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Bioinformatics Software

The Center for Translational Science Activities (CTSA) and the Division of Biomedical Statistics and Informatics at Mayo Clinic collaborate to offer a series of classroom-based professional development courses on bioinformatics software. These courses are taught by Alexey A. Leontovich, Ph.D., of Mayo Clinic in Rochester, Minn., who also oversees bioinformatics consulting in the CTSA.

These courses are intended for researchers who want to learn about the technologies available in the Medical Genome Facility (formerly the Advanced Genomics Technology Center) at Mayo Clinic and receive hands-on training on commercial and public bioinformatics software, public bioinformatics databases and genome browsers.

Effective use of bioinformatics software enables researchers to study — on a genome-wide scale — gene expression, exon composition of transcripts, protein binding sites, genotypes, gene copy number variations, DNA methylation and other molecular events.

CME: College of Medicine, Mayo Clinic, is accredited by the Accreditation Council for Continuing Medical Education to provide continuing medical education for physicians.

College of Medicine, Mayo Clinic, designates this live activity for a maximum of 2 AMA PRA Category 1 Credit(s) TM. Physicians should claim only the credit commensurate with the extent of their participation in the activity.

Upcoming courses

Note: Registration links on this page require users to be logged in to the Mayo network.

"Gene Pathway Analysis: An Overview of Methods and Software"

  • Feb. 28, 2013
  • Commercial and public pathway analysis software uses various analytical methods and databases to construct gene networks and draw functional associations between genes and their products. Understanding the methods is important for correct interpretation of the results of such analysis.
  • Time and location: 1-3 p.m. Central, Gonda 19-101, Rochester
  • Mayo Clinic in Rochester: Register now
  • Other Mayo Clinic sites: Register now

"String, GeneMania and Other Free Software Tools and Databases"

  • March 7, 2013
  • The Gene Ontology is an ontology of defined terms representing gene product properties. The ontology covers three domains: cellular component, molecular function and biological process. A number of software applications allow you to mine the Gene Ontology and find associations of genes from an experimental set to specific categories in the ontology.
  • Time and location: 1-3 p.m. Central, Charter House 1-162, Rochester
  • Mayo Clinic in Rochester: Register now
  • Other Mayo Clinic sites: Register now

"MATISSE: Software for Detection of Biological Functional Modules Using Gene Interaction Networks"

  • March 14, 2013
  • Module Analysis via Topology of Interactions and Similarity Sets (MATISSE) is a program for the detection of functional modules using interaction networks and expression data. A functional module is a group of cellular components and their interactions that can be attributed a specific biological function. MATISSE implements several algorithmic engines that together analyze expression and network data. Each of the algorithms addresses a different research question and scenario.
  • Time and location: 2:30-4:30 p.m. Central, Charter House 1-162, Rochester
  • Mayo Clinic in Rochester: Register now
  • Other Mayo Clinic sites: Register now

"Using GSEA Software for Gene Pathways Analysis"

  • March 21, 2013
  • Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (for example, phenotypes).
  • Time and location: 1-3 p.m. Central, Charter House 1-162, Rochester
  • Mayo Clinic in Rochester: Register now
  • Other Mayo Clinic sites: Register now

"Cytoscape: The Basics"

  • April 4, 2013
  • Cytoscape is the most resourceful free software and data source for gene pathway and function enrichment analysis. It includes a variety of analytical and visualization tools. Cytoscape is developed and maintained by the research community worldwide.
  • Time and location: 1-3 p.m. Central, Charter House 1-160 and 1-162, Rochester
  • Mayo Clinic in Rochester: Register now
  • Other Mayo Clinic sites: Register now

"Cytoscape: Advanced"

  • April 9, 2013
  • Cytoscape is the most resourceful free software and data source for gene pathway and function enrichment analysis. It includes a variety of analytical and visualization tools. Cytoscape is developed and maintained by the research community worldwide. Examples of pathway analysis performed in peer-reviewed publications will be presented.
  • Time and location: 11 a.m.-1 p.m. Central, Charter House 1-160, Rochester
  • Mayo Clinic in Rochester: Register now
  • Other Mayo Clinic sites: Register now

"Genome Browsers: UCSC, Ensembl, IGB"

  • April 25, 2013
  • Genome browsers are essential software tools for the visualization of sequence data and genome annotations.
  • Time and location: 1-3 p.m. Central, Ozmun Center 3-05, Rochester
  • Mayo Clinic in Rochester: Register now
  • Other Mayo Clinic sites: Register now

"Using MetaCore Software for Gene Pathways Analysis: Analytical, Visualization and Discovery Tools"

  • May 16, 2013
  • MetaCore is one of the best applications for the analysis of molecular pathways, analysis of biological networks of genes and proteins, data mining of biological annotations, data visualization, and reporting tools.
  • Time and location: 1-3 p.m. Central, Charter House 1-160 and 1-162, Rochester
  • Mayo Clinic in Rochester: Register now
  • Other Mayo Clinic sites: Register now

"MetaCore Software: Advanced"

  • May 23, 2013
  • MetaCore is one of the best applications for the analysis of molecular pathways, analysis of biological networks of genes and proteins, data mining of biological annotations, data visualization, and reporting tools. Examples of pathway analysis performed in peer-reviewed publications will be presented.
  • Time and location: 2:30-4:30 p.m. Central, Charter House 1-162, Rochester
  • Mayo Clinic in Rochester: Register now
  • Other Mayo Clinic sites: Register now

"Using Ingenuity Software for Gene Pathways Analysis: Analytical, Visualization and Discovery Tools"

  • May 30, 2013
  • Ingenuity is the second-best application for the analysis of molecular pathways, analysis of biological networks of genes and proteins, data mining of biological annotations, data visualization, and reporting tools.
  • Time and location: 1-3 p.m. Central, Charter House 1-160 and 1-162, Rochester
  • Mayo Clinic in Rochester: Register now
  • Other Mayo Clinic sites: Register now

Contact

Our Education Contacts page contains a listing of team members who can assist you with questions.

  • March 28, 2013
  • ART011670