Molecular Design LabResearch workflows · Contextual guidance · Reproducible outputsUSER GUIDE
Research user guide

Choose the right workflow, then validate every step

This guide explains every item in the Molecular Design Lab sidebar: what it is for, when to use it, the recommended workflow, what to verify before trusting an output, and where the result can go next.

One known variantVariant → Experiment → Evidence → Primers / 3D / Report Many variantsBatch VCF → filter/prioritize → single-variant workflow Multiple samplesCohort Analysis → GT/DP/AD/GQ/VAF → candidate prioritization Need PCR primersPrimer Design for ordinary targets; Variant-aware Primers for a validated allele Need specificity QCAssay QC → target validation → reference-panel / optional NCBI BLAST screening Need a plasmid construct?Plasmid Designer → map → cloning primers → Assay QC → GenBank/FASTA Need to choose a candidate?Scientific Decision → compare → rationale → reportNeed a recordScientific Report → PDF / CSV / JSON / reproducibility fingerprint Ready to hand off?Workflow Review → completeness gates → reproducibility bundle

Workflow map

Gene / sequence / VCF→Target or variant mapping→Evidence / prioritization→Primer / 3D experiment design→Assay QC / specificity→Plasmid design / construct record→Scientific Decision→Scientific Report→Workflow Review / handoff

Dashboard

The starting point when you want to choose a tool rather than continue an existing workflow.

Use it when

  • You are not sure which tool fits the research question.
  • You want to open a saved workspace or start a new assay/variant workflow.

Recommended workflow

  1. Define whether your input is a sequence, one variant, a VCF, or a multi-sample VCF.
  2. Choose the matching tool.
  3. Preserve important results in Projects or Scientific Report.
Next: sequence/assay → Design Assay or Primer Design; one variant → Variant → Experiment; many variants → Batch VCF; multiple samples → Cohort Analysis.

Design Assay

A decision entry point for choosing the assay-design workflow that best matches your research goal.

Input

  • Biological target
  • Experimental objective
  • Sequence/accession context when available

Workflow

  1. Define target and assay goal.
  2. Select the recommended specialized tool.
  3. Carry target information forward.
  4. Review assay-specific QC.
Check: organism, target identity and assay type before continuing. Tool selection is research planning, not assay validation.

Primer Design

Design conventional PCR/Sanger primer pairs around a DNA target.

Workflow

  1. Paste/retrieve a 5′→3′ DNA sequence.
  2. Set Tm, GC, product size and number of returned candidates.
  3. Generate primer pairs.
  4. Review hairpin, dimer, Tm balance and specificity.
  5. Export or save the chosen design.

Verify

  • Correct target orientation
  • Amplicon covers intended region
  • Balanced primer Tm
  • Specificity/off-target evidence
  • Appropriate controls
In-silico quality does not guarantee amplification efficiency or laboratory specificity.

RT-qPCR Primer Design

Design short expression-oriented amplicons with transcript/exon context.

Workflow

  1. Use transcript/cDNA sequence and exon ranges when available.
  2. Choose qPCR-compatible product length and Tm.
  3. Generate pairs and inspect exon-junction placement.
  4. Prefer designs minimizing unwanted genomic amplification when relevant.

Verify

  • Transcript isoform
  • Junction/exon context
  • Short amplicon
  • Efficiency, melt curve and reference-gene controls in the lab
A computationally valid qPCR pair still needs efficiency and specificity validation.

Peptide Analysis

Analyze peptide properties and generate research candidates before downstream binding or experimental work.

Workflow

  1. Enter peptide/protein-derived sequence.
  2. Run sequence/property analysis.
  3. Review candidate regions and liabilities.
  4. Send relevant candidates to MHC/HLA Prediction.

Verify

  • Sequence and length
  • Hydrophobic/charged regions
  • Synthesis constraints
  • Biological context
Predicted properties are screening aids and do not establish biological activity.

MHC / HLA Prediction

Rank peptide candidates for predicted binding to supported MHC/HLA alleles.

Workflow

  1. Select class I or II.
  2. Select allele(s).
  3. Submit peptide sequence/candidates.
  4. Rank predicted binders across relevant alleles.
  5. Carry selected peptides to experimental validation.

Verify

  • Correct allele nomenclature
  • Appropriate peptide length
  • Class I vs class II context
  • More than one evidence signal when possible
Binding prediction does not establish processing, presentation, immunogenicity or response.

3D Structure & Binding

Inspect structural context after protein/variant mapping.

Workflow

  1. Open a protein or use the Variant → Experiment handoff.
  2. Confirm accession and residue numbering.
  3. Inspect mapped structures and residue context.
  4. Use structural observations to support a testable hypothesis.

Verify

  • Protein isoform
  • Residue mapping
  • Structure coverage/quality
  • Binding-site context
Structural proximity alone does not prove functional or clinical effect.

Variant → Experiment

The central single-variant workflow: transcript compatibility → protein/cDNA effect → genomic validation → evidence → experiment.

Workflow

  1. Enter gene and organism.
  2. Retrieve RefSeq/UniProt records or enter an exact RefSeq accession.
  3. Enter protein or cDNA variant.
  4. Review the comprehensive RefSeq Match/Mismatch/No usable CDS table.
  5. If several transcripts are compatible, explicitly choose the intended transcript.
  6. For cDNA variants, validate genomic coordinate/reference allele.
  7. Review dbSNP, ClinVar, gnomAD and Phase 7 computational evidence.
  8. Send to Variant-aware Primers, 3D or Scientific Report.

Verify

  • Exact transcript accession
  • CDS/codon/reference match
  • Genomic reference allele
  • Assembly/accession provenance
  • ClinVar review context and population frequency
  • Predictors as supporting evidence only
Outputs: normalized variant, transcript/protein effect, genomic HGVS/SPDI/window, Phase 6 evidence, Phase 7 evidence summary, Primer/3D/report handoffs.
No automatic pathogenicity/clinical classification is assigned.

Batch VCF Analysis

Analyze and prioritize many variants while preserving exact REF/ALT and genome assembly context.

Workflow

  1. Upload/paste VCF.
  2. Select GRCh38, GRCh37 or auto-detect from the VCF header.
  3. Parse and split multi-allelic records.
  4. Run batch VEP annotation.
  5. Filter by gene, consequence, ClinVar, AF or predictor evidence.
  6. Run deep evidence on selected or all visible variants.
  7. Open prioritized variants in Variant → Experiment.

Verify

  • Assembly matches VCF
  • REF/ALT orientation
  • Filters are documented
  • gnomAD dataset/assembly compatibility
  • Deep evidence for high-priority variants
Batch ranking prioritizes research candidates; it is not sample-level or clinical interpretation.

Cohort Analysis

Analyze multi-sample VCFs while retaining genotype and sample information.

Workflow

  1. Load a multi-sample VCF.
  2. Confirm assembly.
  3. Assign roles: case/control, tumor/normal, father/mother/child, or custom context.
  4. Review GT, DP, AD, GQ and calculated VAF.
  5. Annotate variants using Phase 8.
  6. Infer candidate flags using transparent research rules.
  7. Filter, deep-annotate and send selected variants downstream.

Interpret the fields

  • GT: genotype call
  • DP: total depth
  • AD: allele depths
  • GQ: genotype quality
  • VAF: ALT depth / total allele depth
  • Candidate flags: prioritization heuristics, not proof
Candidate modes: de novo, recessive, tumor-specific and case-enriched research candidates.
Candidate flags do not establish inheritance, somatic origin, pathogenicity or actionability. Confirm sample relationships and findings independently.

Variant-aware Primers

Design validation or allele-aware assays around a mapped variant.

Workflow

  1. Prefer handoff from Variant → Experiment.
  2. Confirm sequence window, REF/ALT and variant position.
  3. Generate flanking PCR/Sanger pairs.
  4. For suitable SNVs, inspect WT/ALT allele-specific candidates and probes.
  5. For indels, inspect junction-specific candidates.
  6. Review QC and export candidates.

Verify

  • REF matches sequence
  • Variant is at intended discriminatory position
  • Tm/GC/hairpin/dimer QC
  • Amplicon size
  • Independent specificity testing
Allele specificity must be optimized and demonstrated experimentally.

Assay QC & Specificity

A final in-silico screening layer for a selected primer pair before laboratory optimization.

Workflow

  1. Open from Variant-aware Primers or enter two primers manually in 5′→3′ orientation.
  2. Paste the validated target/genomic window whenever available.
  3. Run Phase 12 QC and review Tm, GC, homopolymers and self/hetero-complementarity.
  4. Confirm whether exactly one intended amplicon is found in the supplied target.
  5. Optionally provide a compact FASTA reference/off-target panel.
  6. For broader screening, start NCBI BLAST manually and wait at least 10 seconds between checks.
  7. Save the result to Scientific Report.

Verify

  • Both primers are correct and written 5′→3′
  • Intended target sequence is the correct assembly/accession/window
  • Primer ΔTm and 3′ complementarity are acceptable
  • Exact target amplicon is unique in the supplied target
  • BLAST organism is correct
  • Potential off-targets are reviewed independently
Outputs: per-primer QC, pair QC score, target amplicon map, compact FASTA-panel hits and optional approximate pair-level NCBI BLAST candidates.
Phase 12 is a research screen. It does not establish amplification efficiency, sensitivity, analytical specificity, diagnostic performance or clinical validity. Wet-lab optimization and independent specificity validation remain required.

Advanced Vector Designer

Select a biological objective and receive a host-aware vector architecture before committing to exact plasmid sequence assembly.

Supported research modes

  • Bacterial expression
  • Mammalian expression
  • Lentiviral transfer-vector architecture
  • AAV transfer-vector architecture
  • CRISPR expression
  • Reporter vector
  • shRNA vector
  • Tag-fusion vector

Smart checks

  • Host/promoter logic
  • Payload frame and size
  • Fusion-tag orientation
  • Reporter/polycistronic logic
  • AAV/lentiviral transfer-cassette size warnings
  • User-supplied CRISPR/shRNA sequence presence

Recommended workflow

  1. Generate Phase 16 architecture.
  2. Review warnings and module order.
  3. Send the architecture to Plasmid Designer.
  4. Use the exact backbone and payload to build the construct.
  5. Design cloning primers and send them to Assay QC.
  6. Save outputs in Project Workspace / Scientific Report.

Safety boundary

Viral modes are limited to transfer-vector research architecture. Packaging/helper genes and infectious-virus rescue design are intentionally outside the tool.

Smart Multi-Site Assembly Designer (Phase 17)

Plan complex research assemblies from a user-supplied backbone, multiple independent insertion sites and multiple variants per site. The tool estimates combinatorial library size, compares assembly strategies, screens common Type IIS sites, partitions long sequences, previews constructs and hands a selected construct to Plasmid Designer.

Workflow

  1. Enter a backbone name and paste the backbone DNA sequence.
  2. Add each insertion site using a unique backbone position.
  3. Add one or more sequence variants for every site.
  4. Choose Auto-select, Gibson, Golden Gate or restriction planning.
  5. Set overlap length and maximum synthesis fragment length when relevant.
  6. Generate the assembly plan.
  7. Review site-level QC, Type IIS findings, coding checks, long-sequence partitions and buildability.
  8. Inspect construct previews and select the construct you want to continue with.
  9. Send the selected assembled construct to Plasmid Designer, or export FASTA/JSON/Print.

Verify

  • Insertion positions are unique and lie within the supplied backbone.
  • Backbone and part sequences contain only A/C/G/T/N characters.
  • Review internal BsaI/BsmBI findings when Type IIS planning is relevant.
  • Interpret frame, start/stop and internal-stop warnings in the intended coding context.
  • Confirm the combinatorial library size matches the variants supplied at each site.
  • Review long-sequence partitioning and overlap settings before experimental use.
  • Treat buildability as a planning heuristic, not a guarantee of cloning success.

Outputs

Strategy summary, site-level QC, Type IIS screening, coding warnings, fragment partitions, combinatorial construct count, construct previews, buildability estimates and FASTA/JSON/Print exports. A selected construct can be transferred to Plasmid Designer for downstream research analysis.

Research-use boundary

Phase 17 is a research planning tool for user-supplied DNA sequences. Its strategy selection, QC flags and buildability score are heuristic. It does not guarantee cloning success, biological function, safety, experimental validity or regulatory suitability.

Smart Multiplex PCR & Targeted Amplicon Panel Designer (Phase 18)

Design multiple primer pairs as a coordinated research panel instead of optimizing each assay in isolation. Phase 18 performs panel-level primer selection, cross-primer conflict screening, pool assignment and compatibility scoring, with an optional tiled-amplicon mode for longer targets.

Workflow

  1. Add each research target and paste its DNA sequence.
  2. Select Multiplex PCR panel or Targeted amplicon tiling.
  3. Set target Tm, amplicon size range, primer constraints and maximum pools.
  4. Run panel design.
  5. Review the globally selected primer pair for each target.
  6. Inspect pool assignments and cross-primer conflicts.
  7. Redesign flagged targets or increase the pool count if strong same-pool interactions remain.
  8. Export JSON/CSV or Print/PDF for research records.

Verify

  • Confirm target sequences and intended orientation before design.
  • Check primer Tm spread across the complete panel.
  • Review self-dimer, hairpin and pair-interaction scores as screening heuristics.
  • Check that high cross-primer interactions are separated between pools.
  • Use the compatibility score for prioritization, not as proof of experimental success.
  • Run an external specificity workflow when genome-wide off-target assessment is required.

Outputs

Globally selected primer pairs, amplicon sizes, pair scores, Tm spread, pool assignments, high-interaction conflict list, unresolved same-pool conflicts, compatibility score, redesign suggestions and exportable JSON/CSV/Print records.

Research-use boundary

Phase 18 is a research planning tool. The current thermodynamic interaction screen is heuristic and does not guarantee multiplex performance, genome-wide specificity, clinical validity or regulatory suitability. Experimental validation remains required.

Plasmid Designer

Create or inspect a plasmid research construct while keeping the complete sequence, feature map, cloning-junction plan and primer handoff together.

Use it when

  • You need to combine a known backbone with an insert or coding cassette.
  • You want a circular feature map and common restriction-site screen.
  • You need cloning-primer planning for restriction cloning, Gibson assembly or Golden Gate.
  • You want GenBank, FASTA and JSON outputs that preserve the exact designed construct.

Recommended workflow

  1. Paste or import the exact backbone and confirm circular/linear topology.
  2. Add the insert and choose the insertion position.
  3. Annotate relevant features before building the construct.
  4. Select a cloning strategy only when you want primer-overhang planning.
  5. Inspect the map, unique/multiple restriction sites, reading-frame checks and strategy warnings.
  6. Send the cloning primer pair to Assay QC and preserve the result in Project Workspace / Scientific Report.

Before you trust the result

  • Confirm the exact backbone version and 5′→3′ insert orientation.
  • Verify coding frame, start/stop codons and fusion boundaries where relevant.
  • Check selected enzymes for unwanted internal sites.
  • Verify Gibson/Golden Gate junction architecture independently.
  • Sequence-verify the final experimental construct.

Outputs

  • Circular plasmid map and feature legend
  • Restriction-site table
  • Cloning-primer plan with basic QC metrics
  • FASTA / GenBank / JSON
  • Research snapshot and Assay QC handoff
Research limitation: Plasmid Designer is a computational planning aid. It does not establish cloning efficiency, expression, phenotype, biosafety or regulatory suitability.

Restriction Enzyme Analyzer

Map restriction-enzyme recognition and cut sites in a supplied DNA sequence and plan single or multiple digests.

Recommended workflow

  1. Paste the DNA sequence and confirm linear or circular topology.
  2. Select the enzyme or enzyme combination.
  3. Run the analysis and inspect recognition/cut positions.
  4. Review predicted fragment sizes and end types.
  5. Check digest-condition and compatibility information before laboratory use.

Verify

  • Correct sequence and topology
  • Recognition/cut convention
  • Expected fragment count and sizes
  • Multi-enzyme compatibility
  • Current manufacturer conditions
Next: Inspect predicted fragments in Virtual Gel Electrophoresis or continue with cloning/sequence planning.
Computational digest planning does not guarantee experimental digestion or account for every enzyme-specific condition.

Virtual Gel Electrophoresis

Visualize predicted DNA fragment separation from fragment-size or restriction-digest results.

Recommended workflow

  1. Load or enter expected DNA fragment sizes.
  2. Choose available gel/display settings appropriate to the size range.
  3. Generate the virtual gel.
  4. Compare band positions and identify closely migrating fragments.
  5. Interpret the image together with numerical fragment-size results.

Verify

  • Fragment sizes and bp units
  • Expected number of bands
  • Source digest/fragment list
  • Closely sized fragments that may not resolve visually
The virtual gel is an approximate planning visualization and does not model every experimental variable affecting migration, intensity or resolution.

Lab Calculators

Perform common molecular-biology calculations while keeping input values and units explicit.

Recommended workflow

  1. Select the calculator matching the laboratory task.
  2. Enter values in the requested units.
  3. Run the calculation.
  4. Review the result and stated assumptions.
  5. Transfer values to a protocol only after an independent unit check.

Verify

  • Units
  • Stock and target concentrations
  • Final volume
  • Dilution factor or molecular-weight assumptions
Critical preparation calculations should be independently rechecked before laboratory use.

FASTA / GenBank Viewer

Inspect FASTA or GenBank sequence records, metadata and annotated features before downstream design.

Recommended workflow

  1. Paste or load a supported sequence record.
  2. Confirm record identity, sequence length and molecule type.
  3. Inspect annotations and feature coordinates when present.
  4. Select the intended sequence or feature for downstream use.
  5. Preserve accession/source information with the research record.

Verify

  • Record/accession
  • DNA versus protein
  • Sequence orientation
  • Feature coordinates
  • No accidental truncation during copy/paste
The viewer displays information in the supplied record; it does not independently validate biological identity or annotation correctness.

Sequence Utilities

Apply routine DNA, RNA and protein sequence transformations while keeping sequence direction and alphabet explicit.

Recommended workflow

  1. Paste the sequence and choose the intended utility.
  2. Confirm the input sequence type.
  3. Run the transformation or calculation.
  4. Review output sequence and length.
  5. Check orientation and biological context before downstream use.

Verify

  • Sequence alphabet
  • 5′→3′ orientation for nucleic acids
  • Reverse versus reverse complement
  • Translation frame when relevant
  • Unintended characters
Sequence transformations are deterministic utilities; biological interpretation remains the researcher's responsibility.

Protein Sequence Analyzer

Inspect protein sequence properties and sequence features before downstream peptide or assay design.

Recommended workflow

  1. Paste the protein sequence and confirm its identity.
  2. Run the available sequence analyses.
  3. Review composition, length and highlighted features.
  4. Interpret PTM or variant annotations in their stated context.
  5. Send the relevant region to downstream peptide/MHC tools when appropriate.

Verify

  • Correct protein isoform
  • Valid amino-acid sequence
  • Residue numbering
  • Annotation source
  • Sequence region transferred downstream
Sequence-derived properties and annotations do not by themselves establish biological function.

Protein → Peptide Designer

Generate candidate peptide windows from a protein sequence for downstream research screening and prioritization.

Recommended workflow

  1. Paste and confirm the source protein sequence.
  2. Choose peptide-length and candidate-generation settings.
  3. Generate candidate windows.
  4. Review sequence liabilities and candidate properties.
  5. Send selected candidates to MHC/HLA or other downstream analysis when appropriate.

Verify

  • Source protein and isoform
  • Peptide length
  • Residue coordinates
  • Synthesis-challenging regions
  • Downstream assay requirements
A computationally attractive peptide is not evidence of binding, immunogenicity or biological activity.

Leader / Signal Peptide

Screen an N-terminal protein region for signal-peptide/leader-sequence characteristics and document the sequence context used for the assessment.

Recommended workflow

  1. Paste the protein sequence and confirm the N-terminus is present.
  2. Run the available leader/signal-peptide analysis.
  3. Inspect the predicted N-terminal region and displayed evidence.
  4. Compare the result with protein annotation and biological context.
  5. Carry the appropriate mature/full-length sequence to downstream tools.

Verify

  • Correct isoform and intact N-terminus
  • Residue numbering
  • Prediction/evidence source
  • Whether downstream analysis requires precursor or mature sequence
Signal/leader prediction is computational evidence and does not establish secretion, localization or cleavage experimentally.

Population Coverage

Estimate HLA population coverage from epitope/HLA restrictions and a cited population allele-frequency dataset.

Recommended workflow

  1. Enter epitope-to-HLA restriction pairs using canonical HLA nomenclature.
  2. Provide the population HLA frequency table and exact source.
  3. Confirm population identity and dataset completeness.
  4. Calculate coverage and review per-locus completeness and missing restricting alleles.
  5. Export results together with population/source provenance.

Verify

  • HLA nomenclature
  • Population and dataset source
  • Frequency scale and locus completeness
  • Restricting alleles represented in the dataset
  • Model assumptions
Coverage depends on supplied frequencies and model assumptions. Missing alleles are not evidence of zero frequency, and modeled coverage is not an individual-level prediction.

Provenance & Evidence

Audit the active research snapshot for source context, methods, versions, parameters, warnings and evidence provenance.

Recommended workflow

  1. Load or refresh the active research snapshot.
  2. Review snapshot identity and fingerprint.
  3. Inspect metadata coverage and the evidence ledger.
  4. Review captured accessions, datasets and source references.
  5. Record the provenance review without rewriting original workflow outputs.
  6. Export the provenance manifest or continue to Scientific Decision/Report.

Verify

  • Project/target identity
  • Source and accession provenance
  • Method/database versions when supplied
  • Parameters and warnings
  • Visible metadata gaps remain explicit
Provenance completeness improves traceability but does not prove scientific, clinical or regulatory validity.

Scientific Decision Workspace — Phase 21

Compare captured candidates while keeping source scores, warnings, methods and provenance visible, then document why one candidate is carried forward, held or excluded from the current research plan.

Recommended workflow

  1. Open Phase 21 after a workflow has generated comparable candidates.
  2. Choose the captured candidate source.
  3. Filter and compare up to three candidates side by side.
  4. Review score meaning, warnings, method/version and database scope.
  5. Select the candidate being carried forward and write a scientific rationale.
  6. Save the decision to the active research snapshot, then continue to Scientific Report, Workflow Review or Project Workspace.

Before you trust the decision record

  • Confirm every compared candidate belongs to the intended workflow and target.
  • Do not compare unlike scores as though they measure the same biological property.
  • Review missing provenance rather than silently inferring it.
  • Keep unresolved warnings visible.
  • Plan the appropriate independent experimental validation.
Output: a Phase 21 decision record containing source, compared candidates, selected candidate, warnings, provenance, research status and rationale.
Phase 21 is research decision documentation. It does not automatically identify a “best” candidate and is not clinical decision support.

Run History & Reproducible Experiment Record — Phase 23

Capture a timestamped research run with its project/target context, snapshot fingerprint, execution status, methods, versions, parameters, reference scope, warnings and downstream decision/provenance context.

Recommended workflow

  1. Open Phase 23 after the active research snapshot contains the workflow state you want to preserve.
  2. Confirm project, target identity and snapshot fingerprint.
  3. Choose the documented execution status; do not use Completed only because results are visible.
  4. Optionally record start/end time and a run note.
  5. Keep metadata-only storage unless you intentionally want the full snapshot payload stored locally.
  6. Capture the run record, then inspect history or compare two runs.
  7. Export a selected run or the complete run-history JSON for archive or handoff.

Verify

  • Run ID and capture time are present.
  • Execution status is explicit.
  • Fingerprint matches the research state being recorded.
  • Methods, versions, parameters and database scope are preserved when available.
  • Warnings and limitations remain visible.
  • Record scope clearly says metadata-only or full snapshot included.
Outputs: browser-local run history, latest-run snapshot pointer, one-run JSON export, full history JSON export and two-run documented-metadata comparison.
Phase 23 documents research execution context. It does not prove experimental reproducibility or establish clinical or regulatory validity.

Reliability & Failure-State Hardening — Phase 24

Use explicit operational states instead of silent failure. Phase 24 provides queued, running, retrying, completed, partially failed, failed and cancelled states plus a browser-local reliability ledger.

Use it when

  • An external service times out or is unavailable.
  • A save/export fails.
  • A retry is needed.
  • A session expires or the browser goes offline.

Verify

  • Current state is explicit.
  • No fake progress percentage is shown.
  • Unresolved events are reviewed before handoff.
  • Operational completion is not treated as scientific validity.
The shared Phase 24 API is non-invasive; existing workflows can adopt it progressively.

Session Recovery & Data Integrity — Phase 25

Create a browser-local full-snapshot checkpoint, verify it with SHA-256, export it when needed, and restore only after explicit confirmation.

Recommended workflow

  1. Create a checkpoint before risky changes.
  2. Confirm the checkpoint fingerprint is verified.
  3. Export important checkpoints outside the browser.
  4. Before restore, inspect project/target/fingerprint.
  5. Type RESTORE and confirm replacement.

Safety behavior

  • Full snapshot storage requires acknowledgement.
  • A pre-restore backup is created automatically.
  • Restore is blocked if checkpoint verification fails.
  • Browser-local storage is not described as a cloud backup.
Recovery checkpoints may contain biological sequences or other research content and remain in this browser unless exported.

Part 1 interpretation key

Use the same meaning for evidence and result labels across Molecular Design Lab.

Calculated property

A value derived directly from supplied data or a defined calculation, such as sequence length, GC content or a thermodynamic quantity.

Computational prediction

A model-, database- or rule-based estimate. A prediction is not experimental confirmation and its interpretation depends on method, version, thresholds and reference scope.

Researcher decision

A documented human choice, rationale or workflow status. It records what was selected or concluded for the research workflow; it does not convert a prediction into experimental evidence.

Experimental evidence

Evidence generated by laboratory experiments or other independently generated observations. Where relevant, MDL outputs should be validated experimentally before laboratory conclusions are relied upon.

A high score, completed workflow, captured report item or verified software record describes the computational/documentation state only unless experimental evidence is explicitly supplied.

Part 1 data handling & storage

Molecular Design Lab uses more than one storage path. The distinction matters when preserving or sharing research work.

Browser-local records

  • Run History, reliability events and recovery checkpoints can be stored in the current browser.
  • Recovery checkpoints may include the complete active research snapshot and therefore may contain biological sequences or other research content.
  • Browser-local storage is not a cloud or institutional backup and may be lost if browser/site data are cleared.

External services & exports

  • External services should be treated separately from browser-local storage; review the relevant data-handling conditions before submitting sensitive information.
  • Use JSON/CSV/PDF exports when a durable copy is required outside the browser.
  • Computational outputs, predictions and documentation records do not replace experimental validation.
Part 1 is research-use software. Storage location, successful computation and complete documentation do not establish scientific, clinical or regulatory validity. Calculated property = direct calculation; computational prediction = model/rule/database estimate; researcher decision = documented human choice; experimental evidence = independently generated observation.

Scientific Report

Create a reproducible research record from captured Phase 5–12 context.

Workflow

  1. Open after completing the analysis/design workflow.
  2. Confirm captured sections and identifiers.
  3. Add project/sample name and notes.
  4. Export PDF, CSV or JSON.
  5. Save locally or to the account when appropriate.

Verify

  • Gene/transcript/assembly
  • Database evidence
  • Primer/design outputs
  • Phase 12 assay-QC/specificity evidence when available
  • Cohort context if applicable
  • Retrieval/software provenance and SHA-256 fingerprint
This is a research report, not a diagnostic/clinical report.

Project Workspace — Phase 13

Bring multi-step research outputs into one project and create a reproducible handoff for another researcher without pretending that the platform is a real-time collaboration or regulated data system.

Recommended workflow

  1. Create a project and set project name, organism, assembly, sample ID and status.
  2. Use Attach active research snapshot after completing Variant, Batch/Cohort, Primer, Assay QC or Scientific Report work.
  3. Add sample context and project notes.
  4. Add collaborator/reviewer names or roles only when appropriate under your institutional policy.
  5. Set review status: not reviewed, ready for review, in review or reviewed.
  6. Save locally, or save to your account when signed in.
  7. Export a portable JSON handoff bundle. A colleague can import the same bundle into Phase 13.

Verify before handoff

  • Correct project/sample context
  • Consistent organism, assembly and transcript across artifacts
  • Expected research snapshot and assay outputs are attached
  • Review status and handoff note are current
  • SHA-256 workspace fingerprint is recorded
  • No patient identifiers, passwords, secrets or prohibited proprietary data are included
Outputs: project workspace, samples, attached research snapshots/artifacts, activity history, review state, local/account persistence, JSON export/import and a portable collaboration handoff.
Phase 13 is a research workflow organizer. It is not real-time shared editing, an ELN/LIMS, a source-control system, a clinical record, or a regulated repository. Keep independent institutional records and follow your data-governance rules.

Workflow Review & Reproducibility — Phase 14

Review workflow completeness before research collaboration, archive or handoff.

Recommended workflow

  1. Select a Phase 13 Project Workspace or use the active research snapshot.
  2. Run the Phase 14 review.
  3. Resolve required gates marked Attention.
  4. Save the review to the Scientific Report snapshot.
  5. Attach it to the selected workspace when useful.
  6. Export the fingerprinted reproducibility bundle for handoff.

What the score means

  • Required gates contribute to the completeness score.
  • Optional and not-applicable stages do not penalize a workflow.
  • Assay QC becomes required when an assay is part of the captured workflow.
  • Cohort checks become required when multi-sample context is present.
  • The SHA-256 fingerprint helps detect changes to the reviewed input context.
Important: a 100/100 completeness score means the expected research documentation gates were captured. It does not establish pathogenicity, diagnostic validity, assay performance, treatment suitability or regulatory compliance.

Account

Manage sign-in and account-linked project/report storage.

Use

  • Sign in for account-linked persistence when enabled.
  • Verify the account before saving.
  • Sign out on shared computers.

Data caution

  • Follow institutional rules for research data.
  • Do not upload prohibited confidential or identifiable data.

Lessons

Short educational material explaining concepts behind the tools.

Use

  1. Choose the concept relevant to your current workflow.
  2. Review the underlying biology/assay principle.
  3. Return to the tool and interpret the output in context.

Remember

  • Educational examples are general.
  • Formal database definitions can change over time.

Glossary

Definitions of terms and abbreviations used across the platform.

Best use

  • Clarify terminology while reading a result.
  • Then return to the relevant tool section in this guide for procedural meaning.

Examples

  • HGVS / SPDI
  • GT / DP / AD / GQ / VAF
  • ClinVar review status
  • Allele frequency

Free Beta Access

Shows current beta access and usage model.

Check

  • Current free-beta status
  • Any usage limits
  • Features marked experimental

During beta

  • Expect iterative changes.
  • Keep independent copies of critical research records.

About & Limitations

Read this before relying on the platform for a new research workflow.

Core limitations

  • Research prototype
  • External databases/services can change or be unavailable
  • Predictors provide supporting evidence, not ground truth
  • Wet-lab confirmation remains essential

Always record

  • Assembly
  • Transcript/accession
  • Database source/version
  • Retrieval date
  • Experimental validation status

Feedback / Beta Survey

Report usability problems, scientific edge cases and missing workflows.

Useful feedback

  • Tool/page name
  • What you entered
  • What you expected
  • What actually happened
  • A non-sensitive reproducible example

Do not submit

  • Patient-identifying information
  • Passwords/secrets
  • Proprietary data you are not allowed to share

Troubleshooting

Quick checks before treating a problem as a code or database failure.

Page / UI

  1. Use Ctrl+F5 after a new deployment.
  2. Confirm the expected page URL.
  3. Check whether the contextual Guide button loads.
  4. Confirm the universal sidebar is identical across pages.

Scientific workflow

  1. Confirm organism and assembly.
  2. Confirm transcript accession/version.
  3. Check REF/ALT or reference residue.
  4. Retry external evidence if a service was temporarily unavailable.
  5. Do not infer absence when a database returns no result.
If a result looks biologically inconsistent, stop the downstream handoff and re-check transcript, assembly, allele orientation and reference sequence first.
Molecular Design Lab — research prototype. This guide describes intended research workflows. Confirm designs and biological interpretations independently before laboratory or downstream use.