Journal Club

    These are just basic guidelines for the topics.presenters
should NOT attempt to cover all of the mentioned items instead use these
as a measure how an article/review fit into the topic.

    If a background review is vital to the topic, presenter may review the
topic in general for 10 mins then focus on a certain paper, or may opt
to go for a general overview for the complete topic not restricting
herself/himself to a certain paper.

    As a final note, I believe we should take these journal clubs as an
opportunity to learn on the topic we are working on, instead of a
task/exam. So it would be great if presenter studies the subject
extensively and charms us with deep insights, but it is also cool if you
just read enough to ignite some discussion and can give most important
facts and pointers.


19 Mon at 11.00 AM: Insight on biological pathways
An ( or a few) examplary pathway will be reviewed to gain
insight into pathways, preferably in human. It would be great if
presenter can also review studies on the overall structure of the big
picture like size, avarage node degree, any exceptional structures,
compertmantalization etc.  Presenter should assume that audience has
minimal background knowledge on biological pathways (i.e. only those
that were discussed at tutorial 12 wed). Read article(?)

To be decided: EcoCyc Database(Emek Demir)
EcoCyc Database will be reviewed in terms of their ontology,approach
and applications. EcoCyc is one of the most succesfull DBs in the field
and share many similarities with PATIKA. I will try to move through the
most important milestones and successes in the EcoCyc story, and will address
points we can learn from EcoCyc.ED (Note: JC hour is not still certain yet)
Article-A nice overview of EcoCyc

To be decided: Pathway data:
Pathway data and ways they are obtained will be reviewed. Presenter
should focus on current/future high throughput techniques as well as the
restrictions/requirements that may be posed on the ontology by the
structure of the data.

To be decided: Pathway Databases
Current pathway databases and database systems( both commercial
and academic) will be reviewed.  Reviewer should focus on the amount and
structure of the data, and the way they are modeled/stored. Presenter
should compare major databases in terms of size, regularity,
completeness, querying, representation strength and collaborativeness.

Part 2: Special Topics:

To be decided: Pathway Data Mining
Methods for identifying pathway information from various data
sources will be reviewed. Focus should be given data mining
applications, specifically mining data from unstructured text like
PubMed abstracts. Presenter should also review the underlying ontology
of the data created by such applications and discuss its suitability to
the PATIKA project.

To be decided: Pathway Inferral Problem
Methods for inferring pathways from various data sources will be
reviewed. Focus should be given to inferring pathways from structured
data such as microarray data or yeast two hybrid systems.

To be decided: Pathway Simulation and Prediction
Methods for simulating pathways or predicting their outcome on
certain conditions will be reviewed. Focus should be on methods that
require modest data/ modeling times and can simulate signaling pathways.
Quantitative to qualitative transitions can also be discussed.

To be decided: Pathway Layout
Issue on automatically creating pathway layouts will be
discussed. Presenter should review general visual features that are
desired to be in Pathway diagrams, constraints (such as compartments) as
well as current solutions. Other layout methods that can be applied to
pathways can also be presented.

Part 3: Applications
To be decided: Applications
Any application that uses or can benefit from pathway infromation can be
covered. Example applications are drug desgin and development, disease
modeling, diagnosis, expert systems, therapy design, knowledge
acquisition. Presenter should discuss benefits and how PATIKA data can
be used in such applications.