Bioinformatics
The Bioinformatics Core Facility team provides services and resources to assist the Notre Dame research community from project development through publication. Our analyst works to identify appropriate experimental design, and provide guidance and services for data processing and analysis of genomics datasets. Often these datasets are from non-model organisms with complex genomic backgrounds. Services are available to support a range of applications including Transcriptomics, small RNA, Whole genome sequencing, ddRAD-seq, Epigenomics, Metagenomics, and more.
Research Collaborations
The GBCF offers project-based collaborations through either fee-for-service or through joint research grants.
Consultation & Office Hours
The GBCF team is happy to offer consultation services for data analysis and project design. Request an appointment by contacting Melissa Stephens.
Office hours are suspended until further notice.
Workshops & Training
Bioinformatics workshops and training sessions, including seminars and lecture events, which cover a range of topics from introductory Linux to complex analysis like those involved in Next Generation Sequencing, are limited until further notice. For more information, please contact Melissa Stephens.
Computing Resources
The software packages below are supported by the GBCF and licensed by the University for faculty use. To establish an account and access the software for either MetaCore or IPA, please contact Melissa Stephens.
- MetaCore Pathway Analysis – Integrated software suite for functional analysis of Next-Gen Sequencing, variant, CNV, microarray, metabolic, SAGE, proteomics, siRNA, miRNA, and screening data
- Ingenuity Pathway Analysis – Web-based software application for the analysis, integration, and interpretation of data derived from gene, transcript, and protein expression data
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Sequencher – DNA sequence assembly software for windows
- Must be connected to the Notre Dame network and have KeyAccess software installed. Cisco Clean Access VPN connection required for remote access.
Biomodules
The GBCF, in conjunction with the Center for Research Computing (CRC), has pre-installed a number of Bioinformatics tools available for users to access. For more information on these tools, please access the Biomodules Wiki.
To see a list of the current titles use cmd: module help bio/2.0
To load biomodules use cmd: module load bio
It is recommended to establish a CRC account for the transfer of raw and processed sequencing data, and for secure long term storage.