A multi-disciplinary scientific research institute powered by 177 specialized skills spanning bioinformatics, drug discovery, clinical research, machine learning, quantum computing, and 37 scientific databases
An Agent Company based on claude-scientific-skills — a large scientific skill library covering bioinformatics, drug discovery, clinical research, quantum computing, and 37 scientific databases
This is an Agent Company package from Paperclip
| Content | Count |
|---|---|
| Agents | 54 |
| Skills | 177 |
| Agent | Role | Reports To |
|---|---|---|
| Dr. Amara Okafor | Engineer | chief-science-officer |
| Dr. Samuel Adeyemi | Engineer | physical-sciences-lead |
| Dr. Henrik Larsen | Engineer | databases-lead |
| Dr. Elena Vasquez | CEO | — |
| Dr. Erik Johansson | Engineer | drug-discovery-lead |
| Dr. Yara Hassan | Engineer | databases-lead |
| Dr. Marcus Chen | Engineer | ceo |
| Dr. Aisha Patel | Engineer | clinical-research-lead |
| Dr. Hannah Fischer | Engineer | chief-science-officer |
| Dr. Mei-Lin Zhou | Engineer | clinical-research-lead |
| Dr. Olivia Hartmann | Engineer | physical-sciences-lead |
| Dr. Zara Nwosu | Engineer | research-methods-lead |
| Dr. Rosa Martinez | Engineer | chief-science-officer |
| Dr. Lin Wei | Engineer | chief-science-officer |
| Dr. Fatima Al-Rashid | Engineer | ml-lead |
| Dr. Andre Dupont | Engineer | sci-comm-lead |
| Dr. Priya Sharma | Engineer | chief-science-officer |
| Dr. Carlos Mendez | Engineer | drug-discovery-lead |
| Dr. Sarah Nakamura | Engineer | chief-science-officer |
| Dr. Hana Suzuki | Engineer | ml-lead |
| Dr. Kenji Watanabe | Engineer | bio-genomics-lead |
| Dr. Anya Kozlova | Engineer | databases-lead |
| Dr. Omar Farouk | Engineer | data-viz-lead |
| Dr. Grace Kim | Engineer | clinical-research-lead |
| Dr. Lucas Bergmann | Engineer | research-methods-lead |
| Dr. Takeshi Yamamoto | Engineer | lab-ops-lead |
| Dr. Elise Bergstrom | Engineer | lab-ops-lead |
| Dr. Catherine Moreau | Engineer | chief-science-officer |
| Dr. Isabelle Moreau | Engineer | databases-lead |
| Dr. Julian Archer | Engineer | sci-comm-lead |
| Dr. Paolo Ricci | Engineer | sci-comm-lead |
| Dr. Rajesh Kumar | Engineer | physical-sciences-lead |
| Dr. Alexander Petrov | Engineer | chief-science-officer |
| Dr. Yuki Tanaka | Engineer | drug-discovery-lead |
| Dr. Sven Eriksson | Engineer | clinical-research-lead |
| Dr. Ingrid Novak | Engineer | ml-lead |
| Dr. Ravi Mehta | Engineer | bio-genomics-lead |
| Dr. Nikolai Volkov | Engineer | chief-science-officer |
| Dr. James O'Brien | Engineer | clinical-research-lead |
| Dr. Naomi Takahashi | Engineer | sci-comm-lead |
| Dr. Thomas Brennan | Engineer | databases-lead |
| Dr. Liam O'Connor | Engineer | financial-research-lead |
| Dr. Clara Fontaine | Engineer | physical-sciences-lead |
| Dr. Kwame Asante | Engineer | databases-lead |
| Dr. Tomas Reyes | Engineer | bio-genomics-lead |
| Dr. Simone Weber | Engineer | sci-comm-lead |
| Dr. Michael Torres | Engineer | chief-science-officer |
| Dr. David Okonkwo | Engineer | ml-lead |
| Dr. Victoria Chang | Engineer | chief-science-officer |
| Dr. Lena Dubois | Engineer | bio-genomics-lead |
| Dr. Sofia Lindgren | Engineer | bio-genomics-lead |
| Dr. Petra Johansen | Engineer | data-viz-lead |
| Dr. Nathan Brooks | Engineer | ml-lead |
| Dr. Leo Tancredi | Engineer | data-viz-lead |
| Skill | Description | Source |
|---|---|---|
| adaptyv | Protein engineering and directed evolution analysis using Adaptyv Bio platform | github |
| aeon | Time series analysis and temporal pattern detection for scientific data | github |
| alpha-vantage | Financial market data retrieval and analysis via Alpha Vantage API | github |
| alphafold-database | Query AlphaFold protein structure predictions database | github |
| anndata | Annotated data matrix operations for single-cell genomics using AnnData | github |
| arboreto | Gene regulatory network inference using tree-based ensemble methods | github |
| arxiv-database | Search and retrieve preprints from the arXiv repository | github |
| astropy | Astronomical computations, coordinate transforms, and celestial data analysis | github |
| benchling-integration | Integration with Benchling laboratory information management system | github |
| bgpt-paper-search | AI-powered academic paper search and retrieval | github |
| bindingdb-database | Query BindingDB for protein-ligand binding affinity data | github |
| biopython | Biological sequence analysis, alignment, and molecular biology computations | github |
| biorxiv-database | Search and retrieve preprints from the bioRxiv repository | github |
| bioservices | Programmatic access to biological web services and databases | github |
| brenda-database | Query BRENDA enzyme information and kinetics database | github |
| cbioportal-database | Query cBioPortal for cancer genomics data exploration | github |
| cellxgene-census | Access and analyze the CZ CELLxGENE Census single-cell data | github |
| chembl-database | Query ChEMBL bioactivity database for drug-like molecules | github |
| cirq | Quantum circuit design and simulation using Google Cirq | github |
| citation-management | Manage, format, and organize scientific citations and bibliographies | github |
| clinical-decision-support | Evidence-based clinical decision support and diagnostic reasoning | github |
| clinical-reports | Generate structured clinical reports from patient and study data | github |
| clinicaltrials-database | Search ClinicalTrials.gov for clinical study information | github |
| clinpgx-database | Query CPIC pharmacogenomics clinical annotations database | github |
| clinvar-database | Query ClinVar for genomic variant clinical significance data | github |
| cobrapy | Constraint-based metabolic modeling and flux balance analysis | github |
| consciousness-council | Multi-perspective deliberation framework for complex scientific questions | github |
| cosmic-database | Query COSMIC somatic mutation database for cancer genomics | github |
| dask | Parallel and distributed computing for large-scale data processing | github |
| datacommons-client | Access Google Data Commons public datasets and statistics | github |
| datamol | Molecular data processing, featurization, and cheminformatics workflows | github |
| deepchem | Deep learning for drug discovery, materials science, and chemistry | github |
| deeptools | Tools for deep-sequencing data analysis and visualization | github |
| denario | Financial data aggregation and economic indicator analysis | github |
| depmap | Access Cancer Dependency Map project data for functional genomics | github |
| dhdna-profiler | DNA sequence profiling and genetic variant characterization | github |
| diffdock | Molecular docking prediction using DiffDock diffusion model | github |
| dnanexus-integration | Integration with DNAnexus genomics data analysis platform | github |
| docx | Generate and manipulate Microsoft Word documents programmatically | github |
| drugbank-database | Query DrugBank for comprehensive drug and target information | github |
| edgartools | SEC EDGAR filings retrieval and financial document analysis | github |
| ena-database | Query European Nucleotide Archive for sequencing data | github |
| ensembl-database | Query Ensembl genome browser for gene annotations and sequences | github |
| esm | Protein language model analysis using Meta ESM models | github |
| etetoolkit | Phylogenetic tree visualization, manipulation, and analysis | github |
| exploratory-data-analysis | Automated exploratory data analysis with statistical summaries and visualizations | github |
| fda-database | Query FDA drug approvals, labels, and adverse event databases | github |
| flowio | Flow cytometry data file parsing and analysis | github |
| fluidsim | Computational fluid dynamics simulation and analysis | github |
| fred-economic-data | Access Federal Reserve Economic Data (FRED) time series | github |
| gene-database | Query NCBI Gene database for gene information and annotations | github |
| generate-image | Generate scientific illustrations and diagrams using AI image generation | github |
| geniml | Genomic interval machine learning for regulatory element analysis | github |
| geo-database | Query NCBI Gene Expression Omnibus for transcriptomics datasets | github |
| geomaster | Geospatial data processing, coordinate transforms, and mapping | github |
| geopandas | Geospatial data analysis and visualization with GeoPandas | github |
| get-available-resources | Discover and list available computational resources and tools | github |
| gget | Efficient querying of genomic databases from the command line | github |
| ginkgo-cloud-lab | Integration with Ginkgo Bioworks cloud laboratory platform | github |
| glycoengineering | Glycan structure analysis and glycoengineering design | github |
| gnomad-database | Query gnomAD for population-level genomic variant frequencies | github |
| gtars | Genomic interval operations and region set analysis | github |
| gtex-database | Query GTEx tissue-specific gene expression database | github |
| gwas-database | Query GWAS Catalog for genome-wide association study results | github |
| hedgefundmonitor | Hedge fund performance tracking and strategy analysis | github |
| histolab | Histopathology image preprocessing and analysis pipeline | github |
| hmdb-database | Query Human Metabolome Database for metabolite information | github |
| hypogenic | Hypothesis generation from scientific literature and data patterns | github |
| hypothesis-generation | Systematic scientific hypothesis formulation and evaluation | github |
| imaging-data-commons | Access NCI Imaging Data Commons for medical imaging datasets | github |
| infographics | Create data-driven scientific infographics and visual summaries | github |
| interpro-database | Query InterPro protein families, domains, and functional sites database | github |
| iso-13485-certification | ISO 13485 medical device quality management compliance guidance | github |
| jaspar-database | Query JASPAR transcription factor binding profile database | github |
| kegg-database | Query KEGG pathway and molecular interaction network database | github |
| labarchive-integration | Integration with LabArchives electronic lab notebook platform | github |
| lamindb | Biological data management and lineage tracking with LaminDB | github |
| latchbio-integration | Integration with Latch bioinformatics workflow platform | github |
| latex-posters | Generate scientific conference posters using LaTeX templates | github |
| literature-review | Systematic literature review with search, screening, and synthesis | github |
| markdown-mermaid-writing | Generate technical documents with Mermaid diagrams and markdown | github |
| market-research-reports | Generate market research reports for scientific and biotech sectors | github |
| markitdown | Convert various document formats to clean markdown | github |
| matchms | Mass spectrometry data matching, comparison, and spectral similarity analysis | github |
| matlab | MATLAB-style numerical computing, matrix operations, and signal processing | github |
| matplotlib | Publication-quality scientific figure generation with Matplotlib | github |
| medchem | Medicinal chemistry analysis, drug-likeness, and molecular optimization | github |
| metabolomics-workbench-database | Query Metabolomics Workbench for metabolomics study data | github |
| modal | Serverless cloud compute for running scientific workloads at scale | github |
| molecular-dynamics | Molecular dynamics simulation setup, execution, and trajectory analysis | github |
| molfeat | Molecular featurization and chemical descriptor computation | github |
| monarch-database | Query Monarch Initiative for disease-gene-phenotype associations | github |
| networkx | Network and graph analysis for biological and scientific networks | github |
| neurokit2 | Neurophysiological signal processing for ECG, EEG, EMG, and more | github |
| neuropixels-analysis | Neuropixels probe electrophysiology data processing and analysis | github |
| offer-k-dense-web | Access K-Dense web platform services and resources | github |
| omero-integration | Integration with OMERO bio-image data management platform | github |
| open-notebook | Open science notebook for documenting experimental procedures | github |
| openalex-database | Query OpenAlex scholarly works, authors, and institutions database | github |
| opentargets-database | Query Open Targets for drug target validation evidence | github |
| opentrons-integration | Integration with Opentrons liquid handling robot platform | github |
| paper-2-web | Convert scientific papers into interactive web presentations | github |
| parallel-web | Parallel web scraping and data collection from multiple sources | github |
| pathml | Computational pathology and whole slide image analysis | github |
| pdb-database | Query Protein Data Bank for 3D macromolecular structure data | github |
| Generate and manipulate PDF documents for scientific publications | github | |
| peer-review | Structured peer review analysis and feedback generation | github |
| pennylane | Quantum machine learning and differentiable quantum computing | github |
| perplexity-search | AI-powered web search using Perplexity for research queries | github |
| phylogenetics | Phylogenetic tree construction, analysis, and evolutionary inference | github |
| plotly | Interactive scientific data visualization with Plotly | github |
| polars | High-performance DataFrame operations for large-scale data analysis | github |
| polars-bio | Bioinformatics-specific data operations using Polars DataFrames | github |
| pptx | Generate and manipulate PowerPoint presentations programmatically | github |
| pptx-posters | Generate scientific posters in PowerPoint format | github |
| primekg | Query PrimeKG precision medicine knowledge graph | github |
| protocolsio-integration | Integration with protocols.io experimental protocol platform | github |
| pubchem-database | Query PubChem for chemical compound and bioassay data | github |
| pubmed-database | Search PubMed biomedical literature database | github |
| pufferlib | Reinforcement learning environment interface and training | github |
| pydeseq2 | Differential gene expression analysis using DESeq2 methodology | github |
| pydicom | DICOM medical image file reading, processing, and analysis | github |
| pyhealth | Healthcare data analytics and clinical prediction modeling | github |
| pylabrobot | Laboratory robotics automation and liquid handling control | github |
| pymatgen | Materials science analysis, crystal structure manipulation, and phase diagrams | github |
| pymc | Bayesian statistical modeling and probabilistic programming | github |
| pymoo | Multi-objective optimization algorithms and evolutionary computation | github |
| pyopenms | Mass spectrometry data processing and proteomics analysis | github |
| pysam | SAM/BAM/CRAM genomic alignment file processing and analysis | github |
| pytdc | Therapeutics Data Commons access for drug discovery benchmarks | github |
| pytorch-lightning | Deep learning model training and experiment management | github |
| pyzotero | Zotero reference manager integration for bibliography management | github |
| qiskit | Quantum computing circuit design and execution using IBM Qiskit | github |
| qutip | Quantum system dynamics simulation with QuTiP | github |
| rdkit | Cheminformatics molecular operations, fingerprints, and property calculations | github |
| reactome-database | Query Reactome biological pathway and reaction database | github |
| research-grants | Research grant writing assistance and funding opportunity analysis | github |
| research-lookup | Targeted research lookup across multiple academic databases | github |
| rowan | Molecular simulation and computational chemistry workflows | github |
| scanpy | Single-cell RNA-seq analysis pipeline with clustering and visualization | github |
| scholar-evaluation | Evaluate research quality, impact, and scholarly contributions | github |
| scientific-brainstorming | Structured scientific brainstorming and ideation framework | github |
| scientific-critical-thinking | Critical analysis of scientific claims, methods, and evidence | github |
| scientific-schematics | Generate scientific diagrams, schematics, and technical illustrations | github |
| scientific-slides | Generate scientific presentation slides with proper formatting | github |
| scientific-visualization | Advanced scientific data visualization and figure composition | github |
| scientific-writing | Scientific manuscript drafting, editing, and style optimization | github |
| scikit-bio | Biological data analysis including diversity metrics and alignments | github |
| scikit-learn | Machine learning model training, evaluation, and feature engineering | github |
| scikit-survival | Survival analysis and time-to-event modeling | github |
| scvelo | RNA velocity analysis for single-cell transcriptomics dynamics | github |
| scvi-tools | Probabilistic models for single-cell omics data analysis | github |
| seaborn | Statistical data visualization with publication-ready aesthetics | github |
| shap | Model interpretability using SHAP values and feature importance analysis | github |
| simpy | Discrete-event simulation for process modeling and optimization | github |
| stable-baselines3 | Reinforcement learning algorithm implementations and training | github |
| statistical-analysis | Comprehensive statistical testing, regression, and inference | github |
| statsmodels | Statistical models, hypothesis tests, and econometric analysis | github |
| string-database | Query STRING protein-protein interaction network database | github |
| sympy | Symbolic mathematics, equation solving, and algebraic computation | github |
| tiledbvcf | Efficient VCF genomic variant data storage and querying with TileDB | github |
| timesfm-forecasting | Time series forecasting using Google TimesFM foundation model | github |
| torch-geometric | Graph neural networks for molecular and scientific graph data | github |
| torchdrug | Drug discovery deep learning with molecular representation learning | github |
| transformers | Transformer model inference for scientific NLP and sequence tasks | github |
| treatment-plans | Evidence-based treatment plan generation and clinical protocol design | github |
| umap-learn | Dimensionality reduction and data visualization using UMAP | github |
| uniprot-database | Query UniProt protein sequence and functional annotation database | github |
| usfiscaldata | U.S. fiscal data retrieval and government financial analysis | github |
| uspto-database | Query USPTO patent database for intellectual property research | github |
| vaex | Out-of-core DataFrame processing for billion-row scientific datasets | github |
| venue-templates | Scientific conference and journal submission templates | github |
| what-if-oracle | Counterfactual scenario analysis and what-if reasoning for science | github |
| writing | General-purpose scientific and technical writing assistance | github |
| xlsx | Generate and manipulate Excel spreadsheets for scientific data | github |
| zarr-python | Chunked, compressed array storage for large scientific datasets | github |
| zinc-database | Query ZINC database for commercially available compound screening | github |
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Exported from Paperclip on 2026-03-23