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PHYLOINF09
Computational PhyloinformaticsCourse Timetable (provisional) |
| PHYLOINF09 | PhyloInformatics - the NESCENT course |
| Thursday, July 9 |
Day #1 |
| 08:00 - 09:00 | Coffee, Check email |
| 09:00 - 10:30 | Unix refresher module |
| 10:30 - 10:45 | Coffee Break |
| 10:45 - 12:15 | Unix lab continued; Introduction to Perl |
| 12:15 - 13:30 | Lunch Break |
| 13:30 - 15:00 | Perl IO Handles |
| 15:00 - 15:30 | Tea Break |
| 15:15 - 16:45 | Truth and Beauty; Arrays, Hashes, Lists |
| 16:45 - | Evening Session: software installations, TBA |
| Friday, July 10 |
Day #2 |
| 08:00 - 09:00 | Coffee, Check email |
| 09:00 - 10:30 | Perl regular expressions |
| 10:30 - 10:45 | Coffee Break |
| 10:45 - 12:15 | Perl subroutines and functions |
| 12:15 - 13:30 | Lunch Break |
| 13:30 - 15:00 | Packages |
| 15:00 - 15:30 | Tea Break |
| 15:15 - 16:45 | CPAN |
| 16:45 - | Evening Session: software installations, TBA |
| Saturday, July 11 |
Day #3 |
| 08:00 - 09:00 | Coffee, Check email |
| 09:00 - 10:30 | Introduction to nexus, Bio::Phylo |
| 10:30 - 10:45 | Coffee Break |
| 10:45 - 12:15 | Matrix objects in Bio::Phylo |
| 12:15 - 13:30 | Lunch Break |
| 13:30 - 15:00 | Large tree inference strategies; Rec-i-DCM3; CIPRES REST interface |
| 15:00 - 15:30 | Tea Break |
| 15:15 - 16:45 | Collecting results from CIPRES; Mesquite |
| 16:45 - | Evening Session: optional student coding and personal research projects |
| Sunday, July 12 |
Day #4 |
| 08:00 - 09:00 | Coffee, Check email |
| 09:00 - 10:30 | Sequence data in Genbank; BioPerl's Bio::SeqIO; Bio::Seq; Bio::Species |
| 10:30 - 10:45 | Coffee Break |
| 10:45 - 12:15 | Genbank taxonomy vs real taxonomy; Bio::Species revisited |
| 12:15 - 13:30 | Lunch Break |
| 13:30 - 15:00 | Bio::Seq Revisited |
| 15:00 - 15:30 | Tea Break |
| 15:15 - 16:45 | Bio::Tools::Run::Alignment::*; Bio::AlignIO; Bio::Align::Alignl |
| 16:45 - | Evening Session: optional student coding and personal research projects |
| Monday, July 13 |
Day #5 |
| 08:00 - 09:00 | Coffee, Check email |
| 09:00 - 10:30 | Substitution models with ModelTest; automating PAUP |
| 10:30 - 10:45 | Coffee Break |
| 10:45 - 12:15 | Substitution model selection; Automating ModelTest |
| 12:15 - 13:30 | Lunch Break |
| 13:30 - 15:00 | Manipulating trees using Bio::Phylo; Tree pruning |
| 15:00 - 15:30 | Tea Break |
| 15:15 - 16:45 | Estimating branch lengths using PAUP |
| 16:45 - | Evening Session: optional student coding and personal research projects |
| Tuesday, July 14 |
Day #6 |
| 08:00 - 09:00 | Coffee, Check email |
| 09:00 - 10:30 | Calibrating relative branch lengths to obtain absolute divergence dates |
| 10:30 - 10:45 | Coffee Break |
| 10:45 - 12:15 | Rate smoothing, penalized likelihood; Automating r8s |
| 12:15 - 13:30 | Lunch Break |
| 13:30 - 15:00 | Divergence rates vs. branch lengths; tree traversal; recursion |
| 15:00 - 15:30 | Tea Break |
| 15:15 - 16:45 | Applying branch lengths to the supertree |
| 16:45 - | Evening Session: software installations, TBA |
| Wednesday, July 15 |
Day #7 |
| All day | Free day to recharge brain cells and visit Lisbon |
| Thursday, July 16 |
Day #8 |
| 08:00 - 09:00 | Coffee, Check email |
| 09:00 - 10:30 | Introduction to Databases |
| 10:30 - 10:45 | Coffee Break |
| 10:45 - 12:15 | Introduction to SQL |
| 12:15 - 13:30 | Lunch Break |
| 13:30 - 15:00 | SQL and the DBI |
| 15:00 - 15:30 | Tea Break |
| 15:15 - 16:45 | SQL and Trees 1 |
| 16:45 - | Evening Session: optional student coding and personal research projects |
| Friday, July 17 |
Day #9 |
| 08:00 - 09:00 | Coffee, Check email |
| 09:00 - 10:30 | SQL and Trees 2 |
| 10:30 - 10:45 | Coffee Break |
| 10:45 - 12:15 | Transitive Closure |
| 12:15 - 13:30 | Lunch Break |
| 13:30 - 15:00 | Transitive Closure |
| 15:00 - 15:30 | Tea Break |
| 15:15 - 16:45 | Building a Simple Web Interface |
| 16:45 - | Evening Session: optional student coding and personal research projects |
| Saturday, July 18 |
Day #10 |
| 08:00 - 09:00 | Coffee, Check email |
| 09:00 - 10:30 | Designing Your Own Database |
| 10:30 - 10:45 | Coffee Break |
| 10:45 - 12:15 | Strongly-typed versus weakly-typed schemas |
| 12:15 - 13:30 | Lunch Break |
| 13:30 - 15:00 | Introducing BioSQL |
| 15:00 - 15:30 | Tea Break |
| 15:15 - 16:45 | Persisting and retrieving data with BioPerl <-> BioSQL |
| 16:45 - | Evening Session: optional student coding and personal research projects |
| Sunday, July 19 |
Day #11 |
| 08:00 - 09:00 | Coffee, Check email |
| 09:00 - 10:30 | Persisting and retrieving data with BioPerl <-> BioSQL |
| 10:30 - 10:45 | Coffee Break |
| 10:45 - 12:15 | Querying a BioSQL using object-relational mapping |
| 12:15 - 13:30 | Lunch Break |
| 13:30 - 15:00 | Querying a BioSQL using object-relational mapping |
| 15:00 - 15:30 | Tea Break |
| 15:15 - 16:45 | Querying BioSQL directly |
| 16:45 - | Evening Session: optional student coding and personal research projects |
| Course Homepage |
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Instituto Gulbenkian de Ciência, Apartado 14, 2781-901 Oeiras, Portugal Last updated: May 17th 2009 |