Ongoing Projects

Projects in progress, including open-source tools and working documents.

Strategy

Annual Planning

A project overview built around the coming year’s decisions: what existing evidence can tell us, what else we need to learn, and where modeling or critical thinking could…

GenAI

synpmx

Generating realistic synthetic PK/PD datasets, so that analysis workflows, teaching material, and tooling can be developed and shared without exposing real clinical data.

Scoping a project using Agentic Engineering Framework

Writing the requirements and the checks before commissioning an agent to build inside them: what is already in place here, how the initial spec gets written, how the work…

Validation Tools Taxonomy

Pharmacometrics

The kinds of validation a pharmacometrics activity needs, from the question through data, code, model and predictions to how the answer was used; the checklists that exist…

Second Brain

A reminder to set up an AI-searchable store of past work, fed first from Google Drive and this site, with the purpose still to scope: which sources go in, which tool, and…

Pharmacometrics modeling skills

Pharmacometrics

Folding published references and internal modeling guidance into a few AI skill files for building and evaluating pharmacometrics models, kept on GitHub for anyone to…

PMX internships in the age of AI and agentic coding

Pharmacometrics

An intern with an AI assistant can do more than a 2020 intern, and so can the mentor alone. What the mentor and the intern should each expect, where the mentor’s time still…

The half-life of facts in immunology

Immunology and T-cell engagers

Can AI estimate how long a fact in immunology survives, or how far immunologists disagree? A first test on how B cell subsets are defined by their markers, building on a…

Pharmacometrics

Validation Tools Taxonomy

Pharmacometrics

The kinds of validation a pharmacometrics activity needs, from the question through data, code, model and predictions to how the answer was used; the checklists that exist…

Pharmacometrics modeling skills

Pharmacometrics

Folding published references and internal modeling guidance into a few AI skill files for building and evaluating pharmacometrics models, kept on GitHub for anyone to…

PMX internships in the age of AI and agentic coding

Pharmacometrics

An intern with an AI assistant can do more than a 2020 intern, and so can the mentor alone. What the mentor and the intern should each expect, where the mentor’s time still…

Exposure metric guide

Pharmacometrics

Turning the Choosing a PK Metric R Markdown file into a PMX Tools page: what the source holds, what changed in the conversion, and what is left.

Sizing studies

Pharmacometrics

How many patients a Phase 1/2 expansion cohort needs to characterize a dose-response or biomarker-response relationship: Frank Harrell’s rule of thumb, Richard Riley’s…

Model Based TDP

Pharmacometrics

Can an integrated dose-response model improve a decision requiring at least 80% biomarker decline in 90% of patients? A literature review, reproducible comparisons for three…

Logistic regression for dose finding

Pharmacometrics

Picking a method, glm against Bayesian alternatives, and picking the right diagnostics for a fitted model. Both drafts, to be extended as time allows.

Publishing the 3 RECIST Lesion Model

Pharmacometrics

Writing up a 2011 ASCO poster as a citable preprint: a model of the RECORD-1 everolimus trial in renal cell carcinoma that describes target, nontarget and new lesions…

Create Videos for Intro to PK and PD slides

Pharmacometrics

Correcting the errors a colleague found in the Introduction to Fundamental PK Concepts and PD Concepts tutorial decks, then recording a video to go with each.

Immunology and T-cell engagers

Faster first-in-human TCE studies

Immunology and T-cell engagers

Three ways to reach a biologically active dose sooner in a first-in-human T-cell engager study: escalating within a patient, finding the dose in healthy volunteers first…

T-cell engagers and target-mediated drug disposition

Immunology and T-cell engagers

T-cell engagers are dosed far below the amount needed to saturate CD3, so the sharp concentration drop of target-mediated drug disposition should be the usual sight and is…

TCE-CRS-tolerance

Immunology and T-cell engagers

Cytokine release syndrome risk often falls as step-up doses rise. Can the published epcoritamab tolerance model explain that, and can it be fit to publicly available data…

One-page TCE dose-finding strategy

Immunology and T-cell engagers

A T-cell engager program owes twenty-one dose and regimen decisions and has nowhere that holds the list. One landscape page that does: where each decision stands, when it is…

ITP-PK-Platelet

Immunology and T-cell engagers

Can a model of pharmacokinetic and platelet-count data for a B-cell depleting agent, fit to a small dose escalation and expansion study in immune thrombocytopenia, select…

imm-bcell-plasma-cause

Immunology and T-cell engagers

Which autoimmune diseases and patients depend on B cells or plasma cells? Evidence for CD19, CD20 and BCMA targeting, a disease ranking, and what rituximab response or…

B cell reset in autoimmune diseases

Immunology and T-cell engagers

What returns after B cell depletion, how to measure it, and whether immunophenotypes and other biomarkers predict lasting remission. Clinical evidence and a proposed…

imm-biopsy

Immunology and T-cell engagers

How well peripheral blood B cells track tissue B cells, and whether a biopsy in one tissue describes depletion and recovery in another. Paired human observations, sampling…

B-cell indirect-response estimation

Immunology and T-cell engagers

Why the EC50 of a B-cell depleting antibody is so hard to estimate: where the information separating Emax from EC50 lives, what the published models found, and what a study…

The half-life of facts in immunology

Immunology and T-cell engagers

Can AI estimate how long a fact in immunology survives, or how far immunologists disagree? A first test on how B cell subsets are defined by their markers, building on a…

Immune biomarkers and infection risk

Immunology and T-cell engagers

Neutrophils, B cells and immunoglobulins are measured at nearly every visit on therapies that deplete them. Can their time courses, pooled across many studies, predict which…

Archive

Projects that are no longer relevant are on the archive page. They keep their pages and their URLs.