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alterlab-ieu/alterlab-academic-skills

245 skills · 12.8K combined installs

Skills from this source

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Skill
Source
8W Activity
Installs
1
alterlab-openalex Query and analyze scholarly literature using the OpenAlex API across 240M+ works, retrieving papers, authors, institu…
alterlab-ieu/alterlab-academic-skills
60
2
alterlab-peer-review Writes structured, checklist-based manuscript and grant peer reviews — assesses methodology, statistical validity, re…
alterlab-ieu/alterlab-academic-skills
60
3
alterlab-plotly Builds INTERACTIVE charts with the Plotly Python library (plotly.express / graph_objects) — hover tooltips, zoom/pan,…
alterlab-ieu/alterlab-academic-skills
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4
alterlab-pymatgen Analyzes and manipulates materials with the pymatgen toolkit — crystal structures and molecules, phase diagrams and t…
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5
alterlab-pyopenms Build complete mass-spectrometry workflows with pyOpenMS — feature detection, peptide identification, protein quantif…
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6
alterlab-qutip Simulates open quantum systems with QuTiP, the Quantum Toolbox in Python, solving Lindblad master equations (mesolve)…
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7
alterlab-research-grants Writes competitive research grant proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC — applies agency-specific forma…
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8
alterlab-research-lookup Look up current research and scholarly papers by auto-routing each query to the best backend — the Parallel Web Syste…
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9
alterlab-scientific-viz Orchestrates matplotlib, seaborn, and plotly with opinionated publication styles to produce journal-ready figures. Us…
alterlab-ieu/alterlab-academic-skills
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10
alterlab-scientific-writing Writes scientific manuscripts in full flowing paragraphs (never bullet points) via a two-stage process — section outl…
alterlab-ieu/alterlab-academic-skills
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11
alterlab-scikit-bio Analyze biological data with scikit-bio — sequence analysis and alignments, phylogenetic trees, alpha/beta diversity …
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12
alterlab-shap Model interpretability and explainability with SHAP (SHapley Additive exPlanations) — feature importance and plots (w…
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13
alterlab-sympy Symbolic mathematics in Python with SymPy — solve equations algebraically, perform calculus (derivatives, integrals, …
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14
alterlab-torch-geometric Graph Neural Networks with PyTorch Geometric (PyG) — node and graph classification, link prediction, GCN, GAT, and Gr…
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15
alterlab-adaptyv Submits and tracks protein-testing experiments on the Adaptyv Bio Foundry cloud lab (wet-lab validation), and optimiz…
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16
alterlab-aeon Runs time series machine learning with the aeon library — classification, regression, clustering, forecasting, anomal…
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17
alterlab-alpha-vantage Accesses real-time and historical stock market data, forex rates, cryptocurrency prices, commodities, economic indica…
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18
alterlab-benchling Integrates the Benchling R&D platform via its REST API and SDK — access the registry (DNA, proteins), inventory, ELN …
alterlab-ieu/alterlab-academic-skills
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19
alterlab-bgpt-search Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP …
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20
alterlab-bindingdb Query BindingDB for measured protein-ligand binding affinities (Ki, Kd, IC50, EC50) via its keyless REST API or the f…
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21
alterlab-brenda Access the BRENDA enzyme database via its SOAP API to retrieve kinetic parameters (Km, kcat, Ki), reaction equations,…
alterlab-ieu/alterlab-academic-skills
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22
alterlab-chembl Query ChEMBL via the chembl_webresource_client Python client for curated bioactive molecules and drug-like compound l…
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23
alterlab-cirq Builds, simulates, and runs quantum circuits with Cirq, Google Quantum AI's framework for NISQ hardware, noise-aware …
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24
alterlab-clinical-decision Generates professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings — …
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alterlab-clinicaltrials Query ClinicalTrials.gov via its API v2 to search trials by condition, drug, location, recruitment status, or phase a…
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26
alterlab-clinpgx Access ClinPGx pharmacogenomics data (the successor to PharmGKB) to query gene-drug interactions, CPIC/DPWG dosing gu…
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alterlab-clinvar Query NCBI ClinVar via the E-utilities API or FTP for the clinical significance (pathogenicity) of human germline gen…
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alterlab-cosmic Access the COSMIC catalogue of somatic mutations in cancer to query somatic mutations, the Cancer Gene Census, mutati…
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alterlab-dask Scales pandas/NumPy workflows beyond memory with Dask distributed computing — parallel DataFrames, arrays, delayed ta…
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alterlab-datacommons Query Google Data Commons for public statistical data aggregated from global sources, resolving geographic entities a…
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alterlab-datamol Wraps RDKit in a high-level, pandas-friendly datamol interface with sensible defaults for everyday drug discovery — S…
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alterlab-deepchem Runs molecular machine learning with DeepChem — diverse featurizers, pre-built MoleculeNet benchmark datasets, and pr…
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33
alterlab-denario Runs Denario (AstroPilot-AI), a multiagent AI system for scientific research assistance that automates end-to-end res…
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alterlab-dnanexus Develops and runs genomics pipelines on the DNAnexus cloud platform using the dxpy Python SDK and dx CLI — build apps…
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35
alterlab-drugbank Access and analyze drug information from the DrugBank database — drug properties, interactions, targets, pathways, ch…
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alterlab-ena Access the European Nucleotide Archive (ENA) via its API and FTP to retrieve DNA/RNA sequences, raw sequencing reads …
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37
alterlab-esm Run ESM protein language models — ESM3 for generative multimodal protein design across sequence, structure, and funct…
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38
alterlab-etetoolkit Manipulate, annotate, and render phylogenetic trees programmatically with the ETE Toolkit (ete3) — parse and edit New…
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39
alterlab-fda Query the openFDA API for drugs, medical devices, adverse event reports, recalls, regulatory submissions (510k, PMA),…
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40
alterlab-flowio Parse and write FCS (Flow Cytometry Standard) files v2.0-3.1 with FlowIO — extract event data as NumPy arrays, read $…
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alterlab-gene-db Query NCBI Gene via the E-utilities and Datasets APIs, searching by gene symbol or Gene ID and retrieving gene inform…
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alterlab-glycoengineering Analyze and engineer protein glycosylation — scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosyl…
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alterlab-hedgefund-monitor Queries the OFR (Office of Financial Research) Hedge Fund Monitor API for time series on hedge fund size, leverage, c…
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44
alterlab-histolab Extract and preprocess tiles from whole-slide images (WSI) with histolab — OpenSlide-backed slide loading, tissue det…
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alterlab-imaging-data-commons Query and download public cancer imaging data from the NCI Imaging Data Commons (IDC) using the idc-index Python pack…
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alterlab-interpro Query the EMBL-EBI InterPro REST API for protein family, domain, and functional-site annotations integrated from memb…
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alterlab-iso13485 Prepares ISO 13485 certification documentation for medical device Quality Management Systems (QMS) — gap analysis of …
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alterlab-lamindb Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets quer…
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alterlab-mermaid Writes Markdown documents and text-based Mermaid diagrams (flowcharts, sequence, class, ER, gantt, state, and more) w…
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alterlab-metabolomics-wb Access the NIH Metabolomics Workbench via its REST API (4,200+ studies), querying metabolites, RefMet standardized no…
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