Overview

The BCMM Computational Core is dedicated to empowering researchers by providing advanced computational analyses of omics data, primarily obtained from microbiome sequencing. This initiative supports translational research aimed at improving patient outcomes. The core's daily responsibilities include processing and analyzing omics datasets and delivering these findings directly to investigators. Additionally, the core manages the development, maintenance, and upgrading of the computational infrastructure necessary for operating sophisticated analytical software and handling the extensive computational demands associated with these tasks.

Requesting InfoCommons Linkage for BCMM Omics Projects Standard Operating Procedure (SOP)

The Computational Core is working to link InfoCommons data with BCMM-associated omics projects. A overview of this process is linked here. Access SOP (requires MyAccess login).

Consultation and project support

Our team has the expertise to assist with all aspects of microbiome data analysis. Prior to starting the project, we will supply an estimate of the required hours, a quote, and a start date as outlined in our Memorandum of Understanding (PDF). Throughout the project, you will be kept informed with detailed monthly billing updates and continuous delivery of analysis results on our project page.

BCMM Computational Hub: Services and Costs 

1. Services 

(1) Analytical Design Consultation

Provide technical support for microbiome study design, including sample size estimation, power analysis, selection of appropriate statistical models, and metadata structuring to ensure compatibility with downstream bioinformatics and statistical pipelines. Early consultation is highly encouraged to ensure proper study design and avoid underpowered or analytically unfeasible setups.

(2) Bioinformatic Processing

We provide end-to-end bioinformatic support for microbiome and host-microbiome sequencing data. This is broken up into primary, secondary, and tertiary analysis.

Primary analysis includes preprocessing raw reads, quality control, and standardized outputs in Excel format, containing raw counts, taxonomic annotations, and functional profiles where applicable. An approximate time allocation for primary analysis is summarized below and used to develop quotes – billing will reflect actual time spent. 

(3) Biostatistical Analysis

Our statistical analysis services are structured into secondary and tertiary analysis tiers to support a broad range of microbiome research goals. 

Secondary analysis focuses on characterizing microbial communities or functional profiles and identifying statistically significant associations with variables of interest. This includes:

1. Preliminary data analysis for summary statistics and visualizations.

2. Diversity analyses to assess within- and between-sample variation using ecological metrics.

3. Feature- and function-level association testing with variables of interest.

Depending on the complexity of the study, the quality of metadata, the number of variables, and comparison groups, secondary analysis typically requires 30+ hours to generate publication-ready figures. Additional time may be billed if metadata require substantial cleaning, restructuring, or clarification - tasks that often take longer than statistical testing itself. 

Tertiary analysis builds upon prior results to address more advanced, hypothesis-driven questions. Tertiary analysis may include, but is not limited to:

1. Predictive modeling to classify samples or predict outcomes based on microbial profiles.

2. Subtype discovery through unsupervised clustering.

3. Network analysis to infer interactions among microbes, between the microbiome and host genes, or across multi-omic layers.

4. Multi-omic data integration with datasets such as metagenomics, metabolomics, transcriptomics, and clinical metadata.

These advanced analyses provide deeper insight into microbial community dynamics and their functional relevance. Tertiary analysis typically requires an additional 30 hours, depending on project scope, and includes more complex statistical modeling and generation of publication-ready figures.

(4) Embedded Training on Microbiome Sequencing Data Analysis

We offer customized training sessions on microbiome sequencing data analysis, tailored to your team’s experience level and project goals. Topics may include data preprocessing, statistical modeling, visualization, and reproducibility best practices.

(5) Data Management Support

We offer support for organizing and managing both sequencing data and associated metadata to facilitate long-term accessibility and reuse. Services include metadata curation, file organization, and preparation of datasets for archiving or harmonization. Our goal is to ensure that your project data is well-structured, easily retrievable, and compliant with FAIR (Findable, Accessible, Interoperable, Reusable) data management principles.

2. Costs

Costs listed below are based on current estimates; additional items may be identified as we transition to the new computing system.

Data Management and Storage

We are developing a BCMM data portal for microbiome–metabolomics data. In parallel, we aim to provide a centralized data management environment to support your project. Our team, in collaboration with the FAC, can assist with archiving and retrieving your data in a standardized, accurate, and easily accessible format. For cost estimates, please visit: https://fac-calc.ucsf.edu/fac-shop and submit an iLab request. The costs listed on FAC reflect our actual storage expenses, does not reflect time our team spent on data management.

Meet our team

 

Lu Yang, PhD

Computational Biologist

 

 

Shwethal Trikannad

Research Associate

Next steps

To discuss new or ongoing projects, submit a Computational Project Request form on iLab and schedule a 30-minute consultation with Dr. Lu Yang.

Ready to get started? Submit a request on iLab.