@saibolla/ada 0.1.2

package/skills/peer-review/references/reporting_standards.md

@@ -0,0 +1,290 @@
+# Scientific Reporting Standards and Guidelines
+
+This document catalogs major reporting standards and guidelines across scientific disciplines. When reviewing manuscripts, verify that authors have followed the appropriate guidelines for their study type and discipline.
+
+## Clinical Trials and Medical Research
+
+### CONSORT (Consolidated Standards of Reporting Trials)
+**Purpose:** Randomized controlled trials (RCTs)
+**Key Requirements:**
+- Trial design, participants, and interventions clearly described
+- Primary and secondary outcomes specified
+- Sample size calculation and statistical methods
+- Participant flow through trial (enrollment, allocation, follow-up, analysis)
+- Baseline characteristics of participants
+- Numbers analyzed in each group
+- Outcomes and estimation with confidence intervals
+- Adverse events
+- Trial registration number and protocol access
+
+**Reference:** http://www.consort-statement.org/
+
+### STROBE (Strengthening the Reporting of Observational Studies in Epidemiology)
+**Purpose:** Observational studies (cohort, case-control, cross-sectional)
+**Key Requirements:**
+- Study design clearly stated
+- Setting, eligibility criteria, and participant sources
+- Variables clearly defined
+- Data sources and measurement methods
+- Bias assessment
+- Sample size justification
+- Statistical methods including handling of missing data
+- Participant flow and characteristics
+- Main results with confidence intervals
+- Limitations discussed
+
+**Reference:** https://www.strobe-statement.org/
+
+### PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses)
+**Purpose:** Systematic reviews and meta-analyses
+**Key Requirements:**
+- Protocol registration
+- Systematic search strategy across multiple databases
+- Inclusion/exclusion criteria
+- Study selection process
+- Data extraction methods
+- Quality assessment of included studies
+- Statistical methods for meta-analysis
+- Assessment of publication bias
+- Heterogeneity assessment
+- PRISMA flow diagram showing study selection
+- Summary of findings tables
+
+**Reference:** http://www.prisma-statement.org/
+
+### SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials)
+**Purpose:** Clinical trial protocols
+**Key Requirements:**
+- Administrative information (title, registration, funding)
+- Introduction (rationale, objectives)
+- Methods (design, participants, interventions, outcomes, sample size)
+- Ethics and dissemination
+- Trial schedule and assessments
+
+**Reference:** https://www.spirit-statement.org/
+
+### CARE (CAse REport guidelines)
+**Purpose:** Case reports
+**Key Requirements:**
+- Patient information and demographics
+- Clinical findings
+- Timeline of events
+- Diagnostic assessment
+- Therapeutic interventions
+- Follow-up and outcomes
+- Patient perspective
+- Informed consent
+
+**Reference:** https://www.care-statement.org/
+
+## Animal Research
+
+### ARRIVE (Animal Research: Reporting of In Vivo Experiments)
+**Purpose:** Studies involving animal research
+**Key Requirements:**
+- Title indicates study involves animals
+- Abstract provides accurate summary
+- Background and objectives clearly stated
+- Ethical statement and approval
+- Housing and husbandry details
+- Animal details (species, strain, sex, age, weight)
+- Experimental procedures in detail
+- Experimental animals (number, allocation, welfare assessment)
+- Statistical methods appropriate
+- Exclusion criteria stated
+- Sample size determination
+- Randomization and blinding described
+- Outcome measures defined
+- Adverse events reported
+
+**Reference:** https://arriveguidelines.org/
+
+## Genomics and Molecular Biology
+
+### MIAME (Minimum Information About a Microarray Experiment)
+**Purpose:** Microarray experiments
+**Key Requirements:**
+- Experimental design clearly described
+- Array design information
+- Samples (origin, preparation, labeling)
+- Hybridization procedures and parameters
+- Image acquisition and quantification
+- Normalization and data transformation
+- Raw and processed data availability
+- Database accession numbers
+
+**Reference:** http://fged.org/projects/miame/
+
+### MINSEQE (Minimum Information about a high-throughput Nucleotide Sequencing Experiment)
+**Purpose:** High-throughput sequencing (RNA-seq, ChIP-seq, etc.)
+**Key Requirements:**
+- Experimental design and biological context
+- Sample information (source, preparation, QC)
+- Library preparation (protocol, adapters, size selection)
+- Sequencing platform and parameters
+- Data processing pipeline (alignment, quantification, normalization)
+- Quality control metrics
+- Raw data deposition (SRA, GEO, ENA)
+- Processed data and analysis code availability
+
+### MIGS/MIMS (Minimum Information about a Genome/Metagenome Sequence)
+**Purpose:** Genome and metagenome sequencing
+**Key Requirements:**
+- Sample origin and environmental context
+- Sequencing methods and coverage
+- Assembly methods and quality metrics
+- Annotation approach
+- Quality control and contamination screening
+- Data deposition in INSDC databases
+
+**Reference:** https://gensc.org/
+
+## Structural Biology
+
+### PDB (Protein Data Bank) Deposition Requirements
+**Purpose:** Macromolecular structure determination
+**Key Requirements:**
+- Atomic coordinates deposited
+- Structure factors for X-ray structures
+- Restraints and experimental data for NMR
+- EM maps and metadata for cryo-EM
+- Model quality validation metrics
+- Experimental conditions (crystallization, sample preparation)
+- Data collection parameters
+- Refinement statistics
+
+**Reference:** https://www.wwpdb.org/
+
+## Proteomics and Mass Spectrometry
+
+### MIAPE (Minimum Information About a Proteomics Experiment)
+**Purpose:** Proteomics experiments
+**Key Requirements:**
+- Sample processing and fractionation
+- Separation methods (2D gel, LC)
+- Mass spectrometry parameters (instrument, acquisition)
+- Database search and validation parameters
+- Peptide and protein identification criteria
+- Quantification methods
+- Statistical analysis
+- Data deposition (PRIDE, PeptideAtlas)
+
+**Reference:** http://www.psidev.info/
+
+## Neuroscience
+
+### COBIDAS (Committee on Best Practices in Data Analysis and Sharing)
+**Purpose:** MRI and fMRI studies
+**Key Requirements:**
+- Scanner and sequence parameters
+- Preprocessing pipeline details
+- Software versions and parameters
+- Statistical analysis approach
+- Multiple comparison correction
+- ROI definitions
+- Data sharing (raw data, analysis scripts)
+
+**Reference:** https://www.humanbrainmapping.org/cobidas
+
+## Flow Cytometry
+
+### MIFlowCyt (Minimum Information about a Flow Cytometry Experiment)
+**Purpose:** Flow cytometry experiments
+**Key Requirements:**
+- Experimental overview and purpose
+- Sample characteristics and preparation
+- Instrument information and settings
+- Reagents (antibodies, fluorophores, concentrations)
+- Compensation and controls
+- Gating strategy
+- Data analysis approach
+- Data availability
+
+**Reference:** http://flowcyt.org/
+
+## Ecology and Environmental Science
+
+### MIAPPE (Minimum Information About a Plant Phenotyping Experiment)
+**Purpose:** Plant phenotyping studies
+**Key Requirements:**
+- Investigation and study metadata
+- Biological material information
+- Environmental parameters
+- Experimental design and factors
+- Phenotypic measurements and methods
+- Data file descriptions
+
+**Reference:** https://www.miappe.org/
+
+## Chemistry and Chemical Biology
+
+### MIRIBEL (Minimum Information Reporting in Bio-Nano Experimental Literature)
+**Purpose:** Nanomaterial characterization
+**Key Requirements:**
+- Nanomaterial composition and structure
+- Size, shape, and morphology characterization
+- Surface chemistry and functionalization
+- Purity and stability
+- Experimental conditions
+- Characterization methods
+
+## Quality Assessment and Bias
+
+### CAMARADES (Collaborative Approach to Meta-Analysis and Review of Animal Data from Experimental Studies)
+**Purpose:** Quality assessment for animal studies in systematic reviews
+**Key Items:**
+- Publication in peer-reviewed journal
+- Statement of temperature control
+- Randomization to treatment
+- Blinded assessment of outcome
+- Avoidance of anesthetic with marked intrinsic properties
+- Use of appropriate animal model
+- Sample size calculation
+- Compliance with regulatory requirements
+- Statement of conflict of interest
+- Study pre-registration
+
+### SYRCLE's Risk of Bias Tool
+**Purpose:** Assessing risk of bias in animal intervention studies
+**Domains:**
+- Selection bias (sequence generation, baseline characteristics, allocation concealment)
+- Performance bias (random housing, blinding of personnel)
+- Detection bias (random outcome assessment, blinding of assessors)
+- Attrition bias (incomplete outcome data)
+- Reporting bias (selective outcome reporting)
+- Other sources of bias
+
+## General Principles Across Guidelines
+
+### Common Requirements
+1. **Transparency:** All methods, materials, and analyses fully described
+2. **Reproducibility:** Sufficient detail for independent replication
+3. **Data Availability:** Raw data and analysis code shared or deposited
+4. **Registration:** Studies pre-registered where applicable
+5. **Ethics:** Appropriate approvals and consent documented
+6. **Conflicts of Interest:** Disclosed for all authors
+7. **Statistical Rigor:** Methods appropriate and fully described
+8. **Completeness:** All outcomes reported, including negative results
+
+### Red Flags for Non-Compliance
+- Methods section lacks critical details
+- No mention of following reporting guidelines
+- Data availability statement missing or vague
+- No database accession numbers for omics data
+- No trial registration for clinical studies
+- Sample size not justified
+- Statistical methods inadequately described
+- Missing flow diagrams (CONSORT, PRISMA)
+- Selective reporting of outcomes
+
+## How to Use This Reference
+
+When reviewing a manuscript:
+1. Identify the study type and discipline
+2. Find the relevant reporting guideline(s)
+3. Check if authors mention following the guideline
+4. Verify that key requirements are addressed
+5. Note any missing elements in your review
+6. Suggest the appropriate guideline if not mentioned
+
+Many journals require authors to complete reporting checklists at submission. Reviewers should verify compliance even if a checklist was submitted.

package/skills/pennylane/SKILL.md

@@ -0,0 +1,224 @@
+---
+name: pennylane
+description: Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with PyTorch/JAX/TensorFlow. For hardware-specific optimizations use qiskit (IBM) or cirq (Google); for open quantum systems use qutip.
+license: Apache-2.0 license
+metadata:
+    skill-author: K-Dense Inc.
+---
+
+# PennyLane
+
+## Overview
+
+PennyLane is a quantum computing library that enables training quantum computers like neural networks. It provides automatic differentiation of quantum circuits, device-independent programming, and seamless integration with classical machine learning frameworks.
+
+## Installation
+
+Install using uv:
+
+```bash
+uv pip install pennylane
+```
+
+For quantum hardware access, install device plugins:
+
+```bash
+# IBM Quantum
+uv pip install pennylane-qiskit
+
+# Amazon Braket
+uv pip install amazon-braket-pennylane-plugin
+
+# Google Cirq
+uv pip install pennylane-cirq
+
+# Rigetti Forest
+uv pip install pennylane-rigetti
+
+# IonQ
+uv pip install pennylane-ionq
+```
+
+## Quick Start
+
+Build a quantum circuit and optimize its parameters:
+
+```python
+import pennylane as qml
+from pennylane import numpy as np
+
+# Create device
+dev = qml.device('default.qubit', wires=2)
+
+# Define quantum circuit
+@qml.qnode(dev)
+def circuit(params):
+    qml.RX(params[0], wires=0)
+    qml.RY(params[1], wires=1)
+    qml.CNOT(wires=[0, 1])
+    return qml.expval(qml.PauliZ(0))
+
+# Optimize parameters
+opt = qml.GradientDescentOptimizer(stepsize=0.1)
+params = np.array([0.1, 0.2], requires_grad=True)
+
+for i in range(100):
+    params = opt.step(circuit, params)
+```
+
+## Core Capabilities
+
+### 1. Quantum Circuit Construction
+
+Build circuits with gates, measurements, and state preparation. See `references/quantum_circuits.md` for:
+- Single and multi-qubit gates
+- Controlled operations and conditional logic
+- Mid-circuit measurements and adaptive circuits
+- Various measurement types (expectation, probability, samples)
+- Circuit inspection and debugging
+
+### 2. Quantum Machine Learning
+
+Create hybrid quantum-classical models. See `references/quantum_ml.md` for:
+- Integration with PyTorch, JAX, TensorFlow
+- Quantum neural networks and variational classifiers
+- Data encoding strategies (angle, amplitude, basis, IQP)
+- Training hybrid models with backpropagation
+- Transfer learning with quantum circuits
+
+### 3. Quantum Chemistry
+
+Simulate molecules and compute ground state energies. See `references/quantum_chemistry.md` for:
+- Molecular Hamiltonian generation
+- Variational Quantum Eigensolver (VQE)
+- UCCSD ansatz for chemistry
+- Geometry optimization and dissociation curves
+- Molecular property calculations
+
+### 4. Device Management
+
+Execute on simulators or quantum hardware. See `references/devices_backends.md` for:
+- Built-in simulators (default.qubit, lightning.qubit, default.mixed)
+- Hardware plugins (IBM, Amazon Braket, Google, Rigetti, IonQ)
+- Device selection and configuration
+- Performance optimization and caching
+- GPU acceleration and JIT compilation
+
+### 5. Optimization
+
+Train quantum circuits with various optimizers. See `references/optimization.md` for:
+- Built-in optimizers (Adam, gradient descent, momentum, RMSProp)
+- Gradient computation methods (backprop, parameter-shift, adjoint)
+- Variational algorithms (VQE, QAOA)
+- Training strategies (learning rate schedules, mini-batches)
+- Handling barren plateaus and local minima
+
+### 6. Advanced Features
+
+Leverage templates, transforms, and compilation. See `references/advanced_features.md` for:
+- Circuit templates and layers
+- Transforms and circuit optimization
+- Pulse-level programming
+- Catalyst JIT compilation
+- Noise models and error mitigation
+- Resource estimation
+
+## Common Workflows
+
+### Train a Variational Classifier
+
+```python
+# 1. Define ansatz
+@qml.qnode(dev)
+def classifier(x, weights):
+    # Encode data
+    qml.AngleEmbedding(x, wires=range(4))
+
+    # Variational layers
+    qml.StronglyEntanglingLayers(weights, wires=range(4))
+
+    return qml.expval(qml.PauliZ(0))
+
+# 2. Train
+opt = qml.AdamOptimizer(stepsize=0.01)
+weights = np.random.random((3, 4, 3))  # 3 layers, 4 wires
+
+for epoch in range(100):
+    for x, y in zip(X_train, y_train):
+        weights = opt.step(lambda w: (classifier(x, w) - y)**2, weights)
+```
+
+### Run VQE for Molecular Ground State
+
+```python
+from pennylane import qchem
+
+# 1. Build Hamiltonian
+symbols = ['H', 'H']
+coords = np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.74])
+H, n_qubits = qchem.molecular_hamiltonian(symbols, coords)
+
+# 2. Define ansatz
+@qml.qnode(dev)
+def vqe_circuit(params):
+    qml.BasisState(qchem.hf_state(2, n_qubits), wires=range(n_qubits))
+    qml.UCCSD(params, wires=range(n_qubits))
+    return qml.expval(H)
+
+# 3. Optimize
+opt = qml.AdamOptimizer(stepsize=0.1)
+params = np.zeros(10, requires_grad=True)
+
+for i in range(100):
+    params, energy = opt.step_and_cost(vqe_circuit, params)
+    print(f"Step {i}: Energy = {energy:.6f} Ha")
+```
+
+### Switch Between Devices
+
+```python
+# Same circuit, different backends
+circuit_def = lambda dev: qml.qnode(dev)(circuit_function)
+
+# Test on simulator
+dev_sim = qml.device('default.qubit', wires=4)
+result_sim = circuit_def(dev_sim)(params)
+
+# Run on quantum hardware
+dev_hw = qml.device('qiskit.ibmq', wires=4, backend='ibmq_manila')
+result_hw = circuit_def(dev_hw)(params)
+```
+
+## Detailed Documentation
+
+For comprehensive coverage of specific topics, consult the reference files:
+
+- **Getting started**: `references/getting_started.md` - Installation, basic concepts, first steps
+- **Quantum circuits**: `references/quantum_circuits.md` - Gates, measurements, circuit patterns
+- **Quantum ML**: `references/quantum_ml.md` - Hybrid models, framework integration, QNNs
+- **Quantum chemistry**: `references/quantum_chemistry.md` - VQE, molecular Hamiltonians, chemistry workflows
+- **Devices**: `references/devices_backends.md` - Simulators, hardware plugins, device configuration
+- **Optimization**: `references/optimization.md` - Optimizers, gradients, variational algorithms
+- **Advanced**: `references/advanced_features.md` - Templates, transforms, JIT compilation, noise
+
+## Best Practices
+
+1. **Start with simulators** - Test on `default.qubit` before deploying to hardware
+2. **Use parameter-shift for hardware** - Backpropagation only works on simulators
+3. **Choose appropriate encodings** - Match data encoding to problem structure
+4. **Initialize carefully** - Use small random values to avoid barren plateaus
+5. **Monitor gradients** - Check for vanishing gradients in deep circuits
+6. **Cache devices** - Reuse device objects to reduce initialization overhead
+7. **Profile circuits** - Use `qml.specs()` to analyze circuit complexity
+8. **Test locally** - Validate on simulators before submitting to hardware
+9. **Use templates** - Leverage built-in templates for common circuit patterns
+10. **Compile when possible** - Use Catalyst JIT for performance-critical code
+
+## Resources
+
+- Official documentation: https://docs.pennylane.ai
+- Codebook (tutorials): https://pennylane.ai/codebook
+- QML demonstrations: https://pennylane.ai/qml/demonstrations
+- Community forum: https://discuss.pennylane.ai
+- GitHub: https://github.com/PennyLaneAI/pennylane
+