The University of Michigan’s Taubman Health Sciences Library is hosting a series of National Center for Biotechnology Information (NCBI) workshops in October 2016. Dr. Peter Cooper and Dr. Wayne Matten, of NCBI will conduct the workshops that will be streamed and available in Room 401, Hardin Library for the Health Sciences. No registration required. Free and open to all.
Tuesday, 10/4, 8am-11am- Navigating NCBI Molecular Data Using the Integrated Entrez System and BLAST. This workshop 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).
Wednesday, 10/5, 9 8am-11am- A Practical Guide to NCBI BLAST. This workshop 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.
Thursday, 10/6, 8am-11am- EDirect: Command Line Access to NCBI’s Biomolecular Databases. The EDirect suite of programs allows easy command line access for searching and retrieving literature (PubMed) and accessing NCBI’s biomolecular (Gene, Nucleotide, sequence databases, etc.) records. Its advantages include direct command-line access to NCBI’s databases without writing Perl or Python scripts, construction of custom pipelines for processing data, built-in batch access, and the ability to generate highly flexible custom output reports. During the optional first hour of this workshop (8-9 AM), you will get a basic introduction to the Unix/Linux command line interface. The main workshop (9am-11am) will cover how to use EDirect to set-up simple pipelines to retrieve and process data from PubMed, Gene, and the Nucleotide and Protein sequence databases. Access to EDirect installed in a Linux environment on a cloud service will be provided.
Individuals with disabilities are encouraged to attend all University of Iowa-sponsored events. If you are a person with a disability who requires a reasonable accommodation in order to participate in this program please call Janna Lawrence at 319-335-9871.