help text, comments, reports, or explanations. Detects and fixes AI patterns (inflated symbolism, promotional language, superficial -ing analyses, vague attributions, em dash overuse, rule of three, AI vocabulary words, ...

When the user wants to research, profile, or analyze competitors from their URLs. Also use when the user mentions 'competitor profile,' 'competitor research,' 'competitor analysis,' 'profile this competitor,' 'analyze competitor,' 'competitive intelligence,' 'competitor deep dive,' 'who are my competitors,' 'competitor landscape,' 'competitor dossier,' 'competitive audit,' or 'research these competitors.' Input is a list of competitor URLs. Output is structured competitor profile markdown fil...

When the user wants to plan, design, or implement an A/B test or experiment, or build a growth experimentation program. Also use when the user mentions "A/B test," "split test," "experiment," "test this change," "variant copy," "multivariate test," "hypothesis," "should I test this," "which version is better," "test two versions," "statistical significance," "how long should I run this test," "growth experiments," "experiment velocity," "experiment backlog," "ICE score," "experimentation prog...

Append a Decision Log entry, rewrite Current State, or resolve an Open Question on the active task note in Channing's vault. Use when the user says "log this decision", "update the task note", "add to the decision log", "current state has changed", "answer to the open question is X", asks for a prompt to continue the task in a new session, or otherwise asks to capture, record, or log something about the task being worked on.

Keep an Obsidian vault project's Topics folder up to date from its Tasks (and Events), and graduate evergreen Topics into shared domain folders. Use when the user wants to refresh or maintain a project's topics, find missing or new topics, add task-to-topic backlinks, audit topic interlinking, fix orphan topics, resolve duplicate/alias collisions, convert a dated retrospective into a Task, or promote a cross-cutting Topic out of the project into a domain folder (graduation). Assumes each proj...

Resolve Channing's Obsidian task context and route the requested action. Use when the user references a task note or a Jira/GitHub issue tracked by one, resumes task work, or asks to capture task state.

Append a Decision Log entry, rewrite Current State, or resolve an Open Question on the active task note in Channing's vault. Use when the user says "log this decision", "update the task note", "add to the decision log", "current state has changed", "answer to the open question is X", asks for a prompt to continue the task in a new session, or otherwise asks to capture, record, or log something about the task being worked on.

Keep an Obsidian vault project's Topics folder up to date from its Tasks (and Events), and graduate evergreen Topics into shared domain folders. Use when the user wants to refresh or maintain a project's topics, find missing or new topics, add task-to-topic backlinks, audit topic interlinking, fix orphan topics, resolve duplicate/alias collisions, convert a dated retrospective into a Task, or promote a cross-cutting Topic out of the project into a domain folder (graduation). Assumes each proj...

Maintain a project's Research layer in an Obsidian vault — scaffold a research note from a question, spawn experiment tasks with backlinks, roll experiment findings up into the research note, sync open questions, and on conclusion graduate durable findings into Topics. Use when the user wants to start a piece of research, add an experiment to a research question, update a research note from its experiments, review open questions, or conclude a research question. Sibling of obsidian-topic-main...

Keep an Obsidian vault project's Topics folder up to date from its Tasks (and Events), and graduate evergreen Topics into shared domain folders. Use when the user wants to refresh or maintain a project's topics, find missing or new topics, add task-to-topic backlinks, audit topic interlinking, fix orphan topics, resolve duplicate/alias collisions, convert a dated retrospective into a Task, or promote a cross-cutting Topic out of the project into a domain folder (graduation). Assumes each proj...

Maintain a project's Research layer in an Obsidian vault — scaffold a research note from a question, spawn experiment tasks with backlinks, roll experiment findings up into the research note, sync open questions, and on conclusion graduate durable findings into Topics. Use when the user wants to start a piece of research, add an experiment to a research question, update a research note from its experiments, review open questions, or conclude a research question. Sibling of obsidian-topic-main...

Use when checking the mathematics of a paper rather than its claims — verifying a theorem's proof, an algebraic derivation, a bound, or an appendix full of lemmas. Triggers on "check this proof", "verify the derivation", "is Lemma 3 correct", "does the algebra work", a paper directory containing theorem/proof environments, or a referee asking whether a mathematical argument holds.

Use when checking a .bib or reference list for incorrect or fabricated entries — wrong titles, invented co-authors, wrong DOI/volume/pages, preprints cited instead of the published venue, or references that do not exist. Triggers on "verify this bibliography", "check my references", "are these citations real", a refs.bib alongside a paper, or suspicion that a bibliography was LLM-generated.

Use when working on a Digital Research Alliance of Canada (DRAC, Alliance, formerly Compute Canada) HPC cluster such as Narval, Rorqual, Fir, TamIA, Killarney, Vulcan, Nibi or Trillium — including ssh to *.alliancecan.ca failing with "Permission denied (keyboard-interactive)", sinfo/sacctmgr reporting "command not found" over ssh, submitting or monitoring Slurm jobs (sbatch, squeue, sacct, job arrays, GPU allocations), choosing between clusters, staging data into /project or /scratch, or jobs...

Use when finding related work a draft may have missed, checking whether a contribution has already been published, or mapping what a research area looks like. Triggers on "what related work did we miss", "has this been done before", "is our contribution novel", "map this field", "survey the literature on X", or a paper draft whose related-work section looks thin.

Use when planning, budgeting, submitting or resuming a multi-job experiment campaign on a Slurm/HPC cluster — sizing walltime, shaping jobs and arrays, deciding what to submit first, or after a job hit its walltime, produced no results, silently ran the wrong configuration, or got the wrong number of GPUs.

Use when asked to review, critique, or assess an academic paper from its LaTeX sources — including pre-submission critique of a student's or collaborator's draft, or a referee report for a venue. Also when the only artifact is a blind PDF with no sources. Triggers on "review this paper", "assess the paper", "read my student's draft", "referee report", a directory holding main.tex/refs.bib/*.cls, a submission PDF to review, or a request to check a paper's claims, figures, bibliography or math.

Use when a proof or derivation needs to be made explicit step by step — expanding a paper's algebra for a reader without formal mathematical training, producing a worked companion document, or establishing whether a derivation can be justified at all. Triggers on "explain this derivation", "walk me through this proof", "expand the algebra", "I can't follow this step", "make this readable for a non-mathematician", or a referee needing to show why a step does not follow.