Objectives
- To support investigators in biomedical, health, and community-based research across the network with data science services.
- To develop and enhance biomedical and health-focused data science knowledge and capacity across the network.
Types of Support Offered
- Experimental design, sample size determination, and power calculations
- Planning and execution of studies using existing datasets, e.g., in public health
- Statistical analysis including data visualization, descriptive statistics, hypothesis testing, and regression modeling
- Use of statistical software including SAS, SPSS, and R
Request Statistical Support
Please use the form below to request support from the Data Science Core. We will review your request and reach out to schedule a meeting to learn more about your project.
National Center for Genome Resources
the NM INBRE Data Science Core is supported by the National Center for Genome Resources.
The National Center for Genome Resources (NCGR), founded in 1993, is a not-for-profit research institute specializing in genomic data science. Renowned for its expertise in DNA sequence analysis, bioinformatics, and software engineering, NCGR collaborates with government, industry, and academia to drive biological discoveries across all forms of life. The institute provides comprehensive support for experimental design, computation, data integration, and workforce training. Its facilities include a sequencing lab, bioinformatics analysis capabilities, and ample office space for hosting collaborators and educational events. NCGR also supports virtual collaborations and offers biweekly mentoring programs on various professional development topics. The research group, consisting of 12 researchers, spans diverse biological fields such as microbiology, human health, and environmental research, utilizing cutting-edge sequencing and bioinformatics techniques. NCGR also manages educational training programs, including INBRE-funded workshops and a high school capstone program that provide hands-on learning in bioinformatics and DNA sequencing.
Available Cores and Institutional Research Facilities at NCGR
Sequencing and Molecular Biology Lab
The lab includes the needed equipment for performing DNA/RNA sequencing and molecular biology experiments. Currently, NCGR only performs Oxford Nanopore Sequencing but has agreements in place for discounted sequencing services on other platforms and have a thorough understanding of the main sequencing technologies.
Bioinformatics Analysis
NCGR provides extensive bioinformatics expertise, covering genomic variation, expression analysis, epigenetics, single-cell studies, genome assembly, structural variation, and metagenomics. NCGR employs advanced tools and techniques like PacBio IsoSeq and pangenomic analyses to link genetic variation with phenotypic traits.
Bioinformatics Training
NCGR trains students in bioinformatics, genomics, genetics, computing and biology. They provide onsite and virtual training across many levels, including K-12, undergraduate and graduate levels, postdoctoral and faculty level. They run in person and virtual bioinformatics workshops for New Mexico/INBRE students and researchers across several topics.
To explore all that NCGR has to offer, click the link below to visit their full website.
Briefings In Bioinformatics
Briefings in Bioinformatics is an international forum for researchers and educators in the life sciences. The journal will also be of interest to mathematicians, statisticians and computer scientists who apply their work to biological problems. The journal publishes reviews for the users of databases and analytical tools of contemporary genetics, molecular and systems biology and is unique in providing practical help and guidance to the non-specialist in computerized methodology. Papers range in scope and depth, from the introductory level to specific details of protocols and analyses encompassing bacterial, plant, fungal, animal and human data.
To view the latest and past issues, please follow the read more link below.
National Institute of General Medical Sciences (NIGMS) Sandbox Modules
The NIGMS Sandbox is a collection of cloud-based biomedical data science learning modules to teach students, researchers, clinicians, and others how to use the power of cloud technology for life sciences applications and research.
Available Modules
If you would like guidance on what order to complete the below modules, follow the learn more link and review the recommended learning pathways section.
Fundamentals of Bioinformatics
Dartmouth College
In this module you will learn to use the Bash shell scripting language to work with common genomics file formats, create Conda environments, and troubleshoot command line errors.
DNA Methylation Sequencing Analysis with WGBS
University of Hawaii at Monoa
In this module you will learn how to download raw sequence data, calculate differentially methylated regions, and run a canonical methylseq pipeline in Nextflow.
Transciptome Assembly Refinemen and Applications
MDI Biological Laboratory
In this module you will learn how to use a Nextflow pipeline to assemble and annotate a novel transcriptome using RNA-Seq data.
RNAseq Differential Expression Analysis
University of Maine
In this module you will learn how to download raw sequence data, run differential gene expression analysis, and produce common plots in R.
Proteome Quantification
University of Arkansas for Medical Sciences
In this module you will learn about mass spectrometry data, statistical terminology for data preprocessing, data normalization, and differential abundance analysis for proteomics.
ATAC-Seq and Single Cell ATAC-Seq Analysis
University of Nebraska Medical Center
In this module you will learn how to download raw sequence data, run differential peak identification, genome annotation, transcription factor footprinting, and produce common plots and visualizations.
Consensus Pathway Analysis in the Cloud
University of Nevada Reno
In this module, you will learn how to download expression data, conduct differential analysis, perform enrichment analysis, meta-analysis and visualization. This cloud-based learning module teaches pathway analysis, a term that describes the set of tools and techniques used in life sciences research to discover the biological mechanism behind a condition from high throughput biological data
Integrating Multi-Omics Datasets
University of North Dakota
In this module you will learn how to analyze RNA-Seq, Epigenetics, and integrated multiomics datasets in R with a Nextflow pipeline. This module will walk you through some of the techniques to integrate transcriptomic and epigenetic data.
Metagenomics Analysis of Biofilm-Microbiome
University of South Dakota
In this module you will learn how to use a Docker container to analyze amplicon sequencing metagenomics data with common tools such as qiime2 and PICRUSt2.
Introduction to Data Science for Biology
San Francisco State University
In this module you will learn how to create a simple decision tree using a structured dataset, evaluate model performance quantitatively, and understand why machine learning models require retraining from time to time.
Analysis of Biomedical Data for Biomarker Discovery
University of Rhode Island
In this module you will learn how to use exploratory data analysis, linear models, regression, and machine learning to discover biomarkers for kidney disease. This learning module will introduce the user to basic concepts in biomarker discovery that the user is likely to encounter in the clinical and biomedical literature.
Biomedical Imaging Analysis Using AI/ML Approaches
University of Arkansas
In this module you will learn how to generate a neural network, manipulate datasets, train a neural network on the dataset, apply the trained neural network to a new dataset, and quantify its performance.
Data Science Core Contacts
Charlotte Gard
Data Science Core Director
Data Science Collaborative Consulting Center Director
New Mexico State University
cgard@nmsu.edu
Patrick Trainor
Data Science Core Associate Director
New Mexico State University
ptrainor@nmsu.edu
Marshall Taylor
Education & Outreach Director
New Mexico State University
mtaylor2@nmsu.edu