Frederik Schulz

Assemble genomes and metagenomes while producing quality control artifacts.

Generate reproducible Methods documentation from workflow run artifacts for bioinformatics.

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

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

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

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

Cluster proteins into orthogroups and derive pangenome matrices efficiently.

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

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

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

Evaluate scientific rigor and evidence quality for claims and studies.

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

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

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

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

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

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

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

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

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

Create interactive components for Marimo notebooks using anywidget.

Create and refactor reproducible analysis notebooks using Marimo or Jupyter.

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

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

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

Search arXiv preprints and generate Markdown summaries from arXiv IDs.

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

Build marker gene alignments and phylogenetic trees efficiently.

Perform functional annotation and taxonomy inference from sequence homology.

Critically evaluate AI scientist outputs in biology and related fields.

Access genomics metadata and download genome files from JGI Lakehouse.

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

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

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

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

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

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

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

Predict protein structures and annotate them based on structural data.

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

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

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