(2 X 2) 2 High-throughput Data Analysis Workshops X 2 on NCBI Public Databases.

19 September 2016 - 10:09am by Rolando Garcia-Milian

Cushing/Whitney Medical Library has organized these four workshops, two of them on high-throughput data analysis tools and two on NCBI public databases. Although these are free and open to any Yale affiliate, registration is required due to limited seating.  

Title:      NGS Data Analysis in Partek® Software: Onsite Workshop

Registration: http://schedule.yale.edu/event/2819565


Morning Session (Overview, Hands On: Analysis on RNA-Seq Data): 9:00AM – 12:00PM

Free access to Partek Flow is provided by the Yale Medical Library. Register for an account here

This session will start with an overview of Partek Software solutions followed with a hands on RNA-Seq Data Analysis in Partek Flow. Topics will include how to use statistical tests to identify differentially expressed transcripts and alternative spliced genes among sample groups, how to generate a list of genes of interest and identify high level biological trends using Gene Ontology.

  • Import data (fastq, bam, text format)
  •  Perform QA/AC (Pre-alignment QA/AC, Post-alignment QA/QC)
  • Trim bases
  • Alignment
  • Gene/transcript abundance estimate (E/M)
  •  Differential expression detection (GSA, ANOVA)
  • Filter gene list
  • GO Enrichment Analysis
  • Visualization
    • Quality score distribution
    • Base composition
    • PCA scatterplot
    • Dotplot
    • Volcano plot
    • Hierarchical clustering
    • Chromosome view

Afternoon Session (Open Lab; Q&A): 1:30PM – 4:00PM

We hope to see you there!

Date & Time:     9:00am - 12:00pm, Thursday, September 29, 2016

Location:           C-103, SHM, 333 Cedar St

Campus:           Medical School

Presenter:          Eric Seiser, PhD, Field Application Scientist, Partek Inc.


Title: Broadcast. Navigating NCBI Molecular Data Using the Integrated Entrez System and BLAST

Registration: http://schedule.yale.edu/event/2832345

Description: This workshop will be broadcasted from the Taubman Health Sciences Library, Univ Michigan, and provides an introduction to the NCBI molecular databases and how to access the data using the Entrez text-based search system and BLAST sequence similarity search tool. You will learn the varied types of available molecular data, and how to find and display sequence, variation, genome information using organism sources (Taxonomy), data sources (Bioproject) and emphasizing the central role of the gene as an organizing concept to navigate across the integrated databases (Gene, Nucleotide, Protein, dbSNP and other resources).

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St

Presenter: Peter Cooper, Ph.D. of the National Center for Biotechnology Information

Date/time: 9:00am - 12:00pm, Tuesday, October 4, 2016


Title: Broadcast. A Practical Guide to NCBI BLAST

Registration: http://schedule.yale.edu/event/2832347

Description: This workshop will be broadcasted from the Taubman Health Sciences Library, Univ Michigan and highlights important features and demonstrates the practical aspects of using the NCBI BLAST service, the most popular sequence similarity service in the world. You will learn about useful but under-used features of the service. These include access from the Entrez sequence databases; the new genome BLAST service quick finder; the integration and expansion of Align-2- Sequences; organism limits and other filters; re-organized databases; formatting options and downloading options; and TreeView displays. You will also learn how to use other important sequence analysis services associated with BLAST including Primer BLAST, an oligonucleotide primer designer and specificity checker; the multiple protein sequence alignment tool, COBALT; and MOLE-BLAST, a new tool for clustering and providing taxonomic context for targeted loci sequences (16S, ITS, 28S). These aspects of BLAST provide easier access and results that are more comprehensive and easier to interpret.

Location: Cushing/Whitney Medical Library, Simbonis Conference Room 101A, 333 Cedar St

Presenter: Peter Cooper, Ph.D. of the National Center for Biotechnology Information

Date/time: 9:00am - 12:00pm, Wednesday, October 5, 2016


Title:      Make new discoveries with your OMICs data: Hypothesis testing and assumption-free exploration

Registration: http://schedule.yale.edu/event/2832289


10AM- Noon:

  • Exemplary workflows for different experiment designs
  • Hypothesis testing and Assumption-free data exploration
  • Working with annotations, dynamic and interactive plots

Input data: any matrix multivariate data (RNAseq, Microarrays, Proteomics, miRNA, Metabolomics, Lipidomics, methDNA, Mulitplex and FACS, Clinical data, Biomarkers, etc.), as well as publicly available GEO data, gene sets files, gene ontology. Complete list is available here.


Getting started session – take advantage of a trial access for Yale! Have a look the info uploaded to the Yale Library folder, including presentation, case studies, tutorials, etc.

Qlucore tools allow researchers to perform advanced visualization, exploration and statistical analysis of omics data with the help of an intuitive GUI. Targets of interest can be further explored in terms of biological insight using GO and GSEA.  Unmatched speed, immediate visual feedback, continuous visualization, and synchronized views significantly shorten both data-to-result and query-to-discovery times.

By combining right annotations with statistical methods, data selection tools, and the eliminated factors function, a very broad range of different experiment designs can be analyzed with exceptional productivity. This solution draws upon both innovative and classical approaches, fueled by best-in-class industrial and academic research.

Qlucore Omics Explorer helps you advance your research by:

  • boosting the speed of your analysis at least by 50%
  • generating new ideas, hypotheses, and giving you a new prospective on your data, and questions you ask of it
  • helping recognize significant insight that is specific to biological process, disease, or function, as well as assumption-free exploration
  • keeping your projects on track with simple QC checks on every step
  • providing publication ready graphics, and intermediate results for collaboration.

Qlucore Omics Explorer is used by big commercial companies as well as major research organizations and Universities across Europe and US. (e.g., Boehringer Ingelheim, Roche Diagnostics,  AstraZeneca, DFCI, BWH, Harvard, MD Anderson, MSKCC, MedImmune, Novo Nordisk, etc.).

Date & Time:     10:00am - 12:00pm, Thursday, October 27, 2016

Location:           C-103 - SHM 333 Cedar St

Campus:            Medical School

Presenter:          Yana Khalina-Stackpole, PhD, Business and Support manager, Qlucore