Scientific Computation Services
Expert consulting in building high-performance computational infrastructure for scientific research, including GPU workstations, data storage solutions, linux server setup, and analysis pipelines.
Computing & Data Infrastructure
Complete hardware and software solutions for AI-powered analysis, data storage, and computational workloads:
High-Performance Workstations
Custom-built workstations with NVIDIA GPUs for accelerated image processing, deep learning, and large-scale data analysis. Optimized for performance while minimizing noise and power draw. Over 20 years of workstation building experience.
AI & ML Servers
Dedicated server infrastructure for running inference, batch processing, and continuous analysis workflows. Docker containerization or virtualization for reproducible environments.
Storage Infrastructure
Network-attached storage systems with redundancy, automated backups, and high-speed access. Optimized for terabyte-scale imaging datasets and long-term archival.
Data Pipelines
Automated workflows for preprocessing, analysis, and visualization of scientific datasets. Integration with cloud services or keep it local with your own hardware.
Data Organization
File structure design, metadata management, and database systems for efficient data retrieval and analysis reproducibility.
Cloud Integration
Hybrid local/cloud strategies for scalable storage and computing. Cost-effective solutions for burst computing needs and disaster recovery.
Single-Cell & Spatial Transcriptomics
Extensive experience with 10x Genomics platforms for single-cell and spatial transcriptomics, including library preparation, sequencing, computational analysis, and visualization. Expertise spans standard scRNA-seq workflows to cutting-edge spatial transcriptomics for tissue-level gene expression mapping.
Comprehensive computational analysis of single-cell and single-nucleus RNA-seq data, from experimental design and quality control through advanced trajectory analysis and differential expression.
Figure 5. Single-cell sequencing of Oxtr KO and Oxtr WT OBs demonstrates transcriptional changes associated with synapse morphology and formation within abGCs. (B) Uniform manifold projection of all OB cells. Dlx5/6-Cre;Oxtrfl/fl, Oxtrfl/fl, and WT samples clustered concurrently. (C) Heat map of the top differentially expressed genes for each cluster in B. (D, left) Uniform manifold projection of subclustered abGCs colored in pseudotime. (Middle) Expression of Sox11 and Slc32a1 maturation markers mapped onto abGC clusters. (Right) χ² analysis of Dlx5/6-Cre;Oxtrfl/fl cluster composition versus WT and Oxtrfl/fl samples. (E) Differential expression GO analysis from just abGCs adapted from EnrichR.
From: Pekarek et al. (2022) "Oxytocin signaling is necessary for synaptic maturation of adult-born neurons" Genes & Development 36:1100-1118.
Analysis Capabilities
- Quality Control & Preprocessing: Cell filtering, normalization, and batch correction
- Dimensional Reduction: PCA, t-SNE, UMAP for visualization
- Clustering & Cell Type Identification: Automated and manual annotation strategies
- Differential Expression: Statistical analysis of gene expression changes
- Trajectory Analysis: Pseudotime and developmental lineage inference
- Integration: Multi-sample and multi-condition dataset integration
- Visualization: Publication-quality plots and interactive reports
Typical Service Offerings
Needs Assessment
Evaluate current infrastructure, data volumes, and computing requirements. Identify bottlenecks and optimization opportunities.
System Design
Develop customized solutions tailored to your specific research needs and budget. Hardware selection, network topology, and software stack recommendations.
Implementation
Hands-on setup and configuration of hardware, network, and software components. Testing and optimization for peak performance.
Training & Support
Comprehensive documentation, user training, and ongoing support for maintaining and troubleshooting your infrastructure.
Ready to Build Your Infrastructure?
Contact me to discuss how computational infrastructure can accelerate your research.
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