Tootfinder

@… for the record I have never dual published a package. When 11ty swapped to ESM we went all-in on ESM with Node 18 and it has worked fine.

TopoBind: Multi-Modal Prediction of Antibody-Antigen Binding Free Energy via Sequence Embeddings and Structural Topology
Ciyuan Yu, Hongzong Li, Jiahao Ma, Shiqin Tang, Ye-Fan Hu, Jian-Dong Huang
https://arxiv.org/abs/2508.19632

TopoBind: Multi-Modal Prediction of Antibody-Antigen Binding Free Energy via Sequence Embeddings and Structural Topology
Predicting the binding free energy between antibodies and antigens is a key challenge in structure-aware biomolecular modeling, with direct implications for antibody design. Most existing methods either rely solely on sequence embeddings or struggle to capture complex structural relationships, thus limiting predictive performance. In this work, we present a novel framework that integrates sequence-based representations from pre-trained protein language models (ESM-2) with a set of topological f…

TL;DR:🧵
Today I lost 2 hours because TypeORM ESM NestJS is a fragile combo when it comes to migrations.
No migration:status.
No ESM-compatible CLI.
No schema awareness.
Class name must match filename (with timestamp!).
So I wrote my own migration-status.ts script to compare database state with the migration folder.
Lesson: if you need INSERT INTO "schema"."table", don’t forget the schema.
ORMs give you boilerplate — and tra…

Day#10 Migrations vs Developer: A story of friction
Today was supposed to be a calm day. I just wanted to add a single value to a lookup table using a TypeORM migration. Two hours later, I ...

PFMBench: Protein Foundation Model Benchmark
Zhangyang Gao, Hao Wang, Cheng Tan, Chenrui Xu, Mengdi Liu, Bozhen Hu, Linlin Chao, Xiaoming Zhang, Stan Z. Li
https://arxiv.org/abs/2506.14796

PFMBench: Protein Foundation Model Benchmark
This study investigates the current landscape and future directions of protein foundation model research. While recent advancements have transformed protein science and engineering, the field lacks a comprehensive benchmark for fair evaluation and in-depth understanding. Since ESM-1B, numerous protein foundation models have emerged, each with unique datasets and methodologies. However, evaluations often focus on limited tasks tailored to specific models, hindering insights into broader generali…

adding more WebC ESM support https://github.com/11ty/webc/pull/229

Day 3 2/2
2. Enabling API documentation with Swagger.
I integrated Swagger into the backend (NestJS v10, ESM, Turbo monorepo), using `@nestjs/swagger@7` to match our current framework version.
The docs are now live at `/api/docs`, fully aligned with our global `ValidationPipe` and `AllExceptionsFilter` — ensuring consistent validation and error responses.
Next: annotate DTOs, describe endpoints properly, and restrict access.

🇺🇦 #NowPlaying on BBCRadio3's #ThroughTheNight
Robert Schumann & Esmé Quartet:
🎵 String Quartet no 3 in A, op 41 no 3
#RobertSchumann #EsméQuartet

Day 3 1/2
TL;DR:
Added global `ValidationPipe` and unified `AllExceptionsFilter` in NestJS. API errors now follow a consistent format: `{ statusCode, error, message, code, details }`.
Today’s work focused on:
1. Standardizing input validation and error handling in the backend of the insurance sales network management system (NestJS, TypeScript, ESM, Turbo monorepo).
- Enabled global `ValidationPipe` with: `whitelist`, `forbidNonWhitelisted`, `transform`, `enableI…

Day 2:
TL;DR:
❌ `composite: true`
❌ `tsconfig.build.json`
✅ `paths` in `tsconfig.base.json`
✅ `include` shared libs explicitly where needed
✅ `turbo run build` just works
Wrestled for hours (~3) with TypeScript `project references` and `paths` in a Turbo monorepo (NestJS, ESM).
Turns out: if you want global aliases like `@my-lib/foo` to *just work* across apps — skip `composite: true` and `tsc --build`.
Project references and alia…

🇺🇦 #NowPlaying on BBCRadio3's #ThroughTheNight
Kui Dong & Esmé Quartet:
🎵 Spring
#KuiDong #EsméQuartet
#Spotify

🇺🇦 #NowPlaying on BBCRadio3's #ThroughTheNight
Joseph Haydn, WonHee Bae, Yuna Ha, Dimitri Murrath, Yeeun Heo & Esmé Quartet:
🎵 String Quartet no 30 in E flat, Op 33 no 2 'The Joke'
#JosephHaydn #WonHeeBae #YunaHa #DimitriMurrath #YeeunHeo #EsméQuartet