Microbial Genome Annotation by Undergraduates Michael Sierk Saint Vincent College NIBLSE Workshop April 17, 2014.

Slides:

Advertisements

Similar presentations

My problem is students don't read graphs and tables effectively. Research Question Does continued practice producing and interpreting graphs increase students’

Advertisements

Presentation to Educational Policy Committee Department of Biology Revised March, 2013 Biology Department: Position Requests.

BioInformatics at FSU - whose job is it and why it needs to be done. Steve Thompson Steve Thompson Florida State University School of Computational Science.

Educational Programs in Bioinformatics at UNO Hesham H. Ali Department of Computer Science College of Info Science and Technology University of Nebraska.

Bioinformatics and the Engineering Library ASEE 2008 Amy Stout.

Goran Šuković, University of Montenegro 1/18 Faculty of Sciences Podgorica University of Montenegro 7 th Workshop on “Software Engineering Education and.

Presented by ORNL–University Partnerships in Computational Biology Igor B. Jouline (Zhulin) Joint Institute for Computational Sciences The University of.

Pathways Bioinformatics & Biomolecular Center at the City College of New York Marshak Science Building, Room 1102 Tel: 212/ Fax: 212/

6/10/2015 ©T. C. Hazen #1 Center for Environmental Biotechnology Center for Environmental Biotechnology Rapid deduction of bacteria stress response pathways:

The Golden Age of Biology DNA -> RNA -> Proteins -> Metabolites Genomics Technologies MECHANISMS OF LIFE Health Care Diagnostics Medicines Animal Products.

BIBM 2009 Education Workshop Nov 2, 2009 Moderators: Sun Kim and Dong Xu.

Scientific Data Mining: Emerging Developments and Challenges F. Seillier-Moiseiwitsch Bioinformatics Research Center Department of Mathematics and Statistics.

BI420 – Course information Web site: Instructor: Gabor Marth Teaching.

FACULTY MEETING September 26, 2008 Marty Wood Assistant Dean for Undergraduate Education Chair, SOE Curricula & Courses Committee.

Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies Lonnie Welch School of Electrical Engineering & Computer Science Biomedical.

Undergraduate Participation in Bioinformatics Training (UPBiT) Ming-Ying Leung, 1,2 Stephen B. Aley, 2,3 Vladik Kreinovich, 2,4 and Elizabeth Walsh 2,3.

8/15/2015Bioinformatics and Computational Biology Undergraduate Major 1 Iowa State University College of Liberal Arts and Sciences Bioinformatics & Computational.

Multiple Associate Degrees - Proposed New Policy 3 rd AGC Presentation & VOTE April 9,

Professional Development In A Workforce Program Linnea Fletcher PhD Department Chair, Biotechnology Co-PI, Bio-Link ATE Center Grant in Biotechnology.

The BIO Directorate Microbial Biology Emphasis BIO Advisory Committee April, 2005.

Is it E. coli O157:H7? Using Bioinformatics to Develop and Test Hypotheses I’d like to thank Shellie Kieke, Concordia University – St. Paul, and Ruth Gyure,

 GPiBS (Graduate Program in Biomedical Sciences) is offered through the Graduate College at the University of Oklahoma Health Sciences Center.  All students.

Genome-scale Metabolic Reconstruction and Modeling of Microbial Life Aaron Best, Biology Matthew DeJongh, Computer Science Nathan Tintle, Mathematics Hope.

Institute of Systems Biology (INBIOSIS)/ School of Biosciences & Biotechnology (Faculty of Science & Technology), Bioinformatics Development in Malaysia.

Not Just for Students: An Archives Workshop for Faculty Rachel Grove Rohrbaugh Chatham University Archives | Pittsburgh, Pa. | (412)

Computer Science Graduate Studies in U of Memphis.

Srebrenka Robic Introducing Bioinformatics to Agnes Scott College.

Integrating Bioinformatics into the Life Sciences – Phase 2 Mark Pauley and Bill Tapprich Group #2: Integration.

University of Texas, El Paso April 7-8, 2005 What About Graduate School? Opportunities in Endocrinology Kenneth L. Campbell Professor of Biology University.

Overview. What is Annotation? Annotation is the process of determining the location and function of all identifiable genes in a genome. Annotation is.

IT Education in Serbia Prof. Dr. Ivan Milentiejvic Computer Science Department Faculty of Electronic Engineering University of Nis University of NisSerbia.

STONY BROOK UNIVERSITY HEALTH SCIENCES LIBRARY CHECK OUT THE SERVICES & RESOURCES AVAILABLE TO YOU.

Master’s Degrees in Bioinformatics in Switzerland: Past, present and near future Patricia M. Palagi Swiss Institute of Bioinformatics.

Research in Education Faculty Development Workshop March 8, 2013 Donna L. Pattison, PhD Instructional Professor Department of Biology & Biochemistry.

A New Oklahoma Bioinformatics Company. Microarray and Bioinformatics.

Second Year (2009) Semester 1 Plants and the Environment ( ) Fundamentals of Cell Biology ( Semester 2 Plant Biodiversity ( ) Ecology.

LORRIE JOHNSON U.S. DEPARTMENT OF ENERGY OFFICE OF SCIENTIFIC AND TECHNICAL INFORMATION (OSTI) ICSTI TECHNICAL ACTIVITIES COORDINATING (TACC) MEETING OCTOBER.

Advancing Science with DNA Sequence Undergraduate Genomics in a Research University Environment A Collaborative Effort between the JGI and UC Merced M.

Help Students Help Themselves - CS291/CS490 Mentoring Program Lisa L. Fan, Ph.D Department of Computer Science, University of Regina.

Bioinformatics Education at North Central College Caroline St.Clair Professor of Computer Science.

Making curricula structure Ghent University Workshop Tempus Making curricula structure with basic, core and optional models February 2006.

Bioinformatics: Theory and Practice – Striking a Balance (a plea for teaching, as well as doing, Bioinformatics) Practice (Molecular Biology) Theory: Central.

Bioinformatics & GCAT-SEEK Vince Buonaccorsi Juniata College Goal: Facilitate massively parallel sequencing projects involving faculty teaching undergrads.

Global Biodiversity Information Facility GLOBAL BIODIVERSITY INFORMATION FACILITY Meredith A. Lane CODATA/ERPANET Workshop: Scientific Data Selection &

GK-12 Saturday Workshop I October 16, 2010 RS: Amy Zimmerman CTs: Roy Center, Lee Kelly Genetic Transformation: Process and Applications.

Master of Science in Biological Informatics PROGRAM DESCRIPTION The MS in Biological Informatics program program aims.

 GEP Implementation at Mt. San Jacinto Community College Nick Reeves, Ph.D.

Western New York Genetics in Research Partnership Expanding Exposure, Career Exploration and Interactive Projects in Basic Genome Analysis and Bioinformatics.

How Virginia is Scaling the Z-Degree Across All 23 Colleges Richard Sebastian Director, Teaching & Learning Technologies Virginia Community College System.

Department of Biotechnology

Joanna Klein, Ph.D. Northwestern Scholarship Symposium May 10, 2013.

The HHMI Science Education Alliance Create Refine Network Disseminate Resources for Science Education Tuajuanda Jordan, Ph.D. Senior Program Officer Howard.

Student Engagement with CUREs, SUREs, and Collaboration OK-INBRE Retreat Promoting Undergraduate Research in Oklahoma Virginia Balke, Ph.D. Delaware Technical.

Bioinformatics Professor: Monica Bianchini Department of Information Engineering and Mathematics E–mail: Phone: 1012.

Bachelor of Science (Major or Honours in Biochemistry) Degree.

Budapest University of Technology and Economics

LB73 - Implementation of Biotechnology Projects of Different Inquiry Level to Promote Career Success of Non-Science Majors Paloma Valverde, PhD;

Third largest private college in MD

Lactase genes and evolution

SEA-PHAGES Bioinformatics Workshop Overview

LEARN WHY COMPUTERS ARE REVOLUTIONIZING BIOLOGY!

New genes can be added to an organism’s DNA.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

General Genetics Biology 184 Fall 2008 Instructor: Dr. Tom Peavy.

Session 2. Understanding and Using the Standard Material Transfer Agreement (SMTA) The International Treaty on Plant Genetic Resources for Food and Agriculture:

EDUCAUSE MARC 2004 E-Portfolios: Two Approaches for Transforming Curriculum & Promoting Student Learning Glenn Johnson Instructional Designer Penn State.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Presentation transcript:

Microbial Genome Annotation by Undergraduates Michael Sierk Saint Vincent College NIBLSE Workshop April 17, 2014

Context Saint Vincent College Small Catholic liberal arts college Moderately Selective Biology, Biochemistry, Bioinformatics majors Biotechnology minor

JGI Microbial Annotation Joint Genome Institute Microbial Genome Annotation Cheryl Kerfeld, Seth Axen Institution picks genome Instructors assign genes to students Students fill out electronic notebook When finished, transfer information from notebook to annotation form Instructor rates quality for subsequent review by JGI staff

Implementation BIN 218 Bioinformatics, Genomics, and Proteomics Required for Bioinformatics major, Biotechnology minor Elective for Biology major, CS major Offered odd-numbered years in the Fall (2011, 2013) Typically ~ 10 students BL 215 Molecular Genetics Lab Required for Bioinformatics major, Cell/Molecular Biology major Offered every Fall (2011, 2012, 2013) Typically ~ 20 students

Benefits Students learn about gene annotation techniques, software, etc. Genuine annotation (not just an exercise) Potential for their work to be used in JGI database Relatively low overhead

Limitations Technical difficulties (minor) Some of the modules are difficult for the students to understand Need more instruction/in-class time Easy genes vs. hard genes Planned expansion into Microbiology, Biochemistry, Cell Biology, General Biology has not occurred yet All voluntary, no external incentives (negative or positive) Faculty uncomfortable with the technology and/or unwilling/unable to adapt/modify their curricula Student annotations not used in IMG database?