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 <ul><li>What can I do with a BSc (Biology) & a BCS? </li></ul><ul><li>- Dean of Science,  </li></ul><...
CS vs Biology <ul><li>ORG $000 </li></ul><ul><li>NUM1 FCB $00,$A1,$99,$23 </li></ul><ul><li>NUM2 FCB $00,$A1,$A0,$A0 </li>...
CS vs Biology Feb. 29, 2008 BiNS
Bioinformatics Feb. 29, 2008 BiNS
Undergraduate Research <ul><li>2002 Summer  </li></ul><ul><ul><li>Computer science supervisor </li></ul></ul><ul><ul><li>P...
Finished Undergrad 2004 <ul><li>Considered: </li></ul><ul><ul><li>Working (potato genomics) </li></ul></ul><ul><ul><li>Med...
<ul><li>Applied and accepted </li></ul><ul><li>4 months later,  </li></ul><ul><li>I was driving across Canada </li></ul><u...
Courses <ul><li>CMPT 881 - Computational Biology </li></ul><ul><li>MBB841 - Bioinformatics </li></ul><ul><li>CMPT 880 - Me...
Research Rotations <ul><li>Bioinformatics encompasses a huge range of projects </li></ul><ul><ul><li>Gene prediction </li>...
1 st  Research Rotation <ul><li>Deconstruction of Data Transformations into Reusable Web Services -> Leading to Data Integ...
2 nd  Research Rotation <ul><li>Comparative Genomics Approach to Identifying Genomic Islands  (Supervised by: Fiona Brinkm...
3 rd  Research Rotation <ul><li>Ontology Development for Flow Cytometry Data (Supervised by: Ryan Brinkman) </li></ul><ul>...
Life during BTP… <ul><li>Everyone goes to their own labs, but still keep in touch! </li></ul><ul><li>Student Representativ...
Conferences <ul><li>One perk of being a graduate student </li></ul><ul><li>BTP has a travel allowance </li></ul>Feb. 29, 2...
Life after graduate school <ul><li>Academia </li></ul><ul><ul><li>Professors, Research Associate, Research Assistants, … <...
My 2 cents <ul><li>Bioinformatics is not a bubble </li></ul><ul><ul><li>The skills you learn will be applicable in the fut...
Acknowledgements Feb. 29, 2008 BiNS http://tinyurl.com/2woa4v
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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 of Students) at SFU.

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A graduate student's experience in bioinformatics

  1. 1. A graduate student's experience in bioinformatics Morgan Langille BiNS, SFU Feb. 29, 2008 http://tinyurl.com/2woa4v
  2. 2. 1999 Graduated High School Sussex, NB No personal computer Feb. 29, 2008 BiNS
  3. 3. Undergraduate at UNB <ul><li>What can I do with a BSc (Biology) & a BCS? </li></ul><ul><li>- Dean of Science, </li></ul><ul><li>“ There is something called ‘Bioinformatics’” </li></ul>Feb. 29, 2008 BiNS
  4. 4. CS vs Biology <ul><li>ORG $000 </li></ul><ul><li>NUM1 FCB $00,$A1,$99,$23 </li></ul><ul><li>NUM2 FCB $00,$A1,$A0,$A0 </li></ul><ul><li>RES FCB $00,$00,$00,$00 </li></ul><ul><li>ORG $E000 </li></ul><ul><li>LDAB #$04 COUNTER </li></ul><ul><li>LDX #NUM1 X point to NUM1 </li></ul><ul><li>LDY #NUM2 Y points to NUM2 </li></ul><ul><li>L1: LDAA 0,X load one byte to ACCa </li></ul><ul><li>CMPA 0,Y compare it to B </li></ul><ul><li>BNE L2 done if not eq </li></ul><ul><li>INX advance the pointers </li></ul>Feb. 29, 2008 BiNS
  5. 5. CS vs Biology Feb. 29, 2008 BiNS
  6. 6. Bioinformatics Feb. 29, 2008 BiNS
  7. 7. Undergraduate Research <ul><li>2002 Summer </li></ul><ul><ul><li>Computer science supervisor </li></ul></ul><ul><ul><li>PSI-BLAST improvements </li></ul></ul><ul><li>2003 & 2004 Summer </li></ul><ul><ul><li>Genetics supervisor </li></ul></ul><ul><ul><li>Retro transposition duplications in Drosophila </li></ul></ul>Feb. 29, 2008 BiNS
  8. 8. Finished Undergrad 2004 <ul><li>Considered: </li></ul><ul><ul><li>Working (potato genomics) </li></ul></ul><ul><ul><li>Med school </li></ul></ul><ul><ul><li>Graduate School </li></ul></ul><ul><li>CIHR/MSFHR Training Program in Bioinformatics </li></ul><ul><ul><li>Actual courses in bioinformatics </li></ul></ul><ul><ul><li>Several supervisors all working in bioinformatics </li></ul></ul><ul><ul><li>Guaranteed funding </li></ul></ul>Feb. 29, 2008 BiNS
  9. 9. <ul><li>Applied and accepted </li></ul><ul><li>4 months later, </li></ul><ul><li>I was driving across Canada </li></ul><ul><li>Upon arrival in Vancouver </li></ul><ul><ul><li>Meet & Greet </li></ul></ul><ul><ul><ul><li>Met several supervisors and other students in the program </li></ul></ul></ul>Feb. 29, 2008 BiNS
  10. 10. Courses <ul><li>CMPT 881 - Computational Biology </li></ul><ul><li>MBB841 - Bioinformatics </li></ul><ul><li>CMPT 880 - Medical Image Analysis </li></ul><ul><li>MBB 659 - Special Topics in Bioinformatics </li></ul><ul><li>MEDG505 - Genome Analysis </li></ul><ul><li>MBB505 - Problem Based Learning in Bioinformatics </li></ul>Feb. 29, 2008 BiNS
  11. 11. Research Rotations <ul><li>Bioinformatics encompasses a huge range of projects </li></ul><ul><ul><li>Gene prediction </li></ul></ul><ul><ul><li>Protein Structure Modeling </li></ul></ul><ul><ul><li>Drug Design </li></ul></ul><ul><ul><li>Protein Interactions </li></ul></ul><ul><ul><li>Data integration and visualization </li></ul></ul><ul><li>BTP allows you to try out 3 different projects and supervisors </li></ul>Feb. 29, 2008 BiNS
  12. 12. 1 st Research Rotation <ul><li>Deconstruction of Data Transformations into Reusable Web Services -> Leading to Data Integration (Supervised by: Mark Wilkinson) </li></ul><ul><li>Goals </li></ul><ul><ul><li>Identify categories of data transformations </li></ul></ul><ul><ul><li>Describe categories in machine readable syntax </li></ul></ul><ul><ul><li>Automate data transformations </li></ul></ul><ul><li>Approach: Break down bioinformatic use cases into smaller generic transformation steps </li></ul><ul><li>Use Case Example: Identification of SNPs that are predictive of variation of disease states </li></ul>Feb. 29, 2008 BiNS
  13. 13. 2 nd Research Rotation <ul><li>Comparative Genomics Approach to Identifying Genomic Islands (Supervised by: Fiona Brinkman) </li></ul><ul><li>Genomic Islands (GIs) are regions of a genome that are thought to have originated from a horizontal transfer event </li></ul><ul><li>Sequence based prediction methods </li></ul><ul><ul><li>Search for genomic anomalies that suggest horizontal transfer </li></ul></ul><ul><ul><ul><li>%G+C, nucleotide bias, presence of mobility genes, etc </li></ul></ul></ul><ul><li>Comparative genomics based methods </li></ul><ul><ul><li>Identify unique regions within a query genome that are not present in any closely related microbial genomes </li></ul></ul>Feb. 29, 2008 BiNS
  14. 14. 3 rd Research Rotation <ul><li>Ontology Development for Flow Cytometry Data (Supervised by: Ryan Brinkman) </li></ul><ul><li>To develop an ontology for flow cytometry data </li></ul><ul><li>Using the OWL (Web Ontology Language) and Protégé ontology editor </li></ul><ul><li>Integrate new ontology with the FuGO upper ontology </li></ul><ul><li>Use existing knowledge base from Experibase </li></ul>Feb. 29, 2008 BiNS
  15. 15. Life during BTP… <ul><li>Everyone goes to their own labs, but still keep in touch! </li></ul><ul><li>Student Representative on the BTP Steering Committee </li></ul><ul><li>Monthly student “meetings” </li></ul><ul><li>VanBUG (Vancouver Bioinformatics User Group) </li></ul><ul><li>BTP Wiki </li></ul><ul><li>Facebook Group </li></ul>Feb. 29, 2008 BiNS
  16. 16. Conferences <ul><li>One perk of being a graduate student </li></ul><ul><li>BTP has a travel allowance </li></ul>Feb. 29, 2008 BiNS
  17. 17. Life after graduate school <ul><li>Academia </li></ul><ul><ul><li>Professors, Research Associate, Research Assistants, … </li></ul></ul><ul><li>Industry </li></ul><ul><ul><li>Pharma </li></ul></ul><ul><ul><ul><li>Drug design </li></ul></ul></ul><ul><ul><li>Agriculture </li></ul></ul><ul><ul><ul><li>Livestock </li></ul></ul></ul><ul><ul><ul><li>Plants </li></ul></ul></ul><ul><ul><li>Personal Genomics </li></ul></ul><ul><ul><ul><li>SNPs </li></ul></ul></ul><ul><ul><ul><li>$1000 personal genome </li></ul></ul></ul><ul><li>http://www.bioinformatics.org/jobs/ </li></ul>Feb. 29, 2008 BiNS
  18. 18. My 2 cents <ul><li>Bioinformatics is not a bubble </li></ul><ul><ul><li>The skills you learn will be applicable in the future </li></ul></ul><ul><li>Think carefully about choosing your supervisor and project </li></ul><ul><ul><li>Talk to the supervisor </li></ul></ul><ul><ul><li>Talk to lab members </li></ul></ul><ul><ul><li>Talk to others in the community </li></ul></ul><ul><ul><li>Read recent papers from the lab </li></ul></ul><ul><li>Masters or PhD? </li></ul><ul><ul><li>Start in Master’s, then after 1 year reassess </li></ul></ul>Feb. 29, 2008 BiNS
  19. 19. Acknowledgements Feb. 29, 2008 BiNS http://tinyurl.com/2woa4v

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