Foundations of Bioinformatics and Searching

MLA Course
Listing Archived: Friday, September 4, 2015

Primary contact information...
University at Buffalo
Health Sciences Library, University at Buffalo Libraries
Abbott Hall, 3435 Main St.
Buffalo NY , 14214
United States
Diane Rein is the primary contact.
Phone: 716 829-5749
Fax: 716 829-2211
Region: Mid-Atlantic

Description: The major goal of this course is to provide the fundamentals for library-based bioinformatics products and services decision-making and implementation. It 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.

Experience Level: Beginning Plus
Continuing Education Experience: None
CE Contact Hours: 4 or 8
Professional Competencies: Health Sciences Information Services, Health Sciences Resource Management, Curriculum Design and Instruction
Subject: Collection Development, Expert Searching, Leadership, Reference Resources & Services, Subject Specific Resources, Teaching/Instruction
Course Type: Face to Face, Hands-on

Educational Objective: NOTE: 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. The full day workshop is divided into two different 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.

Need for This Course: There is a great need to systematically integrate across the library, bioinformatics-related knowledge to support all library functions and decision-making processes. This includes collection development and access service units as well as reference and instruction services. The single attempt to train both bioresearchers and librarians in bioinformatics arose out of the National Center for Biotechnology Information (NCBI) at the National Library of Medicine. In early 2008, after less than five years of providing 1-5 day bioinformatics sessions for librarians and information specialists, all bioinformatics educational librarian outreach programs were discontinued by NCBI. This has left a gap that not only remains unfilled and but has created a new one: those who were initially trained cannot continue their training process as bioinformatics continues to explode into new directions and usage. Discussion of this lack of bioinformatics training has been discussed considerably amongst librarians and their various SIGs. In addition, bioinformatics research is one of the most prodigious producers of both local and global data. Understanding the origins of this data, and how the scientific and medical professions create and manipulate it, has general applications to archiving and managing it in institutional data repositories, particularly in the light of the recent National Science Foundation requirement for grant applicants to provide a local data management policy.

The instructional methods used include Lecture, Demonstration, Slides, Discussion, Brainstorming, Hands-on Exercises, and Problem-based.

Participant Materials: 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.

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.

Additional Evaluation: Pre- and post-testing of through an online survey tool will be implemented.