Qiu Lab Meetings: Difference between revisions
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* Systems Biology | * Systems Biology | ||
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== | ==Informatics Architecture== | ||
* Linux OS | * Operating Systems: Linux OS/Ubuntu, Mac OS | ||
* Programming languages: BASH, Perl/BioPerl, R | * Programming languages: BASH, Perl/BioPerl, R | ||
* Relational Databases: PostgreSQL | * Relational Databases: PostgreSQL | ||
* | * Software architecture | ||
** bb2: Borrelia Genome Database | ** bb2: Borrelia Genome Database | ||
** bb2i: an Perl API for bb2 | ** bb2i: an Perl API for bb2 | ||
| Line 32: | Line 32: | ||
** SimBac: A Perl/Moose package for simulating bacterial genome evolution [http://sourceforge.net/projects/bacsim/files/] | ** 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/] | ** Borrelia Ortholog Retriever: Download ortholog alignments from 23 Borrelia spp genomes. Search by gene names and IDs.[http://borreliagenome.org/orth_get/] | ||
* Hardware Setup | |||
** NSF File Server | |||
** Database and Application Server | |||
** Web Server | |||
** Linux Workstations | |||
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Revision as of 20:07, 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
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