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.

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

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

Access genomics metadata and download genome files from JGI Lakehouse.

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

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.

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

Perform functional annotation and taxonomy inference from sequence homology.

Predict protein structures and annotate them based on structural data.

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.

Critically evaluate AI scientist outputs in biology and related fields.

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

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

Create interactive components for Marimo notebooks using anywidget.

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

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

Cluster proteins into orthogroups and derive pangenome matrices efficiently.

Evaluate scientific rigor and evidence quality for claims and studies.

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

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

Create and refactor reproducible analysis notebooks using Marimo or Jupyter.

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

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

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

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

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

Assemble genomes and metagenomes while producing quality control artifacts.

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

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