Getting Started
Do I need an account?
No. SciKeep works fully as a Guest — open the app and start using any free module immediately. As a guest your work stays in this browser only, so clearing browser data loses it. An account carries your subscription and saves your text records — notebook, protocols, inventories — to your account, so they survive a cleared cache or a change of computer; a Lab plan shares one copy across the lab. Images stay on your machine either way, enforced by a 64 KB server-side cap no image can fit through.
How do I navigate between modules?
Use the sidebar on the left. Modules are grouped by category (DNA & CRISPR, Calculators, Lab Bench, etc.). Click the group header to collapse/expand it. Click the toggle arrow at the bottom of the sidebar to collapse it to icon-only mode for more screen space.
What costs money?
Every analysis tool is free, permanently — with no account, no card and no trial clock. That includes qPCR, the statistics engine with repeated-measures and mixed models, cell imaging, IC50 fitting, multiverse analysis and the manuscript audit. The only paid plan is Lab at $49/month, and it buys SHARED infrastructure for the whole group: a shared -80°C freezer map, antibody, reagent and cell-line registries, a team notebook with a hash-chained audit trail, batch image analysis and reagent ordering. It is priced per lab rather than per seat, so you never have to decide which students get access. The reasoning is simple: the person who most needs a tool that catches statistical errors is usually the person with no budget, so the analysis stays free and the lab pays for coordination.
Where is my data stored?
Two modes, and the difference matters. As a guest, everything lives in your browser's localStorage only — nothing is transmitted to us and we cannot access it. The trade-off is real: clear your browser data, or let the browser evict it on its own, and it is gone with no way for us to recover it. Safari is the sharp edge here — it wipes script-written storage after 7 days without a visit. With an account, your text records — lab notebook entries, freezer, reagent, antibody, cell line and culture inventories — are also saved to your private account, so a cleared cache or a new computer no longer costs you your records. Access is enforced per-account at the database level. Images never sync in either mode: microscopy images, blot scans and canvas data are stripped before any upload, and the database rejects anything over 64 KB, so an image cannot leave your machine even by accident. Export important work regularly using each module's export button — that is the one copy nothing can take away from you.
How do I get the Lab plan?
Click "Upgrade" in the top-right header or at the bottom of the sidebar. You can start a 14-day trial with your email alone — no credit card. Nothing you already use stops working if you never subscribe: the analysis tools are free permanently, and the trial only adds the shared lab features.
Why does the qPCR tool refuse to give me a p-value?
Because your design has one biological replicate per condition. The wells you entered are technical replicates — the same cDNA measured several times — and they estimate pipetting precision, not biological variability. Using them as n is pseudoreplication: it shrinks the error bars and can make an experiment done once look significant. The MIQE guidelines require the distinction to be stated. Repeat the experiment on independent samples — separate animals, passages or transfections — and enter each as its own biological replicate. The tool will then average your technical replicates within each one and report a p-value it can stand behind. This is deliberate, not a limitation.
Open qPCR ΔΔCt Calculator — Biological vs Technical Replicates →
Which statistical test should I use for my design?
If each measurement comes from an independent sample, use the independent t-test (two groups) or one-way ANOVA (more). If the SAME passage, animal or day is measured under every condition, use Repeated measures — treating those as independent pushes the shared subject-level variation into the error term and hides real effects. If a subject is missing a measurement, use Mixed model rather than dropping that subject: it uses the data you have. If your data are clearly skewed or ordinal, use Mann-Whitney or Kruskal-Wallis. The tool screens for normality and says so, but it advises rather than vetoes — you know your experiment better than the test does.
Open Repeated Measures ANOVA & Mixed Model Calculator →
What is deep-learning segmentation and should I turn it on?
For H&E tissue sections you plan to publish, we recommend Cellpose (free and open source). On two samples of 62 hand-annotated NuInsSeg H&E patches it scored F1 65% and 69%, against 23% and 26% for this tool's default engine, which is a watershed that needs gaps between cells (confluent tissue has none) and finds about twice as many objects as there are nuclei. The opt-in deep-learning option here is a model we trained on NuInsSeg: in August it scored 67.2% on seven organs held out of training, against 63.2% for Cellpose on the same patches. That has not been re-run since, so treat it as comparable to Cellpose, not better. It costs a one-time ~17 MB download, cached afterwards, takes roughly a second per 256-pixel tile, and your images are never uploaded because the model runs inside your browser. For fluorescence microscopy leave it off: the default engine scores F1 87% on evenly stained nuclei (BBBC039) and 71% across 30-plus mixed experiments (BBBC038). Per-organ accuracy of the deep model ranged from 76% to 45% in August, so check the overlay against your own slides rather than trusting any average.
Open Cell Counter & Image Segmentation →
DNA & CRISPR
CRISPR gRNA Designer & Dual Scoring (Hsu-Zhang + CFD)
Paste your target DNA sequence. Select your Cas nuclease (SpCas9 uses NGG PAM, Cas12a uses TTTV PAM, SaCas9 uses NNGRRT PAM). The tool scans both strands for valid PAM sites and calculates dual off-target scores: Hsu-Zhang (2013) seed-weighted mismatch penalty matrix and Doench (2016) Cutting Frequency Determination (CFD) score. Always order 3-4 top guides and validate empirically.
Open CRISPR gRNA Designer →
Golden Gate Scarless Assembly Simulator
Designs and validates Type IIS restriction enzyme (BsaI, BsmBI, PaqCI) assembly. The simulator checks 4-bp sticky end directional overhangs, flags self-dimers and palindromic cross-talk, verifies assembly fidelity, and outputs the scarless circular construct.
Open Gibson & HiFi Assembly Planner →
REBASE Methylation Sensitivity Scanner
Scans your sequence for overlapping bacterial Dam (GATC), Dcm (CCWGG), and mammalian CpG methylation motifs that can completely block restriction enzyme cleavage (e.g. ClaI, XbaI, BclI, NotI). Recommends Dam-/Dcm- competent E. coli strains (e.g. JM110, C2925) when blockages are detected.
Open DNA Reverse Complement, Translate & ORF Finder →
ICE Analysis — what is it?
Paste your reference (unedited) and edited sequences. The tool aligns them with affine gap penalties and reports the net indel size, where the first difference falls, whether the reading frame is shifted, and what that means for the protein. It does NOT report an editing efficiency: that describes a mixture of alleles across a population and can only be recovered from the overlapping peaks of a Sanger chromatogram, not from consensus sequence text. For population efficiency, use Synthego ICE or TIDE with your .ab1 files.
Open CRISPR Indel Analysis & Frameshift Caller →
Sequence Toolkit & NCBI Entrez
Functions include: reverse complement, 6-frame translation, GC content profiles, ORF identification, codon optimization (human/mouse/E. coli), nucleotide composition, and direct NCBI GenBank CDS fetching.
Open DNA Reverse Complement, Translate & ORF Finder →
Sanger Trace Viewer & Chromatogram QC
Upload raw .ab1 chromatogram trace files from sequencing providers. The viewer renders the 4-channel electropherogram, computes Phred Q30 quality scores, and identifies heterozygous SNPs/indels relative to your reference sequence.
Open Sanger Trace Chromatogram Viewer →
Cloning Planner (Gibson & HiFi Assembly)
Enter your vector and insert sequences. The tool calculates optimal homology arms (20-30 bp), nearest-neighbor thermodynamic melting temperatures (SantaLucia 1998 Tm), and outputs a complete PCR & assembly protocol.
Open Gibson & HiFi Assembly Planner →
Calculators & Formulation
Biopharmaceutical mAb Formulation & Viscosity Suite
Designed for antibody and therapeutic protein development. Computes exact Van Slyke buffer capacity (β) across pH 5.0–7.5, Mooney / Ross-Minton high-concentration viscosity (up to 250 mg/mL), Debye-Hückel electrostatic screening length (κ⁻¹), total osmolality, and generates a 10-step sterile compounding recipe with 0.22 µm PES filtration SOP.
Open Buffer & Solution Recipe Generator →
Standard Buffer & Solution Calculator
Select a buffer type from the dropdown (PBS, TBS, HEPES, Tris-HCl, RIPA, SDS-PAGE buffers, etc.). Enter your desired final volume. The calculator outputs a step-by-step recipe with exact gram weights, pH adjustment instructions, and temperature compensation notes.
Open Buffer & Solution Recipe Generator →
Oligo Calculator — OD260 resuspension
Paste your oligo sequence. The tool computes molecular weight, molar extinction coefficient (ε260), and GC content. Enter the OD260 reading from your spectrophotometer and target concentration (e.g. 100 µM) to receive the exact volume of nuclease-free water to add.
Open Oligo & Primer Resuspension Calculator →
Protein Calculator — MW, pI & Pace Extinction
Enter your protein amino acid sequence. The calculator outputs: molecular weight (kDa), isoelectric point (pI) using iterative Henderson-Hasselbalch titration with Lehninger pKa values, GRAVY hydropathy index, and Pace et al. (1995) extinction coefficient at 280 nm.
Open Protein MW, pI & Extinction Calculator →
Lentiviral MOI & Transfection Reagent Optimizer
Calculates the volume of viral stock required based on target cell count, titer (TU/mL), and desired Multiplicity of Infection (MOI). Models transduction efficiency via Poisson statistics and computes lipid-to-DNA ratios for transfection reagents.
Open Lentiviral MOI & Titre Calculator →
Lab Bench & Assays
4PL & 5PL Non-Linear Logistic Dose-Response Fitting
Fits 4-parameter and 5-parameter asymmetric sigmoidal curves using non-linear regression. Computes exact IC50/EC50, Hill slope cooperativity coefficients, 95% confidence intervals, and R² goodness-of-fit for small molecules, ELISA, and antibody binding assays.
Open 4PL IC50 & Dose-Response Calculator →
ROUT Outlier Removal (Q=1%) & 96-Well Heatmap
Implements the Motulsky & Brown (2006) False Discovery Rate (FDR) algorithm (GraphPad Prism gold standard) to automatically detect and exclude dispensing bubbles and edge evaporation artifacts across 8×12 microplates.
Open 4PL IC50 & Dose-Response Calculator →
Zhang et al. (1999) Z′-Factor HTS Quality Control
Computes screening quality metrics across positive and negative controls: Z′-Factor (Z′ ≥ 0.5 indicates an excellent HTS assay), Signal-to-Background (S/B), Signal-to-Noise (S/N), and %CV control reproducibility.
Open 4PL IC50 & Dose-Response Calculator →
2D Bivariate Scatter Gating & Subpopulation Profiler
Provides flow-cytometry-style quadrant crosshair gating directly on single-cell microscopy morphometry. Computes subpopulation percentages (Q1-Q4), cell counts, and mean intensities for multi-fluorophore co-transfections (GFP/RFP), cell cycle DNA content staging (DAPI vs Ki-67/EdU), and morphological outlier quality assurance (Area vs Circularity).
Open Cell Counter & Image Segmentation →
Neurite Outgrowth & Angiogenesis Capillary Tube Formation
Applies medial axis topological skeletonization to trace neuronal axons and endothelial capillary networks. Quantifies total network length (µm), mean length per soma (µm/cell), branch junction nodes, terminal growth cone tips, and HUVEC closed polygonal meshes/loops. Computes Sholl Analysis concentric ring intersection profiles (rcrit, Nmax) to measure dendritic arborization complexity under neurotrophic factors (NGF) or VEGFR kinase inhibitors (Sunitinib).
Open Cell Counter & Image Segmentation →
Subcellular Puncta & Foci Spot Counter
Detects diffraction-limited fluorescent spots using Laplacian of Gaussian (LoG) and White Top-Hat filters. Automatically assigns foci to individual nuclei (γH2AX, 53BP1 DNA double-strand breaks, RNA smFISH) or cytoplasm (LC3B, p62 autophagosomes). Computes % foci-positive cells (≥5 foci/cell), single-cell frequency distributions, peak optical density, and drug response curves (e.g. radiation vs ATM/ATR inhibitors).
Open Cell Counter & Image Segmentation →
3D Spheroid & Tumor Organoid Morphometry
Measures 3D multicellular spheroids and patient-derived organoids (PDOs). Computes 3D ellipsoidal volume (V = 4/3·π·a·b² in nL and µm³), Wadell sphericity index (Ψ = 2√(πA)/P), circularity, aspect ratio, central hypoxic/necrotic core formation %, and invasive invadopodia ECM sprouting tips. Supports multi-day growth kinetics tracking under chemotherapy or kinase inhibitor treatments.
Open Cell Counter & Image Segmentation →
In Vitro Scratch Assay & Cell Migration Profiler
Quantifies collective cell migration and wound healing kinetics across multi-timepoint series (0h, 6h, 12h, 24h, 48h). Automatically calculates % Wound Closure (100% = fully closed), mean gap width (µm), collective migration velocity (µm/h = ΔW / 2Δt), half-maximal closure time (t50), and relative wound density (RWD %). Generates multi-curve kinetic comparison plots and 1-click CSV exports for drug screening.
Open Cell Counter & Image Segmentation →
SuperPlots & Single-Cell Variability (%CV)
Upload microscopy images (TIFF, PNG, JPG, LIF). Applies Otsu adaptive thresholding and watershed segmentation to extract nuclear area, circularity, and intensity. Renders SuperPlots (Lord et al. 2020) color-coding single cells by replicate (N=3) to prevent pseudoreplication.
Open Cell Counter & Image Segmentation →
Nucleocytoplasmic (N:C) Translocation Profiler
Automatically measures nuclear mask intensity vs a 5-pixel dilated cytoplasmic ring. Quantifies exact N:C ratio shifts for transcription factor translocation assays (e.g. NF-κB, FOXO, STAT).
Open Cell Counter & Image Segmentation →
Western Blot Analyzer — ChemiDoc Normalization
Quantifies lane densitometry for target proteins and normalizes against loading controls (GAPDH, β-actin, Tubulin, or total protein stain) with automated background subtraction.
Open Western Blot Densitometry Analyzer →
Drug Synergy — Bliss Independence Model
Computes excess over Bliss independent expectation across multi-dose drug combination matrices. Generates color-coded synergy/antagonism heatmaps.
Open Drug Synergy Calculator — Bliss Independence Score →
Flow Cytometry Multi-Laser Panel Designer
Evaluates fluorophore excitation and emission spectra across cytometer laser configurations. Flags spectral overlap (>15% spillover) and recommends compensation controls.
Open Flow Cytometry Panel Designer →
Biostatistics & Publishing
Publication-Grade Vector SVG & Multi-Panel Composer
Assembles publication-ready multi-panel figures (1x2 to 2x4 grids) with journal presets for Nature (89/183 mm), Cell (85/174 mm), Science (55/175 mm), and PNAS (87/178 mm). Features editable vector SVG export, scale bar overlays (µm), channel tag badges, and 300/600 DPI print rendering.
Open Publication Figure Panel Composer (300 DPI) →
Kaplan-Meier Survival Curves & Log-Rank Test
Computes product-limit survival functions S(t) with right-censoring support and Mantel-Cox log-rank test for comparing treatment and control survival curves.
Open Kaplan-Meier Survival Curve Generator →
Statistical Hypothesis Tests (t-Test, ANOVA, Mann-Whitney)
Executes two-sample t-tests, paired t-tests, One-Way ANOVA F-tests, and Mann-Whitney U non-parametric tests with exact regularized incomplete beta CDF p-value calculations.
Open Repeated Measures ANOVA & Mixed Model Calculator →
Statistical Power Calculator & NIH Grant Justification
Sizes animal and clinical sample groups based on Cohen's d effect size, alpha (0.05), and power (80% or 90%). Automatically writes publication- and NIH-compliant sample size justification text.
Open Sample Size & Statistical Power Calculator →
Lab Management
Electronic Lab Notebook (ELN) — SHA-256 Ledger
Timestamped notebook entries with Markdown formatting, tag filtering, and cryptographic SHA-256 blockchain-style hash chaining for complete audit trails. Includes electronic signature seals and 1-click GLP compliance certificate generation.
Open Electronic Lab Notebook (ELN) →
-80°C Freezer Locator & Cryo Box Mapping
Maps samples across freezers, shelves, racks, and 81/100-well cryo boxes with QR/barcode support, thaw count tracking, and concentration/volume logs.
Open -80C Freezer Inventory & Cryo Box Locator →
Reagent Ordering & Budget Allocation Tracker
Tracks reagent orders, catalog numbers, vendors, SDS sheets, unit prices, PO approval statuses, and grant budget codes with CSV export.
Open Reagent Ordering & Inventory Tracking →
Validated Antibody Bank
Maintains institutional records of validated antibody clones, host species, dilution ratios, lot-to-lot variance notes, and validated applications (WB, IHC, IF, Flow, ChIP).
Open Antibody Validation Tracker →
Research Area Guides
Which tools help with cellular senescence, reprogramming or longevity research?
SciKeep has no tool branded for aging or longevity — its 42 tools are organised by technique, not by disease area, so the ones that already fit are the same ones any molecular biology lab uses. The qPCR ΔΔCt tool now offers a curated senescence & SASP gene panel (CDKN2A/p16, CDKN1A/p21, LMNB1, and SASP factors IL6, CXCL8, MMP3, SERPINE1) that adds gene names to your list with one click — no example data, you still enter your own Ct values — plus a caveat that common reference genes (ACTB, GAPDH) are not automatically safe to use here, since both track cell-cycle and metabolic state. Beyond that: Kaplan-Meier for lifespan or healthspan survival curves, the CRISPR gRNA designer for reprogramming-factor knock-ins, Western Blot ChemiDoc for p16/p21 protein levels, and the statistics and power-calculator tools for everything downstream. There is no epigenetic-clock or reprogramming-efficiency tool, and none is planned without real published data to check one against.
Open qPCR ΔΔCt Calculator — Biological vs Technical Replicates →
Which tools help with adipocyte, obesity or metabolic research?
The qPCR ΔΔCt tool has a curated adipogenesis & thermogenic marker panel (PPARG, CEBPA, FABP4, ADIPOQ, LEP for adipogenesis and maturity; UCP1, PPARGC1A, PRDM16 for brown/beige thermogenic fat), loaded the same way as the senescence panel — gene names only, plus a specific warning that GAPDH is a documented poor reference gene here because glycolytic flux itself changes as cells differentiate. The 4PL/5PL IC50 tool fits dose-response curves for any compound screen (GLP-1 agonists, lipolysis agents), the Cell Culture Tracker handles adipocyte differentiation timelines, and Kaplan-Meier covers cardiometabolic outcome studies. As with every SciKeep tool, the panel is a starting list, not a validated protocol — confirm reference-gene stability in your own time course.
Open qPCR ΔΔCt Calculator — Biological vs Technical Replicates →
Which tools help with IVF and fertility research?
The imaging side is still honestly absent, and we would rather say that than stretch a claim: SciKeep has no embryo-grading or oocyte-imaging tool, and will not build one without a public, hand-annotated dataset to benchmark it against — the same standard the Cell Imaging tool is held to (see scripts/benchmarks and the /validation page). An unvalidated embryo score is not a risk we are willing to label our way around, because a number like that can plausibly end up in a real transfer decision no matter how it is captioned. The gene-expression side now has a curated folliculogenesis & oocyte/cumulus-competence panel in the qPCR ΔΔCt tool (AMH, FSHR, LHCGR, ESR2, GDF9, BMP15, HAS2, PTGS2, PTX3 — granulosa- and cumulus-cell genes from the basic-science literature), loaded the same way as the other panels: gene names only, and marked research use only — it is not validated to grade an embryo or oocyte, predict IVF outcome, or inform which embryo to transfer for any specific patient. Beyond that: the statistics tools for group comparisons, the Sample Size & Power Calculator for planning a study, and — the one technique built specifically for this kind of data — Kaplan-Meier survival curves, the standard method for cumulative live-birth or time-to-pregnancy analysis in reproductive medicine, not just cancer trials.
Open Kaplan-Meier Survival Curve Generator →
Which tools help with hair loss, dermatology or trichology research?
The imaging side is still honestly limited: there is no follicle-density or trichoscopy image analysis here, for the same reason IVF imaging is absent — no public annotated dataset exists to benchmark it against, and we do not ship a segmentation tool without measured accuracy on real data. The gene-expression side now has a curated androgen-pathway panel in the qPCR ΔΔCt tool (AR, SRD5A1/SRD5A2, CYP19A1, IGF1, TGFB1/TGFB2, DKK1 — the DHT-synthesis and dermal-papilla signalling genes implicated in androgenetic alopecia), loaded the same way as the senescence and adipogenesis panels: gene names only, plus a note that ACTB/GAPDH have not been separately validated as stable references for DHT-treated dermal papilla cultures. Beyond that: the Cell Culture Tracker for dermal papilla or outer-root-sheath cell work, the 4PL/5PL IC50 tool for dose-response screening of growth-promoting or DHT-pathway compounds (minoxidil, finasteride and similar), and the statistics tools for everything downstream.
Open 4PL IC50 & Dose-Response Calculator →