All authors
Claude Skills by mdbabumiamssm
github.com/mdbabumiamssm1,581 skills3 installs3,534 views
- Multi Ancestry PRS AgentAI-powered multi-ancestry polygenic risk score calculation and optimization for equitable disease risk prediction across diverse global populations.Votes: 0GitHub stars: 32
- PRS Net Deep Learning AgentGeometric deep learning-based polygenic risk score prediction using PRS-Net for modeling gene interactions, enhanced disease prediction, and cross-ancestry portability.Votes: 0GitHub stars: 32
- Pharmacogenomics AgentAI-powered pharmacogenomic analysis for drug response prediction, adverse event risk assessment, and precision dosing using multi-omics data and deep learning models.Votes: 0GitHub stars: 32
- Deep Visual Proteomics AgentAI-driven integration of cellular imaging, laser microdissection, and ultra-sensitive mass spectrometry for spatially-resolved single-cell proteomics.Votes: 0GitHub stars: 32
- Dia AnalysisData-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data with library-free or library-based workflows for deep proteome profiling.Votes: 0GitHub stars: 32
- Peptide IdentificationPeptide-spectrum matching and protein identification from MS/MS data. Use when identifying peptides from tandem mass spectra. Covers database searching, spectral library matching, and FDR estimation using target-decoy approaches.Votes: 0GitHub stars: 32
- Ptm AnalysisPost-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localization, motif analysis, and quantitative PTM analysis. Use when analyzing phosphoproteomic data or other modification-enriched samples.Votes: 0GitHub stars: 32
- QuantificationProtein quantification from mass spectrometry data including label-free (LFQ, intensity-based), isobaric labeling (TMT, iTRAQ), and metabolic labeling (SILAC) approaches. Use when extracting protein abundances from MS data for differential analysis.Votes: 0GitHub stars: 32
- Spectral LibrariesBuild, manage, and search spectral libraries for proteomics. Use when creating or working with spectral libraries for DIA analysis. Covers DDA-based library generation, predicted libraries (Prosit, DeepLC), and library formats.Votes: 0GitHub stars: 32
- BiomniA general-purpose biomedical AI agent capable of executing complex research workflows using over 150 tools and databases.Votes: 0GitHub stars: 32
- Data AnalysisRun the cross-language data analysis workflows (Python, R, SQL, Tableau/Power BI) described in this module to clean, analyze, and visualize biomedical datasets end-to-end.Votes: 0GitHub stars: 32
- NanoBananaAI-powered reasoning image engine for generating and editing high-quality biomedical infographics and realistic images.Votes: 0GitHub stars: 32
- PaperBananaAgentic framework for automating the generation of publication-ready academic illustrations and statistical plots.Votes: 0GitHub stars: 32
- Enrichment VisualizationVisualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clusterProfiler results. Covers dotplot, barplot, cnetplot, emapplot, gseaplot2, ridgeplot, and treeplot.Votes: 0GitHub stars: 32
- Figure ExportExports publication-ready figures in various formats with proper resolution, sizing, and typography. Use when preparing figures for journal submission, creating vector graphics for presentations, or ensuring consistent figure styling across analyses.Votes: 0GitHub stars: 32
- Quarto ReportsBuild reproducible scientific documents, presentations, and websites with Quarto supporting R, Python, Julia, and Observable JS. Use when creating reproducible reports with Quarto.Votes: 0GitHub stars: 32
- Rmarkdown ReportsCreate reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format. Use when generating analysis reports with RMarkdown.Votes: 0GitHub stars: 32
- Primer BasicsDesign PCR primers for a target sequence using primer3-py. Specify target regions, product size, melting temperature, and other constraints. Returns ranked primer pairs with quality metrics. Use when designing standard PCR primers.Votes: 0GitHub stars: 32
- Primer ValidationValidate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculations. Check self-complementarity, heterodimer formation, and 3' stability. Use when validating primer specificity and properties.Votes: 0GitHub stars: 32
- Qpcr PrimersDesign qPCR primers and TaqMan/molecular beacon probes using primer3-py. Configure probe Tm, primer-probe spacing, and hydrolysis probe constraints for real-time PCR assays. Use when designing qPCR primers and probes.Votes: 0GitHub stars: 32
- Enzyme SelectionSelect restriction enzymes by criteria using Biopython Bio.Restriction. Find enzymes that cut once, don't cut, produce specific overhangs, are commercially available, or have compatible ends for cloning. Use when selecting restriction enzymes for cloning or analysis.Votes: 0GitHub stars: 32
- Restriction MappingCreate restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction. Visualize cut sites, calculate distances between sites, and generate text or graphical maps. Use when creating or analyzing restriction maps.Votes: 0GitHub stars: 32
- Restriction SitesFind restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batches of enzymes, or commercially available enzyme sets. Returns cut positions for linear or circular DNA. Use when finding restriction enzyme cut sites in sequences.Votes: 0GitHub stars: 32
- Batch ProcessingProcess multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.Votes: 0GitHub stars: 32
- Filter SequencesFilter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences, removing unwanted records, or selecting by specific criteria.Votes: 0GitHub stars: 32
- Format ConversionConvert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools.Votes: 0GitHub stars: 32
- Paired End FastqHandle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data.Votes: 0GitHub stars: 32
- Read SequencesRead biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. Use when parsing sequence files, iterating multi-sequence files, random access to large files, or high-performance parsing.Votes: 0GitHub stars: 32
- Write SequencesWrite biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences, creating new sequence files, or outputting modified records.Votes: 0GitHub stars: 32
- Reverse ComplementGenerate reverse complements and complements of DNA/RNA sequences using Biopython. Use when working with opposite strands, primer design, or converting between template and coding strands.Votes: 0GitHub stars: 32
- Seq ObjectsCreate and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-place, or building annotated sequence records.Votes: 0GitHub stars: 32
- Sequence PropertiesCalculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython. Use when analyzing sequence composition, computing physical properties, or comparing sequences.Votes: 0GitHub stars: 32
- Sequence SlicingSlice, extract, and concatenate biological sequences using Biopython. Use when extracting subsequences, joining sequences, or manipulating sequence regions by position.Votes: 0GitHub stars: 32
- Transcription TranslationTranscribe DNA to RNA and translate to protein using Biopython. Use when converting between DNA, RNA, and protein sequences, finding ORFs, or using alternative codon tables.Votes: 0GitHub stars: 32
- Core Python Best PracticesEssential guidelines for writing modern, type-safe, and idiomatic Python 3 code.Votes: 0GitHub stars: 32
- Python Pandas Best PracticesStandards for efficient, readable, and performant data manipulation using Python''s Pandas library.Votes: 0GitHub stars: 32
- NextJS Best PracticesGuidelines for building scalable, SEO-friendly applications with Next.js (App Router).Votes: 0GitHub stars: 32
- CryoEM AI Drug Design AgentAI-powered integration of cryo-EM structural data with generative AI and molecular dynamics for structure-based drug design targeting flexible proteins and membrane complexes.Votes: 0GitHub stars: 32
- Time Resolved CryoEM AgentAI-powered time-resolved cryo-EM analysis for capturing protein dynamics, drug-binding kinetics, and conformational transitions for dynamics-based drug discovery.Votes: 0GitHub stars: 32
- Alphafold PredictionsAccess and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without experimental structures, or for confidence scores (pLDDT).Votes: 0GitHub stars: 32
- Geometric AnalysisPerform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and dihedrals, superimposing structures, calculating RMSD, or computing solvent accessible surface area (SASA).Votes: 0GitHub stars: 32
- Modern Structure PredictionPredict protein structures using modern ML models including AlphaFold3, ESMFold, Chai-1, and Boltz-1. Use when predicting structures for novel proteins, protein complexes, or when comparing predictions across multiple methods.Votes: 0GitHub stars: 32
- Structure IoParse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures to various formats.Votes: 0GitHub stars: 32
- Structure ModificationModify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, or building structures programmatically.Votes: 0GitHub stars: 32
- Structure NavigationNavigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over structure levels, or extracting sequences from PDB files.Votes: 0GitHub stars: 32
- Context Specific ModelsBuild tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constraints. Create models that reflect cell-type specific metabolism. Use when building tissue-specific metabolic models or integrating transcriptomics with FBA.Votes: 0GitHub stars: 32
- Flux Balance AnalysisPerform flux balance analysis (FBA) and flux variability analysis (FVA) on genome-scale metabolic models using COBRApy. Predict growth rates, metabolic fluxes, and optimal resource utilization. Use when predicting metabolic phenotypes or optimizing flux distributions.Votes: 0GitHub stars: 32
- Gene EssentialityPerform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions. Predict essential genes and identify synthetic lethal pairs for drug target discovery. Use when identifying essential genes or finding synthetic lethal drug targets.Votes: 0GitHub stars: 32
- Metabolic ReconstructionBuild genome-scale metabolic models from genome sequences using CarveMe and gapseq for automated reconstruction. Generate draft models ready for curation and analysis. Use when creating metabolic models for organisms without existing models.Votes: 0GitHub stars: 32
- Model CurationValidate, gap-fill, and curate genome-scale metabolic models using memote for quality scores and COBRApy for manual curation. Ensure models meet SBML standards and produce biologically meaningful predictions. Use when improving draft models or preparing models for publication.Votes: 0GitHub stars: 32