Coding & Dev Tools

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use when identifying cancer-specific genetic vulnerabilities, finding synthetic lethal interactions, checking whether a gene is essential in given cell lines, or validating oncology drug targets. Part of the AlterLab Academic Skills suite.

Query gnomAD (Genome Aggregation Database) for population allele frequencies and gene constraint scores (pLI, LOEUF) reflecting loss-of-function intolerance. Use when checking how common a variant is across populations, filtering rare-disease candidate variants, assessing variant pathogenicity, or identifying loss-of-function intolerant genes. Part of the AlterLab Academic Skills suite.

Query NCBI Gene via the E-utilities and Datasets APIs, searching by gene symbol or Gene ID and retrieving gene information (RefSeqs, GO terms, genomic locations, associated phenotypes) including batch lookups. Use when resolving gene symbols to IDs, annotating gene lists, or pulling functional and positional gene metadata for downstream analysis. Part of the AlterLab Academic Skills suite.

Process-based discrete-event simulation in Python with SimPy — processes, queues, shared resources, and time-based events. Use when simulating systems where entities contend for shared resources over time, such as manufacturing systems, service operations, network traffic, or logistics. Part of the AlterLab Academic Skills suite.

Symbolic mathematics in Python with SymPy — solve equations algebraically, perform calculus (derivatives, integrals, limits), manipulate algebraic expressions, work with symbolic matrices, and generate executable code from formulas. Use when exact symbolic results are needed rather than numerical approximations, or for physics, number-theory, and geometry computations involving variables and parameters. Part of the AlterLab Academic Skills suite.

Run fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, AlphaFold structures, Enrichr enrichment, and more. Use for quick interactive lookups of genes, sequences, structures, or pathways — for batch processing or advanced BLAST use biopython, for multi-database Python workflows use bioservices. Part of the AlterLab Academic Skills suite.

Designs courses and teaching materials using backward design (Wiggins & McTighe), constructive alignment (Biggs), and Bloom's taxonomy alignment, generating rubrics, formative and summative assessments, syllabi, lesson plans, inclusive-pedagogy guidance, and online/hybrid course architecture. Use when the request mentions course design, syllabus, learning outcomes, rubric, assessment design, lesson plan, backward design, constructive alignment, Bloom's taxonomy, curriculum mapping, course redesign, inclusive pedagogy, hybrid course, or online course design. Part of the AlterLab Academic Skills suite.

Builds, simulates, and runs quantum circuits with Cirq, Google Quantum AI's framework for NISQ hardware, noise-aware low-level circuit design, and noise characterization. Use when targeting Google Quantum AI processors (Sycamore/Weber), designing noise-aware NISQ circuits, or running characterization experiments (randomized benchmarking, XEB). For IBM Quantum hardware and Qiskit Runtime prefer alterlab-qiskit; for gradient-trained quantum ML and hybrid quantum-classical models prefer alterlab-pennylane; for open-system Lindblad/master-equation dynamics prefer alterlab-qutip. Part of the AlterLab Academic Skills suite.

Query Google Data Commons for public statistical data aggregated from global sources, resolving geographic entities and pulling time-series statistics. Use when working with demographic data, economic indicators, health statistics, or environmental data — population counts, GDP figures, unemployment rates, disease prevalence — or when resolving places to DCIDs and exploring relationships between statistical entities. Part of the AlterLab Academic Skills suite.

Simulates open quantum systems with QuTiP, the Quantum Toolbox in Python, solving Lindblad master equations (mesolve), Monte Carlo trajectories (mcsolve), and unitary dynamics (sesolve). Use when studying master-equation or Lindblad dynamics, decoherence, dissipation, quantum optics, cavity QED, or open-system time evolution. NOT for circuit-based quantum computing or hardware execution — for IBM Quantum circuits prefer alterlab-qiskit, for Google Quantum AI or NISQ circuits prefer alterlab-cirq, and for gradient-trained quantum ML prefer alterlab-pennylane. Part of the AlterLab Academic Skills suite.

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against ontologies (genes, cell types, diseases, tissues), tracking data lineage and computational workflows, building data lakehouses, or wiring integrations with Nextflow, Snakemake, W&B, or MLflow. Part of the AlterLab Academic Skills suite.

Builds, transpiles, and runs quantum circuits with Qiskit, IBM's quantum computing framework, including Qiskit Runtime primitives (Sampler/Estimator), circuit transpilation, and error mitigation on IBM Quantum hardware. Use when targeting IBM Quantum backends, transpiling circuits, running Runtime sessions or batches, or applying resilience/error mitigation. For Google Quantum AI hardware and NISQ circuits prefer alterlab-cirq; for gradient-trained quantum ML and hybrid quantum-classical models prefer alterlab-pennylane; for open-system Lindblad/master-equation dynamics prefer alterlab-qutip. Part of the AlterLab Academic Skills suite.

Run differential gene expression analysis on bulk RNA-seq count matrices with PyDESeq2, the Python port of DESeq2 — size-factor normalization, dispersion estimation, Wald tests, FDR (Benjamini-Hochberg) correction, and volcano/MA plots. Use when identifying differentially expressed genes between conditions from raw bulk RNA-seq counts. Part of the AlterLab Academic Skills suite.

Computes mass-spectral similarity and identifies compounds for metabolomics with matchms — comparing mass spectra, scoring similarity (cosine, modified cosine), and searching spectral libraries to annotate unknowns. Use when matching MS/MS spectra, identifying metabolites, or library searching; for full LC-MS/MS proteomics pipelines use pyopenms. Part of the AlterLab Academic Skills suite.

Applies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, and molecular complexity metrics for compound prioritization and library cleanup. Use when filtering or triaging a compound library, flagging PAINS or reactive groups, or assessing drug-likeness of candidate molecules. Part of the AlterLab Academic Skills suite.

Drafts attorney-supervised, state-compliant U.S. Advance Health Care Directives that appoint health care agents, resolve the HIPAA access gap, and record clinically usable treatment preferences. Enforces state-law verification for execution formalities, statutory forms, and special limitations. Addresses adversarial risks from family disputes and institutional challenges. Use when drafting advance directives, health care proxies, living wills, health care powers of attorney, HIPAA medical authorizations, or end-of-life planning documents.

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Drafts a Proprietary Information and Inventions Agreement (PIIA) for employment or consulting relationships. Covers confidentiality, invention assignment with state-law carve-outs, DTSA immunity notice, and prior inventions disclosure. Trigger when onboarding employees/consultants, drafting IP assignment agreements, or creating confidentiality and invention assignment contracts.

Drafts an IRC §2702-compliant Qualified Personal Residence Trust agreement with safe harbor provisions under Rev. Proc. 2003-42 and Treas. Reg. §25.2702-5(c). Generates trust instrument, signature/notarization blocks, property exhibit, beneficiary schedule, and post-execution checklist. Use when drafting a QPRT for estate planning clients transferring a personal or secondary residence with a retained occupancy term to reduce gift tax valuation.

Drafts a Subordination, Non-Disturbance, and Attornment Agreement (SNDA) for commercial real estate. Extracts key terms from lease and loan documents, structures tri-party protections balancing landlord, tenant, and lender interests. Trigger when new financing or refinancing requires subordinating tenant leases to lender liens, drafting non-disturbance protections, or preparing tri-party SNDA agreements.

Drafts a Stormwater Pollution Prevention Plan (SWPPP) compliant with 40 CFR Part 122, EPA Construction General Permit (CGP), and applicable state NPDES requirements for construction projects disturbing one or more acres. Use when drafting SWPPPs, construction stormwater permits, erosion control plans, NPDES compliance documents, or BMP selection memoranda.

Drafts SEC Form D Notice of Exempt Offering for EDGAR filing under Regulation D. Captures issuer details, related persons, offering structure, exemption basis (Rule 504, 506(b), 506(c)), sales compensation, and use of proceeds. Use when filing Form D, preparing an exempt offering notice, or handling Regulation D compliance for unregistered securities.

Drafts ITAR Technology Control Plans (TCPs) for managing USML defense articles and technical data under 22 CFR Parts 120-130. Covers DDTC registration, classification, access controls, deemed export prevention, secure handling, training, audits, and incident response. Use when creating or updating export control compliance plans, technology control plans, or DDTC submission documents.

Compares two document versions and produces AI-powered redline analysis with structured change summaries, risk flags, and clause-by-clause breakdowns. Use when the user mentions "redline", "compare documents", "what changed", "version comparison", "contract diff", "track changes", or needs to understand differences between document versions.

Advises on corporate law matters including entity formation, governance, finance, M&A, securities, venture capital, non-profits, and dissolution. Use when drafting governance documents, structuring transactions, selecting entity types, or navigating fiduciary duties and corporate formalities.

Drafts IRS Form 1023 applications for Section 501(c)(3) tax-exempt recognition. Analyzes organizing documents, finances, governance, and operations to produce a complete, internally consistent application. Use when forming non-profits, applying for tax-exempt status, seeking 501(c)(3) recognition, or preparing exemption applications.

Drafts a state-compliant Last Will and Testament covering declarations, revocation of prior instruments, specific bequests, residuary disposition, guardian nominations, fiduciary appointments, and execution formalities. Conducts structured intake on family structure, asset inventory, fiduciary nominees, and existing estate plan documents. Coordinates with trusts, beneficiary designations, and non-probate transfers. Use when drafting wills, testamentary documents, pour-over wills, codicils, or estate planning instruments involving testamentary dispositions.

Drafts U.S. HACCP plans for food production under FDA or USDA regimes. Triggers on requests involving HACCP plans, food safety plans, hazard analysis, critical control points, FSMA compliance, seafood HACCP (21 CFR 123), or meat/poultry HACCP (9 CFR 417).

Drafts SEC-compliant prospectuses for U.S. securities offerings (IPOs, follow-ons, private placements). Structures cover page, risk factors, use of proceeds, business description, MD&A, financials, and offering terms against uploaded company documents and EDGAR comparables. Use when preparing a Form S-1, S-11, offering circular, or any primary disclosure document for a public or private issuance.

Drafts Qualified Domestic Relations Orders (QDROs) compliant with ERISA §206(d)(3) and IRC §414(p) to divide retirement benefits in divorce. Covers defined benefit pensions, 401(k)s, and defined contribution plans with plan-specific division formulas and alternate payee protections. Use when drafting QDROs, dividing retirement assets post-judgment, or preparing domestic relations orders for plan administrator review.

Navigates regulatory compliance, government relations, and administrative law across financial services, healthcare, environmental, FDA, privacy, energy, government contracts, trade, and securities domains. Use when handling agency interactions, compliance programs, enforcement defense, rulemaking comments, or administrative proceedings.

Produces legally focused summaries of California Environmental Impact Reports (EIRs) under CEQA and federal Environmental Impact Statements (EISs) under NEPA. Extracts impacts, mitigation, alternatives, and compliance vulnerabilities. Reflects the 2025 CEQA reforms (AB 130 + SB 131) and the April 2025 rescission of CEQ NEPA implementing regulations. Triggers on requests for EIR/EIS summary, CEQA/NEPA review, mitigation analysis, alternatives analysis, cumulative impacts review, permit challenge prep, or administrative record review.

Drafts a Receipt of Franchise Disclosure Document proving FTC Franchise Rule compliance under 16 C.F.R. § 436. Produces an execution-ready acknowledgment with franchisee identification, delivery date, FDD version, exhibit inventory, and dual signature blocks. Use when creating FDD receipts, franchise disclosure acknowledgments, or Item 19 FPR attestations.

Drafts a Motion for Judgment Notwithstanding the Verdict (JNOV) under FRCP 50(b) or state equivalents, with alternative new-trial request. Builds element-by-element evidentiary insufficiency arguments using transcript citations and preserves the appellate record. Use when drafting JNOV motions, post-trial motions, renewed judgment as a matter of law, or challenging jury verdicts for insufficient evidence.

Drafts ASTM E1527-21 environmental site assessment reports under 40 CFR Part 312. Classifies RECs, CRECs, and HRECs to establish all appropriate inquiries for CERCLA liability protection. Trigger when the user requests a Phase I ESA, environmental site assessment, recognized environmental conditions analysis, ASTM E1527 compliance, or environmental due diligence for property transactions or lending.

Drafts a Request for Equitable Adjustment (REA) for U.S. federal government contracts under FAR provisions. Enforces element-driven cost/schedule narratives, FAR Part 31 cost structures, FAR 52.233-1 certification, and contemporaneous evidence marshaling. Use when a contractor seeks contract modification relief due to government-directed changes, differing site conditions, defective specifications, or government-caused delays.