Aliya Sadeque BIOC 599 Supervisory Committee Meeting Wednesday December 19, 2007.

Slides:

Advertisements

Similar presentations

CSCE555 Bioinformatics Lecture 3 Gene Finding Meeting: MW 4:00PM-5:15PM SWGN2A21 Instructor: Dr. Jianjun Hu Course page:

Advertisements

LESSON 1: What is Genetic Research? PowerPoint slides to accompany Using Bioinformatics : Genetic Research.

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

Bioinformatics at WSU Matt Settles Bioinformatics Core Washington State University Wednesday, April 23, 2008 WSU Linux User Group (LUG)‏

Bioinformatics and the Engineering Library ASEE 2008 Amy Stout.

UCSC BIOINFORMATICS Richard Hughey Vice-Chair, Biomolecular Engineering.

Panel: Mathematics in CS Iowa Undergraduate Computer Science Consortium October 2005.

Jeff Shen, Morgan Kearse, Jeff Shi, Yang Ding, & Owen Astrachan Genome Revolution Focus 2007, Duke University, Durham, North Carolina Introduction.

The Neuroscience Graduate Program Curriculum Overview.

Introduction to Bioinformatics Spring 2008 Yana Kortsarts, Computer Science Department Bob Morris, Biology Department.

Using Bioinformatics to Make the Bio- Math Connection The Confessions of a Biology Teacher.

Data-intensive Computing: Case Study Area 1: Bioinformatics B. Ramamurthy 6/17/20151.

Introduction to Genomics, Bioinformatics & Proteomics Brian Rybarczyk, PhD PMABS Department of Biology University of North Carolina Chapel Hill.

Integration of Bioinformatics into Inquiry Based Learning by Kathleen Gabric.

Workshop in Bioinformatics 2010 What is it ? The goals of the class… How we do it… What’s in the class Why should I take the class..

Bioinformatics in the Biology Curriculum Gloria Rendon NCSA July 2008.

Structural Bioinformatics Dr. Avraham Samson Course no.: Credit points: 1.5 Final grade is based on 10 assignments Course homepage:

Algorithms in Computational Biology Tanya Berger-Wolf Compbio.cs.uic.edu/~tanya/teaching/CompBio January 13, 2006.

Bioinformatics Prof. William Stafford Noble Department of Genome Sciences Department of Computer Science and Engineering University of Washington

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

EECS 395/495 Algorithmic Techniques for Bioinformatics General Introduction 9/27/2012 Ming-Yang Kao 19/27/2012.

David L. Spooner1 IT Education: An Interdisciplinary Approach David L. Spooner Rensselaer Polytechnic Institute.

Pathways Database System: An Integrated System For Biological Pathways L. Krishnamurthy, J. Nadeau, G. Ozsoyoglu, M. Ozsoyoglu, G. Schaeffer, M. Tasan.

Bachelor of Science in Information Technology California State University Channel Islands.

Bioinformatics Jan Taylor. A bit about me Biochemistry and Molecular Biology Computer Science, Computational Biology Multivariate statistics Machine learning.

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

Bioinformatics.

Ran Libeskind-Hadas, Department of Computer Science Thanks to Eliot Bush (Biology) and Zach Dodds (Computer Science) Bioinformatics Education at Harvey.

Bioinformatics Sean Langford, Larry Hale. What is it?  Bioinformatics is a scientific field involving many disciplines that focuses on the development.

Computer Science Graduate Studies in U of Memphis.

Welcome to Introduction to Bioinformatics Computing aka BIC1.

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

Bioinformatics minor at UNI. What is Bioinformatics? Developing software tools for mining biological databases. Utilizing software tools to perform biological.

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

BLAST: A Case Study Lecture 25. BLAST: Introduction The Basic Local Alignment Search Tool, BLAST, is a fast approach to finding similar strings of characters.

BIOINFORMATICS IN BIOCHEMISTRY Bioinformatics– a field at the interface of molecular biology, computer science, and mathematics Bioinformatics focuses.

CS397-CXZ Algorithms in Bioinformatics ChengXiang (“Cheng”) Zhai, Robert Skeel (Department of Computer Science) Nick Sahinidis (Department of Chemical.

Intelligent systems in bioinformatics Introduction to the course.

The Balance Between Theoretical and Practical Work Within Electrical and Computer Engineering Courses Dr. Bahawodin Baha March Development Partnerships.

What is Genetic Research?. Genetic Research Deals with Inherited Traits DNA Isolation Use bioinformatics to Research differences in DNA Genetic researchers.

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

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

Introduction to Bioinformatics (Lecture for CS397-CXZ Algorithms in Bioinformatics) Jan. 21, 2004 ChengXiang Zhai Department of Computer Science University.

BLAST: Basic Local Alignment Search Tool Altschul et al. J. Mol Bio CS 466 Saurabh Sinha.

Introduction to Bioinformatics Dr. Rybarczyk, PhD University of North Carolina-Chapel Hill

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

AdvancedBioinformatics Biostatistics & Medical Informatics 776 Computer Sciences 776 Spring 2002 Mark Craven Dept. of Biostatistics & Medical Informatics.

Final Project Bioinformatics for Biologists. Alternative A Alternative B.

Bioinformatics Curriculum Issues, goals, curriculum.

COMPUTATIONAL BIOLOGIST DR. MARTIN TOMPA Place of Employment: University of Washington Type of Work: Develops computer programs and algorithms to identify.

Biocomputation: Comparative Genomics Tanya Talkar Lolly Kruse Colleen O’Rourke.

Integration of Bioinformatics into Inquiry Based Learning by Kathleen Gabric.

Impact of the New ASA Undergraduate Curriculum Guidelines on the Hiring of Future Undergraduates Robert Vierkant Mayo Clinic, Rochester, MN.

Interdisciplinary Research Interests.

PROTEIN IDENTIFIER IAN ROBERTS JOSEPH INFANTI NICOLE FERRARO.

Bachelor of science (Major In Biology) degree, KPU PhIllip Quintana.

Figure Molecular Biology of the Cell (© Garland Science 2008)

Figure 14-1 Molecular Biology of the Cell (© Garland Science 2008)

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

Using core competencies in curriculum design

MATLAB Distributed, and Other Toolboxes

Data-intensive Computing: Case Study Area 1: Bioinformatics

Business analytics Lessons from an undergraduate introductory course

Hood College Master of Science in Bioinformatics (Proposed)

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

BSc (Hons) Agri-Biosciences

LESSON 1 INTNRODUCTION HYE-JOO KWON, Ph.D /

Applying principles of computer science in a biological context

Computer Science Dr Hwang Chair, Computer Science Department

Lecture 1 6 September 2019 Course syllabus, food guide and exercise guide Notes and other information are on:

Presentation transcript:

Aliya Sadeque BIOC 599 Supervisory Committee Meeting Wednesday December 19, 2007.

Outline About me Thesis project blueprint Course selection

Curriculum Vitae Queen’s University. Bachelor of Science (Honours) in Biochemistry. Minor in Computing. Graduated May, 2007

Previous Coursework Undergraduate Level Biochemistry: Proteins and Enzymes Physical Biochemistry Metabolism Molecular Biology Introductory Biochemistry Laboratory Protein Structure and Function Current Topics in Biochemistry Biochemistry of the Cell Advanced Molecular Biology

Previous Coursework Undergraduate Level Computing: Database Management Systems Neural and Genetic Computing Introduction to Data Mining System Level Programming Operating Systems Undergraduate Level Mathematics: Introduction to Statistics Discrete Math for Computer Scientists Modeling Techniques in Biology

Thesis Project Blueprint Context Why is this work necessary What kind of tools have been used to address it Longest Common Subsequence Part I: Explore LCSs in poxvirus Visualization Threshold frequency equation Part II: Develop an interface for use by biologists

Background “Promoter sequences might be identified as conserved islands in a divergent sea” Observed: 42-bp sequence showing “unusually high degree of sequence conservation” (Brunetti et al.) Are these claims reasonable? How can they be tested?

Tools Alignment 0 mismatch suffix tree Longest Common Subsequence Algorithm

Visualization

Threshold Frequency Figure 1. Table showing number of hits resulting from LCS trials with varying values of n and k, or subsequence length and error number, respectively. k = 1k=2k=3 length# solutionslength# solutionslength# solutions

User Interface Design with usability in mind Selection of inputs – What kind of genomes can/will this tool be used for? Format of results – How should these be presented in order to allow interpretation? Visualization Further processing of output

Timeline Part I: Poxvirus LCS data collection and analysis 2 months Part II: Interface 4-6 months

Course Selection BIOC completed MICR Virology Courses to sit in for: Biochemistry courses? Computing courses? Data mining Bioinformatics Statistics