Qiu Lab Meetings: Difference between revisions

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==Foundational Readings==
==Foundational Readings==
* Phylogeography of ''Borrelia burgdorferi sensu lato''. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3214628/ A review by Margos et al. 2011]
* Molecular phylogenetics
* Molecular phylogenetics
* Population genetics
* Population genetics
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* Systems Biology
* Systems Biology
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==Informatics Architecture==
==Informatics Architecture==
* Operating Systems: Linux OS/Ubuntu, Mac OS
* Operating Systems: Linux OS/Ubuntu, Mac OS

Revision as of 16:30, 28 June 2013

Projects & Goals

  • Borrelia population genomics: Recombination & Natural Selection (Published)
  • Borrelia pan-genomics (Submitted as of 5/25/2013)
  • Positive and negative selection in Borrelia ORFs and IGS (Submitted as of 6/15/2013)
  • Dr Bargonetti's project (Summer 2013)
  • A population genomics pipeline using MUGSY-FastTree (Summer 2013): Project page
  • Borrelia Genome Database & Browser (Summer 2013) Version 2 screen shot
  • Pseudomonas population genomics (Summer 2013) Project page
  • Hypothesis Testing: Do host-interacting genes show adaptive codon usage? (Summer 2013): Project page
  • Phylogenomics browsing with JavaScript/JQuery, Ajax, and jsPhylosvg
  • Frequency distribution of ospC types in wild tick populations (Fall 2013) Project page

Lab meeting: June 13, 2013

  • Weigang: IGS paper submission should be done by Thursday.
  • Che/Slav: Workshop update (Meeting at 3:30pm?)
  • Che: SILAC project (Meeting at 4pm?)
  • Zhenmao: Tick processing & paired-end Illumina sequencing
  • Pedro: Updates on "ncbi-orf" table
  • Girish: phyloSVG extension; QuBi video
  • Saymon and Deidre: consensus start-codons
  • Reeyes and Raymond: Pseudomonas DB; fleN alignment and phylogeny
  • Valentyna: BLASTn results (4:30pm?)

Lab meeting: May 23, 2013

  • May 24, Friday: End of School Year Party in the Park (we leave from Hunter @ 1:30pm)
  • Recommended reading of the week: Detecting Neanderthal genes using the D' homoplasy statistic
  • Weigang: IGS paper submission
  • Che: Thesis update/SILAC project/Summer teaching
  • Zhenmao: Manuscript update: Material & Methods; Results (Tables and Figures)
  • Pedro: Catlyst web framework
  • Girish: cp26 phylogenomic analysis
  • Saymon and Deidre: consensus start-codons

Lab meeting: May 16, 2013

  • Weigang: IGS paper submitted yet?
  • Che: Thesis update. Chapter 3. Evolution of ospA/ospB gene family
  • Pedro/Zhenmao: Can we wrap up the BLAST identification of ospC types?
  • Girish: Fetch cp26 sequences from DB; Run MUGSY & FastTree
  • Saymon/Deidre: Identification of consensus start-codon positions
  • Pedro/Girish: orth_get/orth_igs website development. Catalyst. Implement graphics (genome map & phylogeny) query interface
  • Raymond: start the Pseudomonas summer project

Foundational Readings

  • Phylogeography of Borrelia burgdorferi sensu lato. A review by Margos et al. 2011
  • Molecular phylogenetics
  • Population genetics
  • Genomics
  • Systems Biology

Informatics Architecture

  • Operating Systems: Linux OS/Ubuntu, Mac OS
  • Programming languages: BASH, Perl/BioPerl, R
  • Relational Databases: PostgreSQL
  • Software architecture
    • bb2: Borrelia Genome Database
    • bb2i: an Perl API for bb2
    • DNATweezer: Perl wrappers of most frequently used BioPerl modules, including Bio::Seq, Bio::SimpleAlign, and Bio::Tree [1]
    • SimBac: A Perl/Moose package for simulating bacterial genome evolution [2]
    • Borrelia Ortholog Retriever: Download ortholog alignments from 23 Borrelia spp genomes. Search by gene names and IDs.[3]
  • Hardware Setup
    • NSF File Server
    • Database and Application Server
    • Web Server
    • Linux Workstations

Perl Challenges

Problem Input Output
DNA transcription A DNA sequence, in 5'-3' direction (e.g., aaatttaaaagacaaaaagactgctctaagtcttgaaaatttggttttcaaagatgat) An RNA sequence, in 5'-3' direction
Genetic code None 64 codons, one per line (using loops)
Count amino acids A protein sequence Frequency counts of individual amino acids
Count codons A protein-coding DNA sequence Frequency counts of individual codons
Random sequence 1 None Generate a random DNA sequence (e.g., 1000 bases) with equal base frequencies
Random sequence 2 None Generate a random DNA sequence with biased base frequencies, e.g., 10% G, 10% C, 40% T, and 40% A.
Graphics I a categorical dataset, e.g., Biology a bar graph & a pie char, using GD::Simple or Postscript::Simple