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Claude Skills by mdbabumiamssm
github.com/mdbabumiamssm1,578 skills3 installs3,530 views
- Msa Statistics--> --- name: bio-alignment-msa-statistics description: Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns. tool_type: python primary_tool: Bio.Align measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Calculate sequence id...Votes: 0GitHub stars: 6
- Pairwise Alignment--> --- name: bio-alignment-pairwise description: Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences. tool_type: python primary_tool: Bio.Align measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Align two sequences ...Votes: 0GitHub stars: 6
- Primer Basics--> --- name: bio-primer-design-primer-basics description: Design 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. tool_type: python primary_tool: primer3-py measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Design PCR primers ...Votes: 0GitHub stars: 6
- Primer Validation--> --- name: bio-primer-design-primer-validation description: Validate 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. tool_type: python primary_tool: primer3-py measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command -...Votes: 0GitHub stars: 6
- Qpcr Primers--> --- name: bio-primer-design-qpcr-primers description: Design 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. tool_type: python primary_tool: primer3-py measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Design primers and internal probes...Votes: 0GitHub stars: 6
- Enzyme Selection--> --- name: bio-restriction-enzyme-selection description: Select 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. tool_type: python primary_tool: Bio.Restriction measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file -...Votes: 0GitHub stars: 6
- Fragment Analysis--> --- name: bio-restriction-fragment-analysis description: Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests. Use when analyzing restriction digest fragment patterns. tool_type: python primary_tool: Bio.Restriction measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Restriction Mapping--> --- name: bio-restriction-mapping description: Create 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. tool_type: python primary_tool: Bio.Restriction measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Restriction Sites--> --- name: bio-restriction-sites description: Find 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. tool_type: python primary_tool: Bio.Restriction measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file...Votes: 0GitHub stars: 6
- Batch Processing--> --- name: bio-batch-processing description: Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Process multiple sequence files efficiently using Biopython.Votes: 0GitHub stars: 6
- Compressed Files--> --- name: bio-compressed-files description: Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with .gz or .bz2 sequence files. Use BGZF for indexable compressed files. tool_type: python primary_tool: Bio.bgzf measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Handle gzip, bzip2, and BGZF compressed sequence files with Biopython.Votes: 0GitHub stars: 6
- Fastq Quality--> --- name: bio-fastq-quality description: Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Analyze and manipulate FASTQ quality scores using Biopython.Votes: 0GitHub stars: 6
- Filter Sequences--> --- name: bio-filter-sequences description: Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences, removing unwanted records, or selecting by specific criteria. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Filter and select sequences based on various criteria using Biopython.Votes: 0GitHub stars: 6
- Format Conversion--> --- name: bio-format-conversion description: Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Convert sequence files between formats using Biopython's Bio.SeqIO module.Votes: 0GitHub stars: 6
- Paired End Fastq--> --- name: bio-paired-end-fastq description: Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Handle paired-end sequencing data (R1/R2 files) using Biopython.Votes: 0GitHub stars: 6
- Read Sequences--> --- name: bio-read-sequences description: Read 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. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Read biological sequence data from files us...Votes: 0GitHub stars: 6
- Sequence Statistics--> --- name: bio-sequence-statistics description: Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, generating QC reports, or comparing assemblies. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Calculate comprehensive statistics for sequence datasets using Biopython.Votes: 0GitHub stars: 6
- Write Sequences--> --- name: bio-write-sequences description: Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences, creating new sequence files, or outputting modified records. tool_type: python primary_tool: Bio.SeqIO measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Write SeqRecord objects to sequence files using Biopython's Bio.SeqIO module.Votes: 0GitHub stars: 6
- Codon Usage--> --- name: bio-codon-usage description: Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when analyzing coding sequences for expression optimization or evolutionary analysis. tool_type: python primary_tool: Bio.SeqUtils.CodonUsage measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Analyze codon usage patterns and calculate codon ada...Votes: 0GitHub stars: 6
- Motif Search--> --- name: bio-motif-search description: Find patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription factor binding sites, regulatory elements, or any sequence pattern. For restriction enzyme analysis, use the restriction-analysis skill. tool_type: python primary_tool: Bio.motifs measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Find patter...Votes: 0GitHub stars: 6
- Reverse Complement--> --- name: bio-reverse-complement description: Generate 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. tool_type: python primary_tool: Bio.Seq measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Generate complementary and reverse complementary sequences using Biopython.Votes: 0GitHub stars: 6
- Seq Objects--> --- name: bio-seq-objects description: Create 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. tool_type: python primary_tool: Bio.Seq measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Create and manipulate biological sequence objects using Biopython.Votes: 0GitHub stars: 6
- Sequence Properties--> --- name: bio-sequence-properties description: Calculate 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. tool_type: python primary_tool: Bio.SeqUtils measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Calculate physical and chemical properties of bi...Votes: 0GitHub stars: 6
- Sequence Slicing--> --- name: bio-sequence-slicing description: Slice, extract, and concatenate biological sequences using Biopython. Use when extracting subsequences, joining sequences, or manipulating sequence regions by position. tool_type: python primary_tool: Bio.Seq measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Extract, slice, and concatenate sequences using Biopython's Seq objects.Votes: 0GitHub stars: 6
- Transcription Translation--> --- name: bio-transcription-translation description: Transcribe 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. tool_type: python primary_tool: Bio.Seq measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Convert between DNA, RNA, and protein sequences using Biopython.Votes: 0GitHub stars: 6
- AgentSkillCatalogGraph Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'agent-skill-catalog-graph' description: 'Use graph-backed catalogs such as ctx to discover, compare, and recommend skills, agents, MCPs, and harnesses for LLM automation workflows.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 6
- AgentSkillPackageManagement Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'agent-skill-package-management' description: 'Install and manage versioned AI agent skills, commands, tools, and knowledge bundles reproducibly with manifests, trust checks, lockfiles, updates, rollback, and safe removal.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 6
- ClaudeCodeSkillMarketplaceOps Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'claude-code-skill-marketplace-ops' description: 'Assess and safely adopt Claude Code skills/plugins from large marketplaces such as ccpi/tonsofskills, covering discovery, trust, dependencies, conflicts, and installation hygiene.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 6
- ClaudeOfficialPluginsOperations Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'claude-official-plugins-operations' description: 'Use Anthropic-managed claude-plugins-official for vetted Claude Code plugin discovery, trust review, installation hygiene, dependency assessment, and migration planning.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 6
- OpenDesignAgenticPrototyping Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'open-design-agentic-prototyping' description: 'Use Open Design to plan safe local-first agentic workflows for design systems, prototypes, previews, and HTML/PDF/PPTX/MP4 exports.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 6
- ReferoDesignResearchSkill Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'refero-design-research-skill' description: 'Research-first UI design skill for using Refero MCP to study real app screens and flows before making product design decisions.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 6
- Codebase Investigator--> --- name: codebase-investigator description: Expertly analyze large codebases to identify patterns, dependencies, and architectural flaws. keywords: - refactoring - analysis - architecture - discovery - search measurable_outcome: Map key components and data flows of a 50k+ LOC repo within 5 minutes, identifying 3+ potential improvements. license: MIT metadata: author: AI Agentic Skills Team version: "2.0.0" compatibility: - system: linux, macos allowed-tools: - list_directory - read_file ...Votes: 0GitHub stars: 6
- Core Python Best Practices--> --- name: 'core-python-best-practices' description: 'Essential guidelines for writing modern, type-safe, and idiomatic Python 3 code.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command - write_file --- This skill defines the coding standards for Python development within the project. It emphasizes modern features, type safety, and readability.Votes: 0GitHub stars: 6
- Python Pandas Best Practices--> --- name: 'pandas-best-practices' description: 'Standards for efficient, readable, and performant data manipulation using Python''s Pandas library.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command - write_file --- This skill provides guidelines for working with tabular data in Python. It focuses on vectorization, memory management, and method chaining to write "Modern Pandas" code.Votes: 0GitHub stars: 6
- GitHub Agent**Domain:** Software Engineering / Agentic AI **Status:** ActiveVotes: 0GitHub stars: 6
- NextJS Best Practices--> --- name: 'nextjs-best-practices' description: 'Guidelines for building scalable, SEO-friendly applications with Next.js (App Router).' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command - write_file --- This skill outlines the standards for developing modern web applications using the Next.js App Router. It covers server components, data fetching, caching strategies, and route handling.Votes: 0GitHub stars: 6
- React Best Practices--> --- name: 'react-best-practices' description: 'A comprehensive guide and rule set for writing clean, performant, and maintainable React code.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command - write_file --- This skill provides a set of architectural and coding standards for React applications. It is designed to be used by agents when generating, refactoring, or reviewing React code to ensure align...Votes: 0GitHub stars: 6
- CryoEM AI Drug Design Agent--> --- name: 'cryoem-ai-drug-design-agent' description: 'AI-powered integration of cryo-EM structural data with generative AI and molecular dynamics for structure-based drug design targeting flexible proteins and membrane complexes.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Cryo-EM AI Drug Design Agent** integrates cryo-electron microscopy structural data with AlphaFold3, generative A...Votes: 0GitHub stars: 6
- Time Resolved CryoEM Agent--> --- name: 'time-resolved-cryoem-agent' description: 'AI-powered time-resolved cryo-EM analysis for capturing protein dynamics, drug-binding kinetics, and conformational transitions for dynamics-based drug discovery.' measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- The **Time-Resolved Cryo-EM Agent** leverages time-resolved cryo-electron microscopy to capture protein dynamics, drug-binding kinet...Votes: 0GitHub stars: 6
- Alphafold Predictions--> --- name: bio-structural-biology-alphafold-predictions description: Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without experimental structures, or for confidence scores (pLDDT). tool_type: python primary_tool: requests measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Download and analyze AlphaFold predicted protein structures...Votes: 0GitHub stars: 6
- Geometric Analysis--> --- name: bio-pdb-geometric-analysis description: Perform 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). tool_type: python primary_tool: Bio.PDB measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Measure distances, angles, and ...Votes: 0GitHub stars: 6
- Modern Structure Prediction--> --- name: bio-structural-biology-modern-structure-prediction description: Predict 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. tool_type: python primary_tool: ESMFold measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Predict ...Votes: 0GitHub stars: 6
- Structure Io--> --- name: bio-pdb-structure-io description: Parse 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. tool_type: python primary_tool: Bio.PDB measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Parse, download, and write protein structure files in PDB, mmCIF, and MMTF ...Votes: 0GitHub stars: 6
- Structure Modification--> --- name: bio-pdb-structure-modification description: Modify 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. tool_type: python primary_tool: Bio.PDB measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Transform coordinates, remove/add entities...Votes: 0GitHub stars: 6
- Structure Navigation--> --- name: bio-pdb-structure-navigation description: Navigate 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. tool_type: python primary_tool: Bio.PDB measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Navigate the Structure-Model-Chain-Residue-Atom (SMCRA...Votes: 0GitHub stars: 6
- Context Specific Models--> --- name: bio-systems-biology-context-specific-models description: Build 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. tool_type: python primary_tool: cobrapy measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - ...Votes: 0GitHub stars: 6
- Flux Balance Analysis--> --- name: bio-systems-biology-flux-balance-analysis description: Perform 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. tool_type: python primary_tool: cobrapy measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file...Votes: 0GitHub stars: 6
- Gene Essentiality--> --- name: bio-systems-biology-gene-essentiality description: Perform 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. tool_type: python primary_tool: cobrapy measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - ...Votes: 0GitHub stars: 6
- Metabolic Reconstruction--> --- name: bio-systems-biology-metabolic-reconstruction description: Build 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. tool_type: cli primary_tool: CarveMe measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Model Curation--> --- name: bio-systems-biology-model-curation description: Validate, 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. tool_type: python primary_tool: memote measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_fil...Votes: 0GitHub stars: 6