Data Science & Computing

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A rate sheet from UNT Health Fort Worth titled “HPC Core: Bioinformatics Analysis Rate 2025 Fall.” The document is formatted as a table with columns labeled Category, Analysis Type, Pricing Basis, Internal Rate (USD), Non-Lab Rate (USD), External Profit Rate (USD), Description, and Pipeline Outline. The table lists five service categories: • Bioinformatics Consulting – Custom project, priced per hour. Internal rate $55, non-lab rate $83, external rate $165. Description includes bioinformatics guidance, support, and solution development. Pipeline outline includes experimental design, literature review, best practices determination, method recommendations, and results interpretation. • AI/ML Consulting – Custom project, priced per hour. Rates are $55 internal, $83 non-lab, and $165 external. Description includes artificial intelligence and machine learning guidance and support. Pipeline outline includes experimental design, literature review, best practices, method recommendations, and results interpretation. • Data Analysis Consulting – Custom project, priced per hour. Rates are $55 internal, $83 non-lab, and $165 external. Description includes data analysis guidance, support, and solution development. Pipeline outline mirrors consulting workflow steps including experimental design and interpretation. • Genomics – Whole Genome Sequencing (WGS), priced per sample. Internal rate $250, non-lab rate $375, external rate $750. Description notes comprehensive FASTQ quality control to detection of genetic variants including single-nucleotide changes and structural alterations. Pipeline includes FASTQ QC, adapter trimming, BWA-MEM alignment, duplicate marking, post-alignment QC, GATK variant calling, basic CNV/SV screening, VEP/ANNOVAR annotation, and QC report with consultation. • Whole Exome Sequencing (WES), priced per sample. Internal rate $230, non-lab rate $345, external rate $690. Description includes identification and annotation of coding-region variants. Pipeline includes FASTQ QC, trimming, alignment with BWA-MEM, post-alignment QC, and GATK processing. The bottom of the page includes UNT Health branding and address information, along with “Page 1.”Page 2 of a rate sheet from UNT Health Fort Worth titled “HPC Core: Bioinformatics Analysis Rate 2025 Fall.” The page continues a structured table listing genomic analysis services with columns for Category, Analysis Type, Pricing Basis, Internal Rate (USD), Non-Lab Rate (USD), External Profit Rate (USD), Description, and Pipeline Outline. Services listed include: • Targeted Gene Sequencing – Priced per sample. Internal rate $250, non-lab rate $375, external rate $750. Description notes focused analysis of specified gene panels to detect known or novel mutations. Pipeline includes FASTQ quality control, trimming, alignment to panel regions, variant calling on target genes, annotation, and QC/variant summary report with consultation. • Copy Number Variation (CNV) Analysis – Priced per sample. Internal rate $200, non-lab rate $300, external rate $600. Description includes detection of genomic regions with gains or losses from sequencing data. Pipeline includes alignment (or use of provided BAM), CNV calling using tools such as CNVkit or ExomeDepth, manual review, gene annotation, and QC metrics report. • Structural Variant (SV) Analysis – Priced per sample. Internal rate $210, non-lab rate $315, external rate $630. Description includes identification of large genomic rearrangements such as deletions, duplications, inversions, and translocations. Pipeline includes alignment (or provided BAM), structural variant calling using tools such as Manta or LUMPY, filtering for high-confidence variants, annotation of breakpoints, and QC report. • Genome-Wide Association Study (GWAS) – Priced per hour. Internal rate $55, non-lab rate $83, external rate $166. Description includes statistical association analysis linking genetic variants to traits or diseases in large cohorts. Pipeline includes genotype quality control using PLINK, principal component analysis for stratification, optional imputation (Minimac or Beagle), association testing, multiple testing corrections, and Manhattan or Q-Q plots. • Whole Genome Assembly – Priced per sample. Internal rate $250, non-lab rate $375, external rate $750. Description includes bioinformatics guidance and support, literature review, methods survey, and tool recommendations. Pipeline includes generation of a high-quality draft genome sequence, including annotation of genes and genomic features. The bottom of the page includes UNT Health branding, the university address in Fort Worth, Texas, and a page number labeled “Page 2.”Page 3 of a rate sheet from UNT Health Fort Worth titled “HPC Core: Bioinformatics Analysis Rate 2025 Fall.” The page continues a structured table listing services in Epigenomics, Accessibility, and Transcriptomics. Columns include Category, Analysis Type, Pricing Basis, Internal Rate (USD), Non-Lab Rate (USD), External Profit Rate (USD), Description, and Pipeline Outline. Epigenomics and Accessibility services: • Methylation and Epigenomics Analysis – Priced per sample. Internal rate $250, non-lab rate $375, external rate $750. Description includes analysis of DNA methylation or histone modification patterns to study gene regulation and epigenetic changes. Pipeline includes whole genome bisulfite sequencing alignment (Bismark) or array processing, differential methylation analysis (DSS or similar), peak calling for ChIP-Seq, annotation, quality control reports, and interpretation. • Chromatin Accessibility (ATAC-Seq) – Priced per sample. Internal rate $250, non-lab rate $375, external rate $750. Description includes mapping open chromatin regions to identify regulatory elements and transcription factor binding sites. Pipeline includes FASTQ quality control, trimming, alignment (Bowtie2 or STAR), transcription factor binding site analysis, differential accessibility analysis (DiffBind), quality control metrics, and report. Transcriptomics services: • Bulk RNA-Seq Analysis – Priced per sample. Internal rate $250, non-lab rate $375, external rate $750. Description includes quantitative profiling of gene expression across samples to identify differentially expressed genes. Pipeline includes FASTQ quality control, trimming, alignment (STAR or HISAT2), gene quantification, differential expression analysis (DESeq2 or edgeR), quality control plots, and summary report. • Single-Cell RNA-Seq (scRNA-Seq) Analysis – Priced per sample. Internal rate $260, non-lab rate $390, external rate $780. Description includes high-resolution, cell-by-cell gene expression profiling to identify distinct cell populations and marker genes. Pipeline includes FASTQ quality control, Cell Ranger or STARsolo processing, filtering and quality control, normalization (SCTransform), dimensionality reduction (PCA and UMAP), clustering, annotation, differential expression analysis, and quality control report. • De Novo Transcriptome Assembly and Annotation – Priced per sample. Internal rate $200, non-lab rate $300, external rate $600. Description includes construction of a reference transcriptome for organisms without a reference genome, including functional annotation of transcripts. Pipeline includes read quality control, de novo assembly (Trinity or Velvet), transcript clustering (CD-HIT), functional annotation (Trinotate), assembly quality assessment (TransRate), and summary report. The bottom of the page includes UNT Health branding, the university address in Fort Worth, Texas, and a page number labeled “Page 3.”Page 4 of a rate sheet from UNT Health Fort Worth titled “HPC Core: Bioinformatics Analysis Rate 2025 Fall.” The page continues a structured table listing services in Spatial Transcriptomics, RNA analysis, and Metabolomics and Lipidomics. Columns include Category, Analysis Type, Pricing Basis, Internal Rate (USD), Non-Lab Rate (USD), External Profit Rate (USD), Description, and Pipeline Outline. Services listed include: • Spatial Transcriptomics Analysis – Priced per sample. Internal rate $280, non-lab rate $420, external rate $840. Description includes mapping gene expression patterns to spatial locations within tissue sections to reveal architecture and microenvironments. Pipeline includes image registration, spot quality control, normalization and clustering (Seurat or Scanpy), spatial gene detection, deconvolution, visualization, pathway enrichment, and report with consultation. • MicroRNA (miRNA-Seq) Analysis – Priced per sample. Internal rate $220, non-lab rate $330, external rate $660. Description includes profiling of small non-coding RNAs to study expression and regulatory roles. Pipeline includes adapter trimming, alignment (miRDeep2 or STAR), miRNA quantification, differential analysis (DESeq2), quality control metrics, and report. • Long Non-Coding RNA (lncRNA-Seq) Analysis – Priced per sample. Internal rate $230, non-lab rate $345, external rate $690. Description includes measurement of long non-coding RNA expression levels to study potential biological functions. Pipeline includes FASTQ quality control, alignment to transcriptome (STAR), quantification (featureCounts or RSEM), differential analysis (DESeq2), and quality control report. • Alternative Splicing Analysis – Priced per hour. Internal rate $55, non-lab rate $110, external rate $220. Description includes identification and quantification of different splice isoforms to understand transcript diversity. Pipeline includes STAR two-pass alignment, isoform assembly (StringTie or Cufflinks), junction quantification (rMATS or LeafCutter), differential splicing analysis, sashimi plots, and report. Metabolomics and Lipidomics services: • Untargeted Metabolomics Analysis – Priced per sample. Internal rate $250, non-lab rate $375, external rate $750. Description includes comprehensive profiling of small-molecule metabolites to identify differences between sample groups. Pipeline includes feature detection (XCMS or MZmine), peak alignment and annotation (HMDB), statistical analysis (MetaboAnalyst), pathway enrichment, quality control, and summary report. • Targeted Metabolomics Analysis – Priced per sample. Internal rate $250, non-lab rate $375, external rate $750. Description includes quantitative measurement of predefined metabolites. Pipeline includes targeted feature extraction, calibration curve integration, quantification, internal standards quality control, and report. The bottom of the page includes UNT Health branding, the university address in Fort Worth, Texas, and a page number labeled “Page 4.”Page 5 of a rate sheet from UNT Health Fort Worth titled “HPC Core: Bioinformatics Analysis Rate 2025 Fall.” The page continues a structured table with columns for Category, Analysis Type, Pricing Basis, Internal Rate (USD), Non-Lab Rate (USD), External Profit Rate (USD), Description, and Pipeline Outline. Services listed include: • Lipidomics Analysis – Priced per sample. Internal rate $250, non-lab rate $375, external rate $750. Description includes identification and quantification of lipid species to study lipid metabolism and related pathways. Pipeline includes lipid feature detection, annotation (LIPID MAPS), differential abundance analysis, quality control calibration, pathway and network analysis, and summary report. Metagenomics and Microbiome services: • Shotgun Metagenomics Analysis – Priced per sample. Internal rate $280, non-lab rate $420, external rate $840. Description includes genome-scale profiling of microbial community composition and function in complex samples. Pipeline includes FASTQ quality control, host read removal (KneadData), taxonomic profiling (Kraken2 or MetaPhlAn), optional assembly, functional profiling (HUMAnN3), diversity metrics, and summary report. • 16S rRNA Sequencing Analysis – Priced per sample. Internal rate $280, non-lab rate $420, external rate $840. Description includes targeted sequencing of bacterial 16S rRNA genes to analyze microbial community structure and diversity. Pipeline includes demultiplexing and quality control (QIIME2 or DADA2), amplicon sequence variant or operational taxonomic unit calling, taxonomic assignment (SILVA or Greengenes), alpha and beta diversity analysis, differential abundance testing, and summary report. • Metatranscriptomics Analysis – Priced per sample. Internal rate $250, non-lab rate $375, external rate $750. Description includes profiling of active microbial gene expression to understand functional activities in environmental or host-associated samples. Pipeline includes rRNA depletion quality control, alignment (Salmon), functional annotation (eggNOG mapper), differential expression analysis, pathway enrichment (KEGG), and summary report. Proteomics and Post-Translational Modification (PTM) services: • Mass Spectrometry Proteomics Analysis – Priced per hour. Internal rate $55, non-lab rate $83, external rate $166. Description includes global analysis of protein abundance and differential expression using mass spectrometry data. Pipeline includes raw file to mzML conversion, database search (MaxQuant or Proteome Discoverer), false discovery rate filtering, quantification, differential protein analysis, pathway enrichment, and summary report. • Post-Translational Modification Analysis – Priced per hour. Internal rate $55, non-lab rate $83, external rate $166. Description includes identification and analysis of protein modifications. Pipeline includes variable modification search and site localization scoring. The bottom of the page includes UNT Health branding, the university address in Fort Worth, Texas, and a page number labeled “Page 5.”Page 6 of a rate sheet from UNT Health Fort Worth titled “HPC Core: Bioinformatics Analysis Rate 2025 Fall.” The page continues a structured table with columns for Category, Analysis Type, Pricing Basis, Internal Rate (USD), Non-Lab Rate (USD), External Profit Rate (USD), Description, and Pipeline Outline. Services listed include: Proteomics and PTM (continued): • Modification (PTM) Analysis – Pricing details not fully visible in this section header. Description includes quantification of protein modifications, such as phosphorylation, to study signaling pathways. Pipeline includes PTMProphet processing, quantification, functional annotation, and summary report. • Protein-Protein Interaction (PPI) Analysis – Priced per hour. Internal rate $55, non-lab rate $83, external rate $166. Description includes mapping and analysis of protein interaction networks to identify key partners and functional modules. Pipeline includes integration of PPI databases (STRING or BioGRID), network construction and analysis (Cytoscape), module detection, pathway identification, and report. Structural Bioinformatics services: • Homology Modeling – Priced per protein. Internal rate $55, non-lab rate $83, external rate $166. Description includes building three-dimensional protein models based on known structures to predict structure-function relationships. Pipeline includes template search and alignment (BLAST or HHblits), model building (MODELLER or SWISS-MODEL), refinement and energy minimization, validation (Ramachandran plot or QMEAN), and report. • Molecular Docking – Priced per protein. Internal rate $55, non-lab rate $83, external rate $166. Description includes predicting how small molecules bind to target proteins for virtual screening or lead optimization. Pipeline includes receptor preparation, ligand preparation, docking runs (AutoDock Vina or Glide), scoring, visualization of top hits, and summary report. • Molecular Dynamics (MD) Simulation – Priced per protein. Internal rate $55, non-lab rate $66, external rate $73. Description includes simulation of atomic motions of biomolecules to study dynamics and stability over time. Pipeline includes system setup (solvation and ion placement), parameterization, equilibration and production runs (GROMACS or NAMD), trajectory analysis, and report. • QM/MM Simulations – Priced per protein. Internal rate $55, non-lab rate $83, external rate $166. Description includes hybrid quantum mechanics and molecular mechanics simulations to investigate enzyme mechanisms or reaction pathways. Pipeline includes partitioning QM/MM regions, QM calculations (Gaussian or ORCA), MM simulations (GROMACS), energy profile analysis, and report. The bottom of the page includes UNT Health branding, the university address in Fort Worth, Texas, and a page number labeled “Page 6.”Page 7 of a rate sheet from UNT Health Fort Worth titled “HPC Core: Bioinformatics Analysis Rate 2025 Fall.” The page continues a structured table with columns for Category, Analysis Type, Pricing Basis, Internal Rate (USD), Non-Lab Rate (USD), External Profit Rate (USD), Description, and Pipeline Outline. Functional Genomics services: • CRISPR Screening Analysis – Priced per sample. Internal rate $110, non-lab rate $165, external rate $330. Description includes identifying genes essential for a phenotype using pooled CRISPR knockout or activation screens. Pipeline includes FASTQ quality control, mapping to sgRNA library (MAGeCK), hit calling and statistics, off-target checks, pathway enrichment analysis, and summary report. • RNAi Screening Analysis – Priced per sample. Internal rate $110, non-lab rate $165, external rate $330. Description includes screening gene knockdowns via RNA interference to discover gene functions or drug targets. Pipeline includes FASTQ quality control, mapping to shRNA library, dropout score calculation, hit calling, and summary report. • Gene Expression Perturbation Analysis – Priced per sample. Internal rate $110, non-lab rate $165, external rate $330. Description includes assessing gene expression changes after treatments or perturbations to understand biological responses. Pipeline includes differential expression analysis (DESeq2), pathway enrichment (clusterProfiler), optional gene regulatory network inference, and summary report. • Gene Regulatory Network (GRN) Analysis – Priced per hour. Internal rate $250, non-lab rate $375, external rate $750. Description includes constructing and analyzing gene networks to uncover regulatory relationships between genes. Pipeline includes data normalization (voom or SCTransform), network inference (ARACNe or WGCNA/GENIE3), module detection, validation, and report. Clinical Trial and Statistics services: • Survival Analysis – Priced per hour. Internal rate $55, non-lab rate $83, external rate $166. Description includes analyzing time-to-event data to estimate survival probabilities and risk factors. Pipeline includes data cleaning, Kaplan–Meier curves, Cox proportional hazards modeling, assumption checks, and report. • Bayesian Statistical Analysis – Priced per hour. Internal rate $55, non-lab rate $83, external rate $166. Description includes performing statistical inference using Bayesian methods to quantify uncertainty in model parameters. Pipeline includes model specification with priors and likelihood, Markov Chain Monte Carlo sampling (Stan or JAGS), convergence diagnostics, posterior predictive checks, and report. The bottom of the page includes UNT Health branding, the university address in Fort Worth, Texas, and a page number labeled “Page 7.”Page 8 of a rate sheet from UNT Health Fort Worth titled “HPC Core: Bioinformatics Analysis Rate 2025 Fall.” The page continues a structured table with columns for Analysis Type, Pricing Basis, Internal Rate (USD), Non-Lab Rate (USD), External Profit Rate (USD), Description, and Pipeline Outline. Clinical Trial and Statistics services listed: • RCT Analysis (Randomized Controlled Trials) – Priced per hour. Internal rate $55, non-lab rate $83, external rate $166. Description includes statistical analysis of clinical trial data to compare treatment effects and account for study design complexities. Pipeline includes data cleaning and randomization checks, intention-to-treat versus per-protocol modeling, mixed-effects models for longitudinal outcomes, multiplicity adjustments, and report. • Adaptive Clinical Trial Analysis – Priced per hour. Internal rate $55, non-lab rate $83, external rate $166. Description includes planning and analyzing adaptive trial designs that allow modifications based on interim results. Pipeline includes interim analysis design and simulations, type I error control and sample size recalculation, interim execution, operating characteristics simulation, and report. Below the table is a section titled “Charge Per Sample with Biological Replicates & Time Points.” It explains that each independent biological sample (for example, different individuals or cell lines) counts as one sample for pricing. If analyzing the same sample across multiple time points, each time point is considered a separate dataset. An “Example Calculation” section states: • 3 replicates multiplied by 3 time points equals 9 data files. • Bulk RNA-Seq analysis at $250 per sample equals 9 multiplied by $250, totaling $2,250. • Single-Cell RNA-Seq analysis at $260 per sample equals 9 multiplied by $260, totaling $2,340. The bottom of the page includes UNT Health branding, the university address in Fort Worth, Texas, and a page number labeled “Page 8.”Page 9 of a rate sheet from UNT Health Fort Worth titled “HPC Core: Bioinformatics Analysis Rate 2025 Fall.” The page contains a section labeled “Notes” with three bullet points. The notes state that: • All rates assume the client provides raw sequencing data, including raw FASTQ files, aligned BAM files, or TIFF files for spatial analysis. Wet-lab services such as extraction, library preparation, sequencing, and imaging are completed separately. • Compute costs are included in the listed rates. External nonprofit rates add 20 percent to internal rates, and external for-profit rates add an additional 10 percent beyond that. • The pipeline descriptions list common open-source tools and packages. Pricing does not include proprietary software unless specified, and pipeline modifications are determined per request. The bottom of the page includes UNT Health branding, the university address in Fort Worth, Texas, and a page number labeled “Page 9.”

Contributions to scientific output is an important metric for Core Labs, as it enables us to obtain financial and other support to ensure continuous high standards of operations to foster innovative research.

Users are encouraged to acknowledge Data Science & Computing Core in presentations, posters, papers and all other publications.

For example: “We acknowledge [name of staff] in the UNT Health Data Science & Computing Core for training and assistance on [following]”.

When to acknowledge or provide co-authorship

  • Include an acknowledgement any time the staff member or the Core provides services that support your research.
  • If a staff member has made a significant intellectual contribution beyond routine sample analysis, please consider co-authorship.