Qiu Lab Meetings: Difference between revisions
Jump to navigation
Jump to search
imported>Weigang (Created page with "==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 identificati...") |
imported>Weigang m (→May 16, 2013) |
||
| Line 1: | Line 1: | ||
==May 16, 2013== | ==Projects & Goals== | ||
* Borrelia population genomics: Recombination & Natural Selection (Published) | |||
* Borrelia pan-genomics (In submission) | |||
* Positive and negative selection in Borrelia ORFs and IGS (In submission) | |||
* Borrelia Genome Database & Browser (Summer 2013) | |||
* Pseudomonas population genomics (Summer 2013) | |||
* Frequency distribution of ospC types in wild tick populations (Fall 2013) | |||
---- | |||
==Lab meeting: May 16, 2013== | |||
* Weigang: IGS paper submitted yet? | * Weigang: IGS paper submitted yet? | ||
* Che: Thesis update. Chapter 3. Evolution of ospA/ospB gene family | * Che: Thesis update. Chapter 3. Evolution of ospA/ospB gene family | ||
| Line 7: | Line 15: | ||
* Pedro/Girish: orth_get/orth_igs website development. Catalyst. Implement graphics (genome map & phylogeny) query interface | * Pedro/Girish: orth_get/orth_igs website development. Catalyst. Implement graphics (genome map & phylogeny) query interface | ||
* Raymond: start the Pseudomonas summer project | * Raymond: start the Pseudomonas summer project | ||
---- | |||
==Foundational Readings== | |||
* Molecular phylogenetics | |||
* Population genetics | |||
* Genomics | |||
* Systems Biology | |||
---- | |||
==Main Software Tools== | |||
* Linux OS | |||
* Programming languages: BASH, Perl/BioPerl, R | |||
* Relational Databases: PostgreSQL | |||
* Informatics 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 [https://sourceforge.net/p/dnatwizzer/home/Home/] | |||
** SimBac: A Perl/Moose package for simulating bacterial genome evolution [http://sourceforge.net/projects/bacsim/files/] | |||
** Borrelia Ortholog Retriever: Download ortholog alignments from 23 Borrelia spp genomes. Search by gene names and IDs.[http://borreliagenome.org/orth_get/] | |||
---- | ---- | ||
Revision as of 20:01, 9 May 2013
Projects & Goals
- Borrelia population genomics: Recombination & Natural Selection (Published)
- Borrelia pan-genomics (In submission)
- Positive and negative selection in Borrelia ORFs and IGS (In submission)
- Borrelia Genome Database & Browser (Summer 2013)
- Pseudomonas population genomics (Summer 2013)
- Frequency distribution of ospC types in wild tick populations (Fall 2013)
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
- Molecular phylogenetics
- Population genetics
- Genomics
- Systems Biology
Main Software Tools
- Linux OS
- Programming languages: BASH, Perl/BioPerl, R
- Relational Databases: PostgreSQL
- Informatics 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]