@nice2dev/ui-tools 1.0.10

package/dist/scientific-research.d.ts

@@ -0,0 +1,1149 @@
+/**
+ * @file scientific-research.ts
+ * @module @nice2dev/ui-tools
+ * @description PRO-29 — Scientific & Research Tools
+ *
+ * Types for lab notebooks, experiment management, data analysis,
+ * and publication/collaboration in scientific environments.
+ */
+/** Scientific unit */
+export interface ScientificUnit {
+    symbol: string;
+    name: string;
+    dimension: UnitDimension;
+    siConversionFactor?: number;
+}
+/** Unit dimension */
+export type UnitDimension = 'length' | 'mass' | 'time' | 'temperature' | 'amount' | 'current' | 'luminosity' | 'dimensionless';
+/** Measurement */
+export interface Measurement {
+    value: number;
+    unit: string;
+    uncertainty?: number;
+    timestamp?: Date;
+}
+/** Digital signature */
+export interface DigitalSignature {
+    signerId: string;
+    signerName: string;
+    timestamp: Date;
+    reason?: string;
+    hash: string;
+    valid: boolean;
+}
+/** Audit trail entry */
+export interface AuditTrailEntry {
+    id: string;
+    timestamp: Date;
+    userId: string;
+    userName: string;
+    action: AuditAction;
+    field?: string;
+    oldValue?: string;
+    newValue?: string;
+    ipAddress?: string;
+    reason?: string;
+}
+/** Audit action */
+export type AuditAction = 'create' | 'update' | 'delete' | 'sign' | 'approve' | 'reject' | 'view' | 'export' | 'print';
+/** Lab notebook config */
+export interface LabNotebookConfig {
+    complianceMode?: ComplianceMode;
+    requireSignatures?: boolean;
+    autoNumbering?: boolean;
+    templates?: NotebookTemplate[];
+    allowedFormats?: string[];
+}
+/** Compliance mode */
+export type ComplianceMode = 'none' | '21_cfr_part_11' | 'glp' | 'gcp' | 'iso_17025';
+/** Notebook template */
+export interface NotebookTemplate {
+    id: string;
+    name: string;
+    type: TemplateType;
+    sections: TemplateSection[];
+    metadata?: Record<string, string>;
+}
+/** Template type */
+export type TemplateType = 'experiment' | 'protocol' | 'sop' | 'meeting' | 'general';
+/** Template section */
+export interface TemplateSection {
+    id: string;
+    name: string;
+    type: SectionType;
+    required?: boolean;
+    defaultContent?: string;
+    placeholder?: string;
+}
+/** Section type */
+export type SectionType = 'rich_text' | 'table' | 'formula' | 'image' | 'data_entry' | 'signature' | 'checklist';
+/** Lab notebook entry */
+export interface LabNotebookEntry {
+    id: string;
+    notebookId: string;
+    title: string;
+    entryNumber: string;
+    createdAt: Date;
+    updatedAt: Date;
+    author: string;
+    status: EntryStatus;
+    content: NotebookContent[];
+    tags?: string[];
+    linkedExperiments?: string[];
+    linkedProtocols?: string[];
+    signatures?: DigitalSignature[];
+    auditTrail: AuditTrailEntry[];
+    version: number;
+    previousVersionId?: string;
+}
+/** Entry status */
+export type EntryStatus = 'draft' | 'in_review' | 'signed' | 'locked';
+/** Notebook content */
+export interface NotebookContent {
+    id: string;
+    type: ContentType;
+    order: number;
+    data: ContentData;
+}
+/** Content type */
+export type ContentType = 'text' | 'heading' | 'table' | 'image' | 'formula' | 'data_form' | 'file_attachment' | 'signature_block' | 'checklist';
+/** Content data - union type for different content types */
+export type ContentData = TextContent | TableContent | ImageContent | FormulaContent | DataFormContent | FileAttachmentContent | ChecklistContent;
+/** Text content */
+export interface TextContent {
+    type: 'text' | 'heading';
+    html: string;
+    headingLevel?: 1 | 2 | 3 | 4 | 5 | 6;
+}
+/** Table content */
+export interface TableContent {
+    type: 'table';
+    rows: TableRow[];
+    headers?: string[];
+    caption?: string;
+}
+/** Table row */
+export interface TableRow {
+    cells: TableCell[];
+}
+/** Table cell */
+export interface TableCell {
+    value: string | number;
+    type?: 'text' | 'number' | 'formula';
+    format?: string;
+}
+/** Image content */
+export interface ImageContent {
+    type: 'image';
+    url: string;
+    alt?: string;
+    caption?: string;
+    width?: number;
+    height?: number;
+    annotations?: ImageAnnotation[];
+}
+/** Image annotation */
+export interface ImageAnnotation {
+    id: string;
+    type: 'arrow' | 'circle' | 'rectangle' | 'text';
+    x: number;
+    y: number;
+    width?: number;
+    height?: number;
+    text?: string;
+    color?: string;
+}
+/** Formula content */
+export interface FormulaContent {
+    type: 'formula';
+    latex: string;
+    displayMode?: boolean;
+    numbering?: string;
+}
+/** Data form content */
+export interface DataFormContent {
+    type: 'data_form';
+    fields: DataFormField[];
+    values: Record<string, unknown>;
+}
+/** Data form field */
+export interface DataFormField {
+    id: string;
+    label: string;
+    type: FieldType;
+    unit?: string;
+    required?: boolean;
+    validation?: FieldValidation;
+}
+/** Field type */
+export type FieldType = 'text' | 'number' | 'date' | 'time' | 'datetime' | 'select' | 'checkbox' | 'measurement';
+/** Field validation */
+export interface FieldValidation {
+    min?: number;
+    max?: number;
+    pattern?: string;
+    options?: string[];
+}
+/** File attachment content */
+export interface FileAttachmentContent {
+    type: 'file_attachment';
+    fileId: string;
+    fileName: string;
+    fileSize: number;
+    mimeType: string;
+    checksum?: string;
+}
+/** Checklist content */
+export interface ChecklistContent {
+    type: 'checklist';
+    items: ChecklistItem[];
+}
+/** Checklist item */
+export interface ChecklistItem {
+    id: string;
+    text: string;
+    checked: boolean;
+    checkedBy?: string;
+    checkedAt?: Date;
+}
+/** Protocol */
+export interface Protocol {
+    id: string;
+    title: string;
+    version: string;
+    status: DocumentStatus;
+    createdBy: string;
+    createdAt: Date;
+    updatedAt: Date;
+    approvedBy?: string;
+    approvedAt?: Date;
+    objective: string;
+    materials: ProtocolMaterial[];
+    equipment: ProtocolEquipment[];
+    safetyWarnings?: SafetyWarning[];
+    steps: ProtocolStep[];
+    expectedResults?: string;
+    troubleshooting?: TroubleshootingItem[];
+    references?: Reference[];
+    attachments?: string[];
+}
+/** Document status */
+export type DocumentStatus = 'draft' | 'in_review' | 'approved' | 'superseded' | 'retired';
+/** Protocol material */
+export interface ProtocolMaterial {
+    name: string;
+    catalogNumber?: string;
+    vendor?: string;
+    quantity: number;
+    unit: string;
+    concentration?: string;
+    storageConditions?: string;
+    notes?: string;
+}
+/** Protocol equipment */
+export interface ProtocolEquipment {
+    name: string;
+    model?: string;
+    calibrationRequired?: boolean;
+    settings?: Record<string, string>;
+}
+/** Safety warning */
+export interface SafetyWarning {
+    type: SafetyWarningType;
+    message: string;
+    ppe?: string[];
+}
+/** Safety warning type */
+export type SafetyWarningType = 'biohazard' | 'chemical' | 'radiation' | 'electrical' | 'fire' | 'temperature' | 'pressure' | 'general';
+/** Protocol step */
+export interface ProtocolStep {
+    number: number;
+    instruction: string;
+    duration?: number;
+    durationUnit?: 'seconds' | 'minutes' | 'hours' | 'days';
+    temperature?: string;
+    criticalStep?: boolean;
+    notes?: string;
+    subSteps?: string[];
+    imageUrl?: string;
+}
+/** Troubleshooting item */
+export interface TroubleshootingItem {
+    problem: string;
+    possibleCause: string;
+    solution: string;
+}
+/** Reference */
+export interface Reference {
+    type: ReferenceType;
+    title: string;
+    authors?: string[];
+    year?: number;
+    journal?: string;
+    volume?: string;
+    pages?: string;
+    doi?: string;
+    pmid?: string;
+    url?: string;
+}
+/** Reference type */
+export type ReferenceType = 'journal_article' | 'book' | 'book_chapter' | 'thesis' | 'conference' | 'website' | 'patent' | 'preprint';
+/** SOP (Standard Operating Procedure) */
+export interface SOP {
+    id: string;
+    sopNumber: string;
+    title: string;
+    version: string;
+    status: DocumentStatus;
+    effectiveDate?: Date;
+    reviewDate?: Date;
+    department?: string;
+    scope: string;
+    responsibilities?: SOPResponsibility[];
+    procedure: Protocol;
+    trainingRecords?: TrainingRecord[];
+    relatedSOPs?: string[];
+    changeHistory: ChangeHistoryEntry[];
+}
+/** SOP responsibility */
+export interface SOPResponsibility {
+    role: string;
+    description: string;
+}
+/** Training record */
+export interface TrainingRecord {
+    userId: string;
+    userName: string;
+    trainedDate: Date;
+    method: TrainingMethod;
+    trainer?: string;
+    expirationDate?: Date;
+    assessment?: AssessmentResult;
+}
+/** Training method */
+export type TrainingMethod = 'read_understand' | 'classroom' | 'hands_on' | 'online' | 'demonstration';
+/** Assessment result */
+export interface AssessmentResult {
+    passed: boolean;
+    score?: number;
+    attempts?: number;
+    completedAt: Date;
+}
+/** Change history entry */
+export interface ChangeHistoryEntry {
+    version: string;
+    date: Date;
+    author: string;
+    description: string;
+    approvedBy?: string;
+}
+/** Research proposal */
+export interface ResearchProposal {
+    id: string;
+    title: string;
+    status: ProposalStatus;
+    fundingAgency?: string;
+    submissionDeadline?: Date;
+    submittedDate?: Date;
+    principalInvestigator: Researcher;
+    coInvestigators?: Researcher[];
+    sections: ProposalSection[];
+    budget: ProposalBudget;
+    timeline: ProposalTimeline[];
+    attachments?: string[];
+}
+/** Proposal status */
+export type ProposalStatus = 'draft' | 'internal_review' | 'submitted' | 'under_review' | 'funded' | 'rejected' | 'withdrawn';
+/** Researcher */
+export interface Researcher {
+    id: string;
+    name: string;
+    title?: string;
+    institution: string;
+    department?: string;
+    email: string;
+    orcid?: string;
+}
+/** Proposal section */
+export interface ProposalSection {
+    id: string;
+    name: string;
+    type: ProposalSectionType;
+    content: string;
+    wordCount?: number;
+    wordLimit?: number;
+}
+/** Proposal section type */
+export type ProposalSectionType = 'abstract' | 'specific_aims' | 'background' | 'methodology' | 'expected_outcomes' | 'significance' | 'innovation' | 'timeline' | 'budget_justification' | 'references' | 'appendix';
+/** Proposal budget */
+export interface ProposalBudget {
+    totalRequested: number;
+    currency: string;
+    years: BudgetYear[];
+    justification?: string;
+}
+/** Budget year */
+export interface BudgetYear {
+    year: number;
+    personnel: BudgetLine[];
+    equipment: BudgetLine[];
+    supplies: BudgetLine[];
+    travel: BudgetLine[];
+    other: BudgetLine[];
+    indirectCosts?: number;
+    total: number;
+}
+/** Budget line */
+export interface BudgetLine {
+    description: string;
+    amount: number;
+    justification?: string;
+}
+/** Proposal timeline */
+export interface ProposalTimeline {
+    milestone: string;
+    startMonth: number;
+    endMonth: number;
+    year: number;
+}
+/** Bibliography entry */
+export interface BibliographyEntry {
+    id: string;
+    citeKey: string;
+    reference: Reference;
+    abstract?: string;
+    keywords?: string[];
+    notes?: string;
+    pdfFile?: string;
+    addedDate: Date;
+    readStatus?: ReadStatus;
+    rating?: number;
+    collections?: string[];
+    highlights?: Highlight[];
+}
+/** Read status */
+export type ReadStatus = 'unread' | 'reading' | 'read' | 'archived';
+/** Highlight */
+export interface Highlight {
+    id: string;
+    text: string;
+    page?: number;
+    color?: string;
+    note?: string;
+    createdAt: Date;
+}
+/** Citation style */
+export type CitationStyle = 'apa' | 'mla' | 'chicago' | 'ieee' | 'vancouver' | 'harvard' | 'nature' | 'science' | 'cell' | 'custom';
+/** Experiment */
+export interface Experiment {
+    id: string;
+    experimentNumber: string;
+    title: string;
+    objective: string;
+    status: ExperimentStatus;
+    type: ExperimentType;
+    startDate: Date;
+    endDate?: Date;
+    researcher: string;
+    collaborators?: string[];
+    protocolId?: string;
+    design: ExperimentDesign;
+    samples?: ExperimentSample[];
+    results?: ExperimentResult[];
+    conclusions?: string;
+    notebookEntries?: string[];
+    linkedExperiments?: string[];
+    tags?: string[];
+}
+/** Experiment status */
+export type ExperimentStatus = 'planned' | 'in_progress' | 'completed' | 'failed' | 'cancelled' | 'on_hold';
+/** Experiment type */
+export type ExperimentType = 'screening' | 'optimization' | 'validation' | 'pilot' | 'full_scale' | 'replication';
+/** Experiment design */
+export interface ExperimentDesign {
+    type: DesignType;
+    variables: ExperimentVariable[];
+    controls: ExperimentControl[];
+    replicates: number;
+    randomization?: boolean;
+    blindingLevel?: BlindingLevel;
+    statisticalPower?: number;
+}
+/** Design type */
+export type DesignType = 'factorial' | 'randomized_block' | 'latin_square' | 'split_plot' | 'crossover' | 'case_control' | 'cohort' | 'single_factor';
+/** Experiment variable */
+export interface ExperimentVariable {
+    name: string;
+    type: VariableType;
+    levels?: string[] | number[];
+    unit?: string;
+    description?: string;
+}
+/** Variable type */
+export type VariableType = 'independent' | 'dependent' | 'controlled' | 'confounding';
+/** Experiment control */
+export interface ExperimentControl {
+    type: ControlType;
+    description: string;
+    sampleIds?: string[];
+}
+/** Control type */
+export type ControlType = 'positive' | 'negative' | 'blank' | 'vehicle' | 'sham' | 'placebo';
+/** Blinding level */
+export type BlindingLevel = 'none' | 'single' | 'double' | 'triple';
+/** Experiment sample */
+export interface ExperimentSample {
+    sampleId: string;
+    group: string;
+    condition: string;
+    measurements: Measurement[];
+}
+/** Experiment result */
+export interface ExperimentResult {
+    id: string;
+    type: ResultType;
+    variable: string;
+    dataPoints: DataPoint[];
+    statistics?: ResultStatistics;
+    visualizationUrl?: string;
+}
+/** Result type */
+export type ResultType = 'quantitative' | 'qualitative' | 'categorical' | 'image' | 'spectrum';
+/** Data point */
+export interface DataPoint {
+    x?: number;
+    y: number;
+    label?: string;
+    error?: number;
+    metadata?: Record<string, unknown>;
+}
+/** Result statistics */
+export interface ResultStatistics {
+    mean?: number;
+    median?: number;
+    standardDeviation?: number;
+    standardError?: number;
+    min?: number;
+    max?: number;
+    n: number;
+    pValue?: number;
+    confidenceInterval?: [number, number];
+}
+/** Sample */
+export interface Sample {
+    id: string;
+    sampleId: string;
+    name: string;
+    type: SampleType;
+    status: SampleStatus;
+    source?: string;
+    collectionDate?: Date;
+    collectionMethod?: string;
+    quantity: number;
+    quantityUnit: string;
+    concentration?: number;
+    concentrationUnit?: string;
+    storageLocation: StorageLocation;
+    storageConditions: StorageConditions;
+    expirationDate?: Date;
+    parentSampleId?: string;
+    aliquots?: string[];
+    chainOfCustody: CustodyEvent[];
+    barcode?: string;
+    qrCode?: string;
+    metadata?: Record<string, unknown>;
+}
+/** Sample type */
+export type SampleType = 'biological' | 'chemical' | 'environmental' | 'clinical' | 'reagent' | 'standard' | 'control' | 'other';
+/** Sample status */
+export type SampleStatus = 'available' | 'in_use' | 'depleted' | 'expired' | 'quarantined' | 'disposed';
+/** Storage location */
+export interface StorageLocation {
+    room: string;
+    equipment: string;
+    shelf?: string;
+    rack?: string;
+    box?: string;
+    position?: string;
+}
+/** Storage conditions */
+export interface StorageConditions {
+    temperature: number;
+    temperatureUnit: 'C' | 'F' | 'K';
+    humidity?: number;
+    lightSensitive?: boolean;
+    specialRequirements?: string[];
+}
+/** Custody event */
+export interface CustodyEvent {
+    timestamp: Date;
+    action: CustodyAction;
+    userId: string;
+    userName: string;
+    fromLocation?: StorageLocation;
+    toLocation?: StorageLocation;
+    notes?: string;
+}
+/** Custody action */
+export type CustodyAction = 'received' | 'stored' | 'retrieved' | 'transferred' | 'aliquoted' | 'tested' | 'disposed';
+/** Instrument */
+export interface Instrument {
+    id: string;
+    name: string;
+    model: string;
+    manufacturer: string;
+    serialNumber: string;
+    location: string;
+    status: InstrumentStatus;
+    purchaseDate?: Date;
+    warrantyExpiration?: Date;
+    maintenanceSchedule: MaintenanceSchedule[];
+    calibrationRecords: CalibrationRecord[];
+    usageLog: UsageLogEntry[];
+    documents?: string[];
+}
+/** Instrument status */
+export type InstrumentStatus = 'operational' | 'under_maintenance' | 'calibration_due' | 'out_of_service' | 'retired';
+/** Maintenance schedule */
+export interface MaintenanceSchedule {
+    type: MaintenanceType;
+    frequency: string;
+    lastPerformed?: Date;
+    nextDue: Date;
+    assignedTo?: string;
+}
+/** Maintenance type */
+export type MaintenanceType = 'preventive' | 'corrective' | 'calibration' | 'validation' | 'cleaning';
+/** Calibration record */
+export interface CalibrationRecord {
+    id: string;
+    date: Date;
+    performedBy: string;
+    standard: string;
+    results: CalibrationResult[];
+    passed: boolean;
+    certificateUrl?: string;
+    nextCalibrationDate?: Date;
+}
+/** Calibration result */
+export interface CalibrationResult {
+    parameter: string;
+    expectedValue: number;
+    measuredValue: number;
+    tolerance: number;
+    passed: boolean;
+}
+/** Usage log entry */
+export interface UsageLogEntry {
+    id: string;
+    userId: string;
+    userName: string;
+    startTime: Date;
+    endTime?: Date;
+    purpose: string;
+    experimentId?: string;
+    notes?: string;
+}
+/** Research dataset */
+export interface ResearchDataset {
+    id: string;
+    name: string;
+    description: string;
+    type: DatasetType;
+    format: string;
+    size: number;
+    sizeUnit: 'B' | 'KB' | 'MB' | 'GB' | 'TB';
+    createdDate: Date;
+    modifiedDate: Date;
+    creator: string;
+    license?: string;
+    doi?: string;
+    version: string;
+    metadata: DatasetMetadata;
+    accessLevel: AccessLevel;
+    dataLineage?: DataLineage;
+    qualityScore?: number;
+}
+/** Dataset type */
+export type DatasetType = 'raw' | 'processed' | 'analyzed' | 'simulated' | 'reference';
+/** Dataset metadata (FAIR principles) */
+export interface DatasetMetadata {
+    title: string;
+    description: string;
+    keywords: string[];
+    subjects?: string[];
+    temporalCoverage?: string;
+    spatialCoverage?: string;
+    methodology?: string;
+    instruments?: string[];
+    relatedPublications?: string[];
+    fundingSource?: string;
+    customFields?: Record<string, string>;
+}
+/** Access level */
+export type AccessLevel = 'public' | 'restricted' | 'embargoed' | 'private';
+/** Data lineage */
+export interface DataLineage {
+    sourceDatasets?: string[];
+    processingSteps: ProcessingStep[];
+    toolsUsed?: string[];
+}
+/** Processing step */
+export interface ProcessingStep {
+    order: number;
+    name: string;
+    description: string;
+    parameters?: Record<string, unknown>;
+    timestamp?: Date;
+}
+/** Statistical analysis config */
+export interface StatisticalAnalysisConfig {
+    significanceLevel: number;
+    confidenceLevel: number;
+    multipleTestingCorrection?: MultipleTestingCorrection;
+    missingDataHandling?: MissingDataHandling;
+}
+/** Multiple testing correction */
+export type MultipleTestingCorrection = 'none' | 'bonferroni' | 'holm' | 'fdr_bh' | 'fdr_by';
+/** Missing data handling */
+export type MissingDataHandling = 'listwise_deletion' | 'pairwise_deletion' | 'mean_imputation' | 'median_imputation' | 'multiple_imputation';
+/** Descriptive statistics */
+export interface DescriptiveStatistics {
+    n: number;
+    mean: number;
+    median: number;
+    mode?: number[];
+    standardDeviation: number;
+    variance: number;
+    standardError: number;
+    min: number;
+    max: number;
+    range: number;
+    q1: number;
+    q3: number;
+    iqr: number;
+    skewness?: number;
+    kurtosis?: number;
+}
+/** Statistical test result */
+export interface StatisticalTestResult {
+    testName: string;
+    testStatistic: number;
+    degreesOfFreedom?: number | [number, number];
+    pValue: number;
+    effectSize?: number;
+    effectSizeType?: string;
+    confidenceInterval?: [number, number];
+    conclusion: string;
+    assumptions?: AssumptionCheck[];
+}
+/** Assumption check */
+export interface AssumptionCheck {
+    assumption: string;
+    testUsed?: string;
+    result: 'met' | 'violated' | 'unclear';
+    details?: string;
+}
+/** Regression result */
+export interface RegressionResult {
+    type: RegressionType;
+    equation: string;
+    coefficients: RegressionCoefficient[];
+    rSquared: number;
+    adjustedRSquared: number;
+    standardError: number;
+    fStatistic?: number;
+    pValue: number;
+    residuals?: number[];
+    predictedValues?: number[];
+}
+/** Regression type */
+export type RegressionType = 'linear' | 'multiple_linear' | 'logistic' | 'polynomial' | 'ridge' | 'lasso';
+/** Regression coefficient */
+export interface RegressionCoefficient {
+    variable: string;
+    estimate: number;
+    standardError: number;
+    tStatistic: number;
+    pValue: number;
+    confidenceInterval: [number, number];
+}
+/** PCA result */
+export interface PCAResult {
+    components: PrincipalComponent[];
+    loadings: number[][];
+    scores: number[][];
+    totalVariance: number;
+    explainedVarianceRatio: number[];
+    cumulativeVarianceRatio: number[];
+}
+/** Principal component */
+export interface PrincipalComponent {
+    index: number;
+    eigenvalue: number;
+    explainedVariance: number;
+    cumulativeVariance: number;
+}
+/** Survival analysis result */
+export interface SurvivalAnalysisResult {
+    method: SurvivalMethod;
+    survivalCurve: SurvivalPoint[];
+    medianSurvival?: number;
+    confidenceInterval?: [number, number];
+    atRiskTable: AtRiskTableEntry[];
+    comparisonTest?: StatisticalTestResult;
+    coxModel?: CoxModelResult;
+}
+/** Survival method */
+export type SurvivalMethod = 'kaplan_meier' | 'nelson_aalen' | 'cox_proportional_hazards';
+/** Survival point */
+export interface SurvivalPoint {
+    time: number;
+    survivalProbability: number;
+    standardError?: number;
+    lowerCI?: number;
+    upperCI?: number;
+    nEvents: number;
+    nCensored: number;
+}
+/** At-risk table entry */
+export interface AtRiskTableEntry {
+    time: number;
+    nAtRisk: number;
+    nEvents: number;
+    nCensored: number;
+}
+/** Cox model result */
+export interface CoxModelResult {
+    coefficients: HazardRatioCoefficient[];
+    concordance: number;
+    logLikelihood: number;
+    likelihoodRatioTest: StatisticalTestResult;
+}
+/** Hazard ratio coefficient */
+export interface HazardRatioCoefficient {
+    variable: string;
+    coefficient: number;
+    hazardRatio: number;
+    standardError: number;
+    zStatistic: number;
+    pValue: number;
+    confidenceInterval: [number, number];
+}
+/** Heatmap config */
+export interface HeatmapClusterConfig {
+    data: number[][];
+    rowLabels: string[];
+    columnLabels: string[];
+    clustering: ClusteringConfig;
+    colorScale: ColorScale;
+    cellSize?: {
+        width: number;
+        height: number;
+    };
+    showDendrogram?: boolean;
+    annotations?: HeatmapAnnotation[];
+}
+/** Clustering config */
+export interface ClusteringConfig {
+    method: ClusteringMethod;
+    metric: DistanceMetric;
+    linkage?: LinkageMethod;
+    k?: number;
+    rowCluster?: boolean;
+    columnCluster?: boolean;
+}
+/** Clustering method */
+export type ClusteringMethod = 'hierarchical' | 'kmeans' | 'dbscan' | 'none';
+/** Distance metric */
+export type DistanceMetric = 'euclidean' | 'manhattan' | 'cosine' | 'correlation' | 'jaccard';
+/** Linkage method */
+export type LinkageMethod = 'single' | 'complete' | 'average' | 'ward';
+/** Color scale */
+export interface ColorScale {
+    type: 'sequential' | 'diverging' | 'categorical';
+    colors: string[];
+    domain?: [number, number];
+    midpoint?: number;
+}
+/** Heatmap annotation */
+export interface HeatmapAnnotation {
+    type: 'row' | 'column';
+    index: number;
+    label?: string;
+    color?: string;
+}
+/** Sequence */
+export interface Sequence {
+    id: string;
+    name: string;
+    type: SequenceType;
+    sequence: string;
+    length: number;
+    features?: SequenceFeature[];
+    description?: string;
+    organism?: string;
+    accession?: string;
+}
+/** Sequence type */
+export type SequenceType = 'dna' | 'rna' | 'protein';
+/** Sequence feature */
+export interface SequenceFeature {
+    type: string;
+    start: number;
+    end: number;
+    strand?: '+' | '-';
+    name?: string;
+    color?: string;
+    qualifiers?: Record<string, string>;
+}
+/** Sequence alignment */
+export interface SequenceAlignment {
+    sequences: AlignedSequence[];
+    consensusSequence?: string;
+    conservationScores?: number[];
+    method?: AlignmentMethod;
+    score?: number;
+}
+/** Aligned sequence */
+export interface AlignedSequence {
+    id: string;
+    name: string;
+    alignedSequence: string;
+}
+/** Alignment method */
+export type AlignmentMethod = 'clustalw' | 'muscle' | 'mafft' | 'needleman_wunsch' | 'smith_waterman';
+/** Molecule */
+export interface Molecule {
+    id: string;
+    name: string;
+    formula?: string;
+    molecularWeight?: number;
+    smiles?: string;
+    inchi?: string;
+    pdbId?: string;
+    atoms?: Atom[];
+    bonds?: Bond[];
+    coordinates?: Coordinate3D[];
+}
+/** Atom */
+export interface Atom {
+    id: number;
+    element: string;
+    x: number;
+    y: number;
+    z: number;
+    charge?: number;
+    residue?: string;
+    chain?: string;
+}
+/** Bond */
+export interface Bond {
+    atom1: number;
+    atom2: number;
+    order: 1 | 2 | 3 | 'aromatic';
+}
+/** 3D coordinate */
+export interface Coordinate3D {
+    x: number;
+    y: number;
+    z: number;
+}
+/** Molecule viewer config */
+export interface MoleculeViewerConfig {
+    representation: MoleculeRepresentation;
+    colorScheme: MoleculeColorScheme;
+    showHydrogens?: boolean;
+    showLabels?: boolean;
+    backgroundColor?: string;
+    spinAnimation?: boolean;
+}
+/** Molecule representation */
+export type MoleculeRepresentation = 'ball_and_stick' | 'space_filling' | 'ribbon' | 'cartoon' | 'wireframe' | 'surface';
+/** Molecule color scheme */
+export type MoleculeColorScheme = 'element' | 'chain' | 'residue' | 'secondary_structure' | 'bfactor' | 'custom';
+/** Scientific paper */
+export interface ScientificPaper {
+    id: string;
+    title: string;
+    authors: PaperAuthor[];
+    affiliations: Affiliation[];
+    abstract: string;
+    keywords: string[];
+    sections: PaperSection[];
+    figures: PaperFigure[];
+    tables: PaperTable[];
+    references: BibliographyEntry[];
+    supplementaryMaterials?: SupplementaryMaterial[];
+    status: PaperStatus;
+    targetJournal?: string;
+    wordCount: number;
+    characterCount: number;
+    submissionHistory?: SubmissionRecord[];
+}
+/** Paper author */
+export interface PaperAuthor {
+    id: string;
+    name: string;
+    email?: string;
+    affiliationIds: string[];
+    isCorresponding?: boolean;
+    orcid?: string;
+    contribution?: string;
+}
+/** Affiliation */
+export interface Affiliation {
+    id: string;
+    institution: string;
+    department?: string;
+    address?: string;
+    country: string;
+}
+/** Paper section */
+export interface PaperSection {
+    id: string;
+    type: PaperSectionType;
+    title?: string;
+    content: string;
+    wordCount: number;
+    subsections?: PaperSection[];
+}
+/** Paper section type */
+export type PaperSectionType = 'abstract' | 'introduction' | 'methods' | 'results' | 'discussion' | 'conclusion' | 'acknowledgments' | 'author_contributions' | 'data_availability' | 'conflicts_of_interest' | 'funding' | 'appendix' | 'custom';
+/** Paper figure */
+export interface PaperFigure {
+    id: string;
+    number: string;
+    caption: string;
+    panels: FigurePanel[];
+    width?: number;
+    height?: number;
+    dpi?: number;
+    format: ImageFormat;
+}
+/** Figure panel */
+export interface FigurePanel {
+    label: string;
+    imageUrl: string;
+    description?: string;
+}
+/** Image format */
+export type ImageFormat = 'tiff' | 'eps' | 'pdf' | 'png' | 'jpg' | 'svg';
+/** Paper table */
+export interface PaperTable {
+    id: string;
+    number: string;
+    title: string;
+    caption?: string;
+    headers: string[];
+    rows: string[][];
+    footnotes?: string[];
+}
+/** Supplementary material */
+export interface SupplementaryMaterial {
+    id: string;
+    type: SupplementaryType;
+    title: string;
+    description?: string;
+    fileUrl?: string;
+    content?: string;
+}
+/** Supplementary type */
+export type SupplementaryType = 'figure' | 'table' | 'dataset' | 'video' | 'code' | 'methods' | 'other';
+/** Paper status */
+export type PaperStatus = 'draft' | 'internal_review' | 'submitted' | 'under_review' | 'revision_requested' | 'resubmitted' | 'accepted' | 'published' | 'rejected';
+/** Submission record */
+export interface SubmissionRecord {
+    journal: string;
+    submittedDate: Date;
+    decision?: SubmissionDecision;
+    decisionDate?: Date;
+    reviewerComments?: ReviewerComment[];
+    revisionDeadline?: Date;
+}
+/** Submission decision */
+export type SubmissionDecision = 'accept' | 'minor_revision' | 'major_revision' | 'reject';
+/** Reviewer comment */
+export interface ReviewerComment {
+    reviewerId: string;
+    commentNumber: number;
+    section?: string;
+    comment: string;
+    response?: string;
+    status?: 'open' | 'addressed' | 'in_progress';
+}
+/** Collaboration hub config */
+export interface CollaborationHubConfig {
+    projectId: string;
+    members: CollaborationMember[];
+    sharedDocuments: SharedDocument[];
+    discussionThreads: DiscussionThread[];
+    tasks: CollaborationTask[];
+    meetings: MeetingNote[];
+}
+/** Collaboration member */
+export interface CollaborationMember {
+    userId: string;
+    name: string;
+    email: string;
+    role: CollaborationRole;
+    institution?: string;
+    permissions: Permission[];
+}
+/** Collaboration role */
+export type CollaborationRole = 'principal_investigator' | 'co_investigator' | 'postdoc' | 'graduate_student' | 'research_assistant' | 'technician' | 'external_collaborator';
+/** Permission */
+export type Permission = 'read' | 'write' | 'comment' | 'approve' | 'admin';
+/** Shared document */
+export interface SharedDocument {
+    id: string;
+    title: string;
+    type: string;
+    url: string;
+    lastModified: Date;
+    lastModifiedBy: string;
+    version: number;
+    permissions: Record<string, Permission[]>;
+}
+/** Discussion thread */
+export interface DiscussionThread {
+    id: string;
+    title: string;
+    createdBy: string;
+    createdAt: Date;
+    status: 'open' | 'resolved' | 'closed';
+    documentId?: string;
+    comments: DiscussionComment[];
+}
+/** Discussion comment */
+export interface DiscussionComment {
+    id: string;
+    author: string;
+    content: string;
+    timestamp: Date;
+    reactions?: Record<string, string[]>;
+    replies?: DiscussionComment[];
+}
+/** Collaboration task */
+export interface CollaborationTask {
+    id: string;
+    title: string;
+    description?: string;
+    assignee?: string;
+    dueDate?: Date;
+    status: 'todo' | 'in_progress' | 'review' | 'done';
+    priority: 'low' | 'medium' | 'high';
+    linkedDocuments?: string[];
+}
+/** Meeting note */
+export interface MeetingNote {
+    id: string;
+    title: string;
+    date: Date;
+    attendees: string[];
+    agenda?: string[];
+    notes: string;
+    actionItems: CollaborationTask[];
+    recordingUrl?: string;
+}
+//# sourceMappingURL=scientific-research.d.ts.map