Results for “biomarker”

Use when masking columns or coordinate ranges in multiple-sequence alignments before downstream HMMER or alignment-processing steps.

Use when searching DNA or RNA queries against nucleotide sequence databases with HMMER's nucleotide homology search engine.

Apply a text watermark to a photo using layer-based image composition for brand protection and copyright.

Use when searching protein sequences against profile hidden Markov models (HMMs) such as Pfam or other HMM databases.

Generates Mermaid diagrams from code graphs, including call graphs, class hierarchies, module dependency maps, and data flow visualizations.

Runs full Trailmark structural analysis by building a graph and computing pre-analysis passes for hotspots, taint, blast radius, privilege boundaries, and attack surface.

Runs a Trailmark summary analysis on a codebase to auto-detect languages, count entry points, and list dependencies.

This skill recommends performing an imaging study to assess tumor size, appearance, and parasellar extent once biochemical diagnosis of acromegaly is confirmed. Trigger when IGF-1 is elevated and GH fails to suppress to <0.4 µg/L during an oral glucose tolerance test.

Use when running HMMER master or worker daemon services that front `phmmer`, `hmmsearch`, and `hmmscan` against cached databases.

Applies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, and molecular complexity metrics for compound prioritization and library cleanup. Use when filtering or triaging a compound library, flagging PAINS or reactive groups, or assessing drug-likeness of candidate molecules. Part of the AlterLab Academic Skills suite.

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against ontologies (genes, cell types, diseases, tissues), tracking data lineage and computational workflows, building data lakehouses, or wiring integrations with Nextflow, Snakemake, W&B, or MLflow. Part of the AlterLab Academic Skills suite.

Monitors a watchlist of Polymarket markets and surfaces meaningful shifts in price, volume, comments, or resolution proximity, with position context and optional Bankr integration.

Track investment theses across their lifecycle — from screening idea to closed position with postmortem. Register theses from screener outputs, manage state transitions, attach position sizing, review due dates, and generate postmortem reports with P&L and MAE/MFE analysis.

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores, drug sensitivity data, and gene effect profiles to identify cancer-specific vulnerabilities, synthetic lethal interactions, and validate oncology drug targets.

Predict molecular properties, train graph neural networks, and run drug discovery workflows using DeepChem's featurizers, models, and MoleculeNet benchmarks.

Query ChEMBL via the chembl_webresource_client Python client for curated bioactive molecules and drug-like compound libraries at scale — search compounds by structure or physicochemical properties, retrieve bioactivity measurements (IC50, Ki, EC50), and find inhibitors of a target. Use when screening chemical libraries, mining curated bioactivity for a protein, running SAR studies, or sourcing medicinal-chemistry data; for measured protein-ligand binding affinities (Ki/Kd/IC50) prefer alterlab-bindingdb instead. Part of the AlterLab Academic Skills suite.

Use when searching one or more protein query sequences against a protein sequence database with HMMER's one-pass sequence-vs-sequence searcher.

Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs), searching by TF name, species, or class, scanning DNA sequences for binding sites, and comparing matrices. Use when doing motif analysis, regulatory genomics, transcription factor binding prediction, or interpreting regulatory/non-coding GWAS variants. Part of the AlterLab Academic Skills suite.