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Orchestrates end-to-end autonomous AI research projects using a two-loop architecture. The inner loop runs rapid experiment iterations with clear optimization targets. The outer loop synthesizes resul…
Create an academic presentation as a LaTeX Beamer source and reviewed PDF with an original theme. Use when the requested deliverable is a conference, seminar, or lecture deck in Beamer. Not for PowerP…
Define benchmark runs and log outcomes with consistent metrics, acceptance criteria, and reproducible artifact references.
Compare a project .bib against a Paperpile project/topic folder to find uncited papers or unfiled entries. Use when the user asks to compare a project .bib against a Paperpile project/topic folder to …
turn a single-image bioimage workflow into a reproducible batch pipeline for folders of microscopy images. use when the task involves processing many tiff, ome-tiff, png, jpeg, czi, nd2, or lif files …
Design and implementation of reproducible bioinformatics and ML pipelines using workflow managers (Snakemake, Nextflow), containers (Singularity/Apptainer, Docker), conda environments with lock files,…
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downl…
Vision-language pre-training framework bridging frozen image encoders and LLMs. Use when you need image captioning, visual question answering, image-text retrieval, or multimodal chat with state-of-th…
Activation-aware weight quantization for 4-bit LLM compression with 3x speedup and minimal accuracy loss. Use when deploying large models (7B-70B) on limited GPU memory, when you need faster inference…
Deploy BEHAVIOR-1K (OmniGibson + Isaac Sim) on RTX 5080/50-series Blackwell GPUs. Use this skill whenever setting up BEHAVIOR-1K, OmniGibson, or Isaac Sim on RTX 5080, RTX 5090, or any Blackwell-archi…
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Extract citations from a PDF and generate a validated .bib file. Use when the user asks to extract citations from a PDF and generate a validated .bib file. Reads the PDF, identifies referenced works, …
detect, inspect, and load common bioimage files into python and napari with a tiff-first workflow. use when a task starts from microscopy image files or folders, especially tiff or ome-tiff, but also …
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biome…
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analys…
Autonomous VTI sourcing. Discovers popular repositories that depend on a target SDK, fans out a fleet of subagents to scout each one for silent footguns, proves every candidate RED→GREEN, auto-promote…
Expert guidance for fine-tuning LLMs with Axolotl - YAML configs, 100+ models, LoRA/QLoRA, DPO/KTO/ORPO/GRPO, multimodal support
AI operational modes (brainstorm, implement, debug, review, teach, ship, orchestrate). Use to adapt behavior based on task type.
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, qual…
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measure segmented bioimage objects, generate qc summaries, and export tables, plots, scripts, and notebooks for microscopy analysis. use when labels or masks already exist or when a segmentation resul…
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, cu…
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Sends an agent on a scouting mission to find real-world coding traps (footguns in popular SDKs/protocols), synthesize the finding into a proven brainblast rule pack, and submit it to the pack registry…