Foundations of Bioinformatics and Searching

For more information or to schedule this course, please contact Diane Rein <drein@buffalo.edu> .

The goal of this face-to-face course is to provide the fundamentals for library-based bioinformatics products and services decision-making and implementation. The course encompasses visualizing bioinformatics end-user practice, resource identification and collection, and acquisition of bioinformatics search competencies.

The morning Bioinformatics Overview and Resources will cover bioinformatics practice in end-user communities, its databases, tools and scholarly literature, resource evaluation and authority, and strategies to locate peer-reviewed databases and tools.

The afternoon Searching and Molecular Biology Vocabulary Module will concentrate to developing effective bioinformatics search strategies from within the NCBI resources, by making use of the unique and robust NCBI Entrez search engine (sometimes referred to as the “poor man’s programming script search tool”). In the process, participants will develop a working molecular biology vocabulary related to genes, proteins and organisms, as well as acquire knowledge of the various bioinformatics file formats.

Participants will be provided with a full-color combination workbook/handout, both as print and electronically. The handout will also include step-by-step instructions and screenshots to resolving the problems and exercises covered in the workshop, and an appendix of resources.

Learning Objectives

The full day workshop is divided into two modules: a morning Bioinformatics Overview and Resource Module and an afternoon Bioinformatics Search and Vocabulary Module. In addition, the course will provide an opportunity for participants to network and brainstorm library-based bioinformatics services.

Upon completion of the Bioinformatics Overview and Resource Module participants will:

1) be able to identify how bioinformatics is practiced as both discipline and research process;

2) be able to identify and classify the bioinformatics scholarly literature;

3) have the strategies to identify and locate authoritative bioinformatics databases, software, and data analysis tools to support end-users.

The Bioinformatics Search and Vocabulary Module will provide participants with competencies in:

1) understanding the biological relationship of DNA to RNA to protein and how this drives bioinformatics database organization, navigation, provenance and searching;

2) a working DNA/RNA/protein/gene molecular biology vocabulary; and

3) bioinformatics data files and their provenance.

Agenda

NOTE: Bioinformatics changes rapidly. The agenda below is a representative framework. 

This workshop is available in three different formats:
8 C.E. hours for the complete full -day workshop
4 C.E. hours for the Module 1 Bioinformatics Overview and Resource Module 
4 C.E. hours for the Module 2 Searching and Molecular Biology Vocabulary Module

MODULE 1: 8:00 -8:15, Introductions and workshop overview; 8:15-8:30, pre-test; 8:30-9:15, Bioinformatics Research and Practice lecture and discussion; 9:15-9:45, Bioinformatics Resources—Monographs and Journals; 9:45-10:00, BREAK; 10:00-10:45, Bioinformatics Resources—Databases, Software and Tools; 10:45-noon, Locating and Evaluating Bioinformatics Resources—Lecture, demonstrations, and exercises; Noon-1—LUNCH and networking; MODULE 2: 1:00-1:30—Introduction to Bioinformatics Database Searching and Vocabulary lecture and demonstration; 1:30-2:45—Small Group search exercise 1; 2:30-2:45, BREAK; 2:45-4:15, continued hands-on practice, with concentration to NCBI database function; 4:15-4:30, summary and discussion; 4:30-5:00, evaluations and post-test.

Facility Requirements

Computer work stations for both participants and instructor with access to the Internet. LAN connection preferred over wireless, if possible. Projector and screen required. Most recent web browser version of either Safari (Mac), Internet Explorer or Firefox. Firefox is preferred. Instructor’ computer connected to external room speakers and sound.

This project has been funded in whole or in part with Federal funds from the National Library of Medicine, National Institutes of Health, Department of Health and Human Services, under contract No. N01-LM-6-3501 with the New York University School of Medicine.

MLA CE Credits: 4 or 8

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