A graduate student's experience in bioinformatics

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Information about A graduate student's experience in bioinformatics

Published on February 29, 2008

Author: mlangill

Source: slideshare.net

Description

I present my experiences in bioinformatics with a focus of graduate school in the MSFHR/CIHR Strategic Training Program for Bioinformatics. This presentation was given to BiNS (Bioinformatics Network of Students) at SFU.

A graduate student's experience in bioinformatics Morgan Langille BiNS, SFU Feb. 29, 2008 http://tinyurl.com/2woa4v

1999 Graduated High School Sussex, NB No personal computer Feb. 29, 2008 BiNS

Undergraduate at UNB What can I do with a BSc (Biology) & a BCS? - Dean of Science, “ There is something called ‘Bioinformatics’” Feb. 29, 2008 BiNS

What can I do with a BSc (Biology) & a BCS?

- Dean of Science,

“ There is something called ‘Bioinformatics’”

CS vs Biology ORG $000 NUM1 FCB $00,$A1,$99,$23 NUM2 FCB $00,$A1,$A0,$A0 RES FCB $00,$00,$00,$00 ORG $E000 LDAB #$04 COUNTER LDX #NUM1 X point to NUM1 LDY #NUM2 Y points to NUM2 L1: LDAA 0,X load one byte to ACCa CMPA 0,Y compare it to B BNE L2 done if not eq INX advance the pointers Feb. 29, 2008 BiNS

ORG $000

NUM1 FCB $00,$A1,$99,$23

NUM2 FCB $00,$A1,$A0,$A0

RES FCB $00,$00,$00,$00

ORG $E000

LDAB #$04 COUNTER

LDX #NUM1 X point to NUM1

LDY #NUM2 Y points to NUM2

L1: LDAA 0,X load one byte to ACCa

CMPA 0,Y compare it to B

BNE L2 done if not eq

INX advance the pointers

CS vs Biology Feb. 29, 2008 BiNS

Bioinformatics Feb. 29, 2008 BiNS

Undergraduate Research 2002 Summer Computer science supervisor PSI-BLAST improvements 2003 & 2004 Summer Genetics supervisor Retro transposition duplications in Drosophila Feb. 29, 2008 BiNS

2002 Summer

Computer science supervisor

PSI-BLAST improvements

2003 & 2004 Summer

Genetics supervisor

Retro transposition duplications in Drosophila

Finished Undergrad 2004 Considered: Working (potato genomics) Med school Graduate School CIHR/MSFHR Training Program in Bioinformatics Actual courses in bioinformatics Several supervisors all working in bioinformatics Guaranteed funding Feb. 29, 2008 BiNS

Considered:

Working (potato genomics)

Med school

Graduate School

CIHR/MSFHR Training Program in Bioinformatics

Actual courses in bioinformatics

Several supervisors all working in bioinformatics

Guaranteed funding

Applied and accepted 4 months later, I was driving across Canada Upon arrival in Vancouver Meet & Greet Met several supervisors and other students in the program Feb. 29, 2008 BiNS

Applied and accepted

4 months later,

I was driving across Canada

Upon arrival in Vancouver

Meet & Greet

Met several supervisors and other students in the program

Courses CMPT 881 - Computational Biology MBB841 - Bioinformatics CMPT 880 - Medical Image Analysis MBB 659 - Special Topics in Bioinformatics MEDG505 - Genome Analysis MBB505 - Problem Based Learning in Bioinformatics Feb. 29, 2008 BiNS

CMPT 881 - Computational Biology

MBB841 - Bioinformatics

CMPT 880 - Medical Image Analysis

MBB 659 - Special Topics in Bioinformatics

MEDG505 - Genome Analysis

MBB505 - Problem Based Learning in Bioinformatics

Research Rotations Bioinformatics encompasses a huge range of projects Gene prediction Protein Structure Modeling Drug Design Protein Interactions Data integration and visualization BTP allows you to try out 3 different projects and supervisors Feb. 29, 2008 BiNS

Bioinformatics encompasses a huge range of projects

Gene prediction

Protein Structure Modeling

Drug Design

Protein Interactions

Data integration and visualization

BTP allows you to try out 3 different projects and supervisors

1 st Research Rotation Deconstruction of Data Transformations into Reusable Web Services -> Leading to Data Integration (Supervised by: Mark Wilkinson) Goals Identify categories of data transformations Describe categories in machine readable syntax Automate data transformations Approach: Break down bioinformatic use cases into smaller generic transformation steps Use Case Example: Identification of SNPs that are predictive of variation of disease states Feb. 29, 2008 BiNS

Deconstruction of Data Transformations into Reusable Web Services -> Leading to Data Integration (Supervised by: Mark Wilkinson)

Goals

Identify categories of data transformations

Describe categories in machine readable syntax

Automate data transformations

Approach: Break down bioinformatic use cases into smaller generic transformation steps

Use Case Example: Identification of SNPs that are predictive of variation of disease states

2 nd Research Rotation Comparative Genomics Approach to Identifying Genomic Islands (Supervised by: Fiona Brinkman) Genomic Islands (GIs) are regions of a genome that are thought to have originated from a horizontal transfer event Sequence based prediction methods Search for genomic anomalies that suggest horizontal transfer %G+C, nucleotide bias, presence of mobility genes, etc Comparative genomics based methods Identify unique regions within a query genome that are not present in any closely related microbial genomes Feb. 29, 2008 BiNS

Comparative Genomics Approach to Identifying Genomic Islands (Supervised by: Fiona Brinkman)

Genomic Islands (GIs) are regions of a genome that are thought to have originated from a horizontal transfer event

Sequence based prediction methods

Search for genomic anomalies that suggest horizontal transfer

%G+C, nucleotide bias, presence of mobility genes, etc

Comparative genomics based methods

Identify unique regions within a query genome that are not present in any closely related microbial genomes

3 rd Research Rotation Ontology Development for Flow Cytometry Data (Supervised by: Ryan Brinkman) To develop an ontology for flow cytometry data Using the OWL (Web Ontology Language) and Protégé ontology editor Integrate new ontology with the FuGO upper ontology Use existing knowledge base from Experibase Feb. 29, 2008 BiNS

Ontology Development for Flow Cytometry Data (Supervised by: Ryan Brinkman)

To develop an ontology for flow cytometry data

Using the OWL (Web Ontology Language) and Protégé ontology editor

Integrate new ontology with the FuGO upper ontology

Use existing knowledge base from Experibase

Life during BTP… Everyone goes to their own labs, but still keep in touch! Student Representative on the BTP Steering Committee Monthly student “meetings” VanBUG (Vancouver Bioinformatics User Group) BTP Wiki Facebook Group Feb. 29, 2008 BiNS

Everyone goes to their own labs, but still keep in touch!

Student Representative on the BTP Steering Committee

Monthly student “meetings”

VanBUG (Vancouver Bioinformatics User Group)

BTP Wiki

Facebook Group

Conferences One perk of being a graduate student BTP has a travel allowance Feb. 29, 2008 BiNS

One perk of being a graduate student

BTP has a travel allowance

Life after graduate school Academia Professors, Research Associate, Research Assistants, … Industry Pharma Drug design Agriculture Livestock Plants Personal Genomics SNPs $1000 personal genome http://www.bioinformatics.org/jobs/ Feb. 29, 2008 BiNS

Academia

Professors, Research Associate, Research Assistants, …

Industry

Pharma

Drug design

Agriculture

Livestock

Plants

Personal Genomics

SNPs

$1000 personal genome

http://www.bioinformatics.org/jobs/

My 2 cents Bioinformatics is not a bubble The skills you learn will be applicable in the future Think carefully about choosing your supervisor and project Talk to the supervisor Talk to lab members Talk to others in the community Read recent papers from the lab Masters or PhD? Start in Master’s, then after 1 year reassess Feb. 29, 2008 BiNS

Bioinformatics is not a bubble

The skills you learn will be applicable in the future

Think carefully about choosing your supervisor and project

Talk to the supervisor

Talk to lab members

Talk to others in the community

Read recent papers from the lab

Masters or PhD?

Start in Master’s, then after 1 year reassess

Acknowledgements Feb. 29, 2008 BiNS http://tinyurl.com/2woa4v

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