Frederik Schulz

Build marker gene alignments and phylogenetic trees efficiently.

Create marimo notebooks using Python with a simple and structured format.

Search bioRxiv preprints using the official API for recent biology research.

Expert data visualization specialist for creating publication-quality figures and dashboards.

CodexLoop is a plan-driven orchestration agent for executing and tracking implementation tasks.

Expert scientific writer and editor for high-quality manuscripts and peer reviews.

Evaluate scientific rigor and evidence quality for claims and studies.

Assess the impact of academic papers and journals using citation counts and impact factors.

Access genomics metadata and download genome files from JGI Lakehouse.

Create and refactor reproducible analysis notebooks using Marimo or Jupyter.

Automate web interactions with the agent-browser CLI for tasks like scraping and UI testing.

A collection of agents and skills for bioinformatics and data visualization.

Perform metagenomic binning, refinement, and quality control with completeness and contamination checks.

Expert computational biologist for omics workflows including QC, assembly, and phylogenomics.

Initialize a bioinformatics project scaffold with reproducible environments and data cataloging.

Assemble genomes and metagenomes while producing quality control artifacts.

Perform functional annotation and taxonomy inference from sequence homology.

Search arXiv preprints and generate Markdown summaries from arXiv IDs.

Create polished, publication-quality visualizations using matplotlib and seaborn.

Generate reproducible Methods documentation from workflow run artifacts for bioinformatics.

Streamline the drafting and revision of scientific manuscripts with a structured multi-agent workflow.

Create production-ready Plotly Dash dashboards with consistent theming and clear layouts.

Design and scaffold bioinformatics pipelines using Prefect+Dask or Nextflow for efficient execution.

Convert Jupyter notebooks (.ipynb) into marimo notebooks (.py) efficiently.

Automatically implement research papers in a marimo notebook without user input.

Search the PMC Open Access literature using structured JSON queries with polars-dovmed.

Critically evaluate AI scientist outputs in biology and related fields.

Aggregate results, train ML models, and produce validated reports.

Detect, classify, and perform quality control on viral contigs efficiently.

Ingest, QC, and map reads with reproducible outputs for raw read processing.

Cluster proteins into orthogroups and derive pangenome matrices efficiently.

Run a Codex-native planning and implementation loop with progress tracking and failure memory.

Call genes and annotate features for prokaryotes, viruses, and eukaryotes.

Predict protein structures and annotate them based on structural data.

Easily add 'Open in molab' badges linking to marimo notebooks in markdown or HTML.

Conduct a comprehensive multi-agent review of scientific manuscripts with specialized reviewers and editor oversight.

Query the Crossref REST API for DOI validation and citation metadata management.

Quickly fetch the latest API and SDK documentation using the chub CLI.

Create interactive components for Marimo notebooks using anywidget.

Expert agent for literature discovery, citation metadata, and evidence-based search triage.

Track and reconcile taxonomy updates from multiple authoritative sources with versioned provenance.

Structured review framework for evaluating AI/ML and bioscience proposals.