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A graduate student's experience in bioinformatics
 

A graduate student's experience in bioinformatics

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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 ...

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.

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    A graduate student's experience in bioinformatics A graduate student's experience in bioinformatics Presentation Transcript

    • 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
    • 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
    • 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
    • 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
      • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • Conferences
      • One perk of being a graduate student
      • BTP has a travel allowance
      Feb. 29, 2008 BiNS
    • 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
    • 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
    • Acknowledgements Feb. 29, 2008 BiNS http://tinyurl.com/2woa4v