Fall 2005 projects
BE290B, fall 2005.
Assessment and deadlines
Four milestones will be assessed toward the final grade for this class:
Dates and assessment criteria for these milestones follow beneath.
- Summary paragraph on wiki page (approx 20% of grade);
- Ten-minute presentation (approx 20% of grade);
- Written report (approx 50% of grade);
- Updated wiki page (approx 10% of grade).
Summary paragraph on wiki page
Your first assessed milestone is to edit this wiki page by adding a WikiName link (within a brief one-sentence summary)
to a new wiki page for your project.
The new wiki page should contain a one-paragraph (or more) summary of your approach to the project.
The WikiName for your page should be your name, with capitalized initials and no spaces, followed by "GraduateProject"
(e.g. "IanHolmesGraduateProject"). The wiki server auto-expands this and inserts spaces (i.e. to IanHolmesGraduateProject).
If you're using a Holmes lab project, click on the name of the project below
(e.g. EvolutionaryHmmForProteinSecondaryStructurePrediction) to get to the project stub,
then click on the "Edit" link (top right) and add a link to your GraduateProject page.
If you've designed your own project, click on StudentDesignedGraduateProjects and
edit that page to add a link to your GraduateProject page.
It's OK to work in teams: use a compound WikiName reflecting your team members' surnames,
Also feel free to add wiki pages for your own WikiName (e.g. IanHolmes).
Note that you can use EFetchPlugin to include links to PubMed abstracts in your wiki page,
although you cannot add links to external sites without an account (for reasons of spam prevention).
Assessment for the summary paragraph milestone will begin on November 18th, 2005.
Strictly time-limited presentations to take place in class on December 5th, 2005.
Written project report
The project report is due December 19th, 2005. It should be emailed to IanHolmes in PDF format.
Assessment criteria will include
Teams are encouraged to submit a single report,
with attributions for the various aspects of the work
(i.e. who did what on the project).
- Design of probabilistic model;
- Computational application;
- Biological interpretation of results;
- Suggestions for experiments in order to further validate or test model.
Updated wiki page
Review of the updated wiki page will commence midnight December 19th, 2005.
In the event that you might consider submitting your Bioe290b project--or any other work--to a compbio conference in 2006,
here are some ideas:
Note: Included topic Teaching.CompbioConferences does not exist yet
Holmes lab projects
(This page is pretty out of date now... for an overview of research projects, contact IanHolmes.)
Holmes lab projects are annotated as follows:
See lecture notes on Hidden Markov models for brief intro to
- Unix - some Unix and scripting experience recommended
- bio - biological intuition helpful
- coding - programming experience would be good (e.g. C++)
- math - I classify these as mathematical
- physics - stochastic biophysics simulations
xprot and projects based on Evolutionary HMMs.
- EvolutionaryHmmForProteinSecondaryStructurePrediction (bio, Unix)
- EvolutionaryHmmForTransmembraneStructurePrediction (bio, Unix)
- EvolutionaryHmmForSignalPeptidePrediction (bio, Unix)
- EvolutionaryHmmForGenefinding (bio, Unix)
- EvolutionaryGrammarForOperonPrediction (bio, Unix)
- GenomeWideMeasurementsOfSubstitutionRates (bio)
- McmcAlignmentSamplingWithEvolutionaryHmm (bio, Unix)
- McmcAlignmentSamplingWithEvolutionaryScfg (bio, Unix)
- PredictingOoiNumberViaIndelModeling (bio, Unix, coding)
- PredictingRamachandranPlotAnglesUsingHmmWithDiscreteAndGaussianCharacters (math,coding)
- EstimatingSparseSubstitutionModelForBindingSitesViaEM (math, coding)
- KaKsRatios (math, coding)
- OptimizingTreeBranchLengthsViaEM (math, coding)
- McmcTrajectorySamplerForRateGrammars (math, coding)
- HierarchicalModelsOfPathwayGainAndLoss (math, bio)
- ModelingEvolutionOfFunction (math, bio)
- RNACellularAutomata (physics, coding)
- MesoscaleMolecularDynamicsSimulationOfMicroarrayProbeTargetBinding (physics, coding)
- MesoscaleMolecularDynamicsSimulationOfRnai (physics, coding)
- TkfIndelModelEigenfunctions (math)
- PrincipledApproximationToLongIndelModel (math)
Enter your project stubs here. For example: