Product & Planning

fridrichmethod Bundle

Deep learning for drug discovery. 60+ models (GCN, GAT, AttentiveFP, MPNN, ChemBERTa, GROVER), 50+ featurizers, MoleculeNet benchmarks, HPO, transfer learning. Unified load-featurize-split-train-evaluate API. For fingerprints use rdkit-cheminformatics; for featurization-only use molfeat.

fridrichmethod Skill

PyTorch-based ML platform for drug discovery: graph molecular representation learning, property prediction (ADMET, activity), retrosynthesis, drug-target interaction (DTI), and pretraining on large molecular datasets. Provides GNN layers (GraphConv, GAT, MPNN), pretrained models, and benchmark datasets.

fridrichmethod Bundle

Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.

26zl Bundle

Detects rootkit presence on compromised systems by identifying hidden processes, hooked system calls, modified kernel structures, hidden files, and covert network connections using memory forensics, cross-view detection, and integrity checking techniques. Activates for requests involving rootkit detection, hidden process discovery, kernel integrity checking, or system call hook analysis.

26zl Bundle

Discover and inventory shadow API endpoints that operate outside documented specifications using traffic analysis, code scanning, and API discovery platforms.

26zl Bundle

Manages the end-to-end cyber threat intelligence lifecycle from planning and direction through collection, processing, analysis, dissemination, and feedback to ensure intelligence products meet stakeholder requirements and continuously improve. Use when establishing or maturing a CTI program, defining intelligence requirements with business stakeholders, or building feedback loops between intelligence consumers and producers. Activates for requests involving CTI program maturity, intelligence requirements, PIRs, or intelligence lifecycle management.

26zl Bundle

Audit service accounts across enterprise infrastructure to identify orphaned, over-privileged, and non-compliant accounts. This skill covers discovery of service accounts in Active Directory, cloud pl

26zl Bundle

Conducts comprehensive network penetration tests against authorized target environments by performing host discovery, port scanning, service enumeration, vulnerability identification, and controlled exploitation to assess the security posture of network infrastructure. The tester follows PTES methodology from reconnaissance through post-exploitation and reporting. Activates for requests involving network pentest, infrastructure security assessment, internal network testing, or external perimeter testing.

26zl Bundle

Perform coverage-guided fuzzing of compiled binaries using AFL++ (American Fuzzy Lop Plus Plus) to discover memory corruption, crashes, and security vulnerabilities. The tester instruments target binaries with afl-cc/afl-clang-fast, manages input corpora with afl-cmin and afl-tmin, runs parallel fuzzing campaigns with afl-fuzz, and triages crashes using CASR or GDB scripts. Activates for requests involving binary fuzzing, crash discovery, coverage-guided testing, or AFL++ fuzzing campaigns.

26zl Bundle

Analyze binary exploitation techniques including buffer overflows and ROP chains using pwntools Python library. Covers checksec analysis, gadget discovery with ROPgadget, and exploit development for CTF and authorized security assessments.

26zl Bundle

Discover and inventory all privileged accounts across enterprise infrastructure including domain admins, local admins, service accounts, database admins, cloud IAM roles, and application admin account

26zl Bundle

Indicator lifecycle management tracks IOCs from initial discovery through validation, enrichment, deployment, monitoring, and eventual retirement. This skill covers implementing systematic processes f

26zl Bundle

Monitors Certificate Transparency (CT) logs to detect unauthorized certificate issuance, discover subdomains via CT data, and alert on suspicious certificate activity for owned domains. Uses the crt.sh API and direct CT log querying based on RFC 6962 to build continuous monitoring pipelines that catch rogue certificates, track CA behavior, and map the external attack surface. Activates for requests involving certificate transparency monitoring, CT log auditing, subdomain discovery via certificates, or certificate issuance alerting.

fridrichmethod Bundle

Orchestrates neoantigen discovery from somatic variants to ranked vaccine candidates, chaining HLA typing (OptiType/arcasHLA + LOHHLA), VEP annotation (Wildtype+Frameshift plugins) + expression/readcount annotation, proximal-variant phasing, pVACseq MHC-I/II binding, CCF/clonality, and immunogenicity/quality ranking. Use when recognizing that binding is single-digit PPV and the critical steps are downstream (full-resolution HLA + LOH gating, proximal-variant phasing, clonality from purity+CN not raw VAF, expression), sequencing normalize+annotate -> phase -> HLA -> binding -> quality in the defensible order, dropping candidates on LOH-lost alleles, supplying --phased-proximal-variants-vcf so the mutant peptide is real, or ranking WITHIN patient rather than a fixed IC50 threshold. Hands mechanism to the immunoinformatics component skills; not a re-teach of any single step.

fridrichmethod Bundle

Infer or annotate TCR antigen specificity by unsupervised clustering (TCRdist/tcrdist3, GLIPH2, clusTCR, GIANA) and database lookup (VDJdb, IEDB, McPAS-TCR), and rank candidates with supervised predictors (ERGO-II, NetTCR-2.x, pMTnet) under explicit caveats. Encodes the central truth that general TCR-epitope prediction for UNSEEN epitopes essentially does not work (collapses to near-random; IMMREP22, Grazioli 2022) because labeled data is dominated by a few immunodominant epitopes and there is no true negative set — so clustering for discovery is the honest task and de-novo binding needs wet-lab validation. Use when annotating TCR specificity or grouping a repertoire. Epitope/MHC context lives in mhc-binding-prediction.

fridrichmethod Bundle

End-to-end bulk time-course analysis from an expression matrix to temporal gene modules and per-cluster pathway enrichment. Orchestrates temporal DE (limma splines or DESeq2 LRT), Mfuzz/tslearn soft clustering of expression-profile shapes, GAM trajectory fitting, per-cluster GO enrichment against a temporal-gene background, and an OPTIONAL circadian rhythm-detection branch (MetaCycle/CosinorPy) that runs only when the design covers >=2 full cycles with >=6-8 evenly spaced samples per cycle. Use when analyzing a bulk time-series expression experiment from any omics platform and deciding limma-splines vs DESeq2-LRT for temporal DE, soft vs hard clustering, whether the sampling design even licenses rhythm detection, and which background to use for enrichment. Not for single-cell pseudotime (see temporal-genomics/trajectory-modeling for the bulk-vs-pseudotime boundary) or unknown-period discovery (see temporal-genomics/periodicity-detection).

fridrichmethod Bundle

Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking distal enhancers to target genes, choosing between contact-aware (ABC, ENCODE-rE2G), accessibility-only (Cicero), and orthogonal (HiChIP H3K27ac, EpiMap) approaches, validating predictions against CRISPRi-FlowFISH gold-standard, or building cell-type-specific regulatory maps for fine-mapping or therapeutic target discovery.

26zl Bundle

Implements external attack surface management (EASM) using Shodan, Censys, and ProjectDiscovery tools (subfinder, httpx, nuclei) for asset discovery, subdomain enumeration, service fingerprinting, and exposure scoring. Includes a weighted risk scoring algorithm based on OWASP attack surface analysis methodology and the Relative Attack Surface Quotient (RSQ). Use when building continuous ASM programs or performing external reconnaissance for security assessments.

26zl Bundle

Configure and execute agentless vulnerability scanning using network protocols, cloud snapshot analysis, and API-based discovery to assess systems without installing endpoint agents.

26zl Bundle

Perform comprehensive ICS/OT asset discovery using Claroty xDome platform, leveraging passive monitoring, Claroty Edge active queries, and integration ecosystem to gain full visibility into industrial control system assets including PLCs, RTUs, HMIs, and network infrastructure across Purdue Model levels.

26zl Bundle

Triage and prioritize vulnerabilities using CISA's Stakeholder-Specific Vulnerability Categorization (SSVC) decision tree framework to produce actionable remediation priorities.

26zl Bundle

Automates GDPR Data Subject Access Request (DSAR) workflows including identity verification, PII discovery across databases and files using regex and NER, data mapping, response templating per Article 15 requirements, deadline tracking, and audit logging. Covers ICO/EDPB guidance compliance, exemption handling, and scalable batch processing. Use when building or auditing DSAR response capabilities under GDPR/UK GDPR.

paulasilvatech Skill

Import existing Azure resources into Terraform with Azure CLI discovery, dependency mapping, Azure Verified Modules, exact import addresses, and drift-safe plans. Use when asked to reverse-engineer live Azure infrastructure, generate IaC from subscriptions, resource groups, or ARM resource IDs, map dependencies, use AVM modules, or validate imported Terraform.

paulasilvatech Bundle

Convert frontend intent and repository evidence into INVEST-shaped user stories, Given/When/Then acceptance criteria, journey and state maps, and story-to-test traceability. Use this skill when feature discovery, acceptance criteria, Definition of Done, or an implementation handoff is needed.

paulasilvatech Skill

Design Azure API Center as the enterprise inventory and governance plane for APIs, agent tools, OpenAPI definitions, environments, deployments, metadata, linting, and MCP server discovery. Use when building an API or tool catalog, enforcing API standards, registering MCP servers, or making approved tools discoverable to agent builders.

paulasilvatech Skill

Guides Qdrant search strategy selection. Use when someone asks 'should I use hybrid search?', 'BM25 or sparse vectors?', 'how to rerank?', 'results are not relevant', 'I don't get needed results from my dataset but they're there', 'retrieval quality is not good enough', 'results too similar', 'need diversity', 'MMR', 'relevance feedback', 'recommendation API', 'discovery API', 'ColBERT reranking', or 'missing keyword matches'

paulasilvatech Bundle

Foundation skill for Power Automate through the FlowStudio MCP server: authentication, JSON-RPC helper code, tool discovery with list_skills and tool_search, oversized response parsing, and workflow-skill routing. Use this skill when connecting an agent to Power Automate, setting up FlowStudio MCP, checking auth, discovering flow tools, or preparing build, debug, monitoring, or governance workflows.

paulasilvatech Bundle

Design and plan end-to-end Azure IoT and Smart City solutions with requirements, architecture, device and edge strategy, ingestion, analytics, security, operations, cost controls, and phased delivery artifacts. Use when asked to build an IoT solution on Azure, design Smart City traffic, lighting, waste, water, energy, or public safety platforms, or create an urban IoT roadmap.

paulasilvatech Skill

Migrate a Backstage adopter app from the legacy frontend system to the new extension-based frontend system through hybrid and full-migration phases. Use when converting createApp, feature discovery, routes, sidebar, APIs, themes, or app-level frontend compatibility.

paulasilvatech Bundle

Configure, secure, and validate Backstage technical integrations with GitHub, Azure and Azure DevOps, and ServiceNow across catalog discovery, events, software templates, CI/CD views, incidents, and provider credentials. Use when setting up or troubleshooting integrations outside user sign-in.

paulasilvatech Skill

Model, register, discover, validate, and troubleshoot Backstage Software Catalog entities, providers, processors, ownership, relations, locations, and lifecycle. Use when handling catalog-info YAML, entity ingestion, org discovery, duplicate entities, or catalog governance.

paulasilvatech Skill

Install, configure, authorize, and troubleshoot Backstage Kubernetes frontend and backend plugins, cluster discovery, entity annotations, authentication, permissions, proxies, custom resources, and service-owner views. Use when working with Kubernetes tabs, clusters, pods, or integration errors.

paulasilvatech Skill

Imports existing Azure resources into Terraform through read-only discovery, dependency mapping, Azure Verified Module selection, source-derived import addresses, and drift-safe plans. Use when reverse-engineering a subscription, resource group, or ARM resource ID into maintainable IaC.

paulasilvatech Skill

Generate production-ready Product Requirements Documents for software systems and AI-powered features. Use when starting a product or feature cycle, translating a vague idea into requirements, defining AI system requirements, planning a feature, or creating a stakeholder source of truth.

paulasilvatech Skill

Design Azure API Center as the enterprise inventory and governance plane for APIs, agent tools, OpenAPI definitions, environments, deployments, metadata, linting, and MCP server discovery. Use when building an API or tool catalog, enforcing API standards, registering MCP servers, or making approved tools discoverable to agent builders.

paulasilvatech Bundle

Azure CLI operations run az commands for cloud resource discovery, subscription context, identity, AKS, ACR, Key Vault, RBAC, managed identity, and federated credential workflows. Use this skill when working with az login, az account, az aks, az acr, az keyvault, resource group checks, or Azure day-2 operations.