More exercises?

January 17, 2007

Some of you have asked for more exercises lest they forget what they have learnt in the workshop.

I will add some links below, but remember: Google is your friend!

http://www.macalester.edu/~shoop/courses/CHEM58_S03/index.html


PDB educational features and new tools

January 5, 2007

The Protein Data Bank (PDB) is currently evolving. The new beta site is out and is expected to be released soon in a stable version.

Also, there are two interesting features that need to be highlighted in PDB:

Educational resources, especially the “Molecule of the month” feature

– For any given molecule, try to view the structures in “Protein Workshop” format. This format does not require you to download/install any software. Once you click on the link, an java-based application will open. This should work on most new systems (i.e., not older than 3-4 computers)

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Bioinformatics and the epidemiology of Influenza A

December 9, 2006

A very recent and very powerful study was recently published in the open-access journal: PLOS Pathogens, one of the top journals on Microbiology and Infectious disesases…

Stochastic Processes Are Key Determinants of Short-Term Evolution in Influenza A Virus

The article is not very easy and is full of terms that need background knowledge, but you should get a good idea on the work from the Abstract (Synopsis) and Introduction.


Literature Mining Tools

December 5, 2006

We have discussed today two different literature-mining tools.

1) PubMed Reminer: Detailed analysis of PubMed search results.

PubReMiner will query pubmed with your specified searchquery, get all abstracts and generate frequency tables.
The first table will show you journals in which your query is published the most.
The second table will show you the authors which are most active in the field of your query.
The third table will show you words that have been used most in the title and abstract of the articles.
furthermore, Addressfields, MESH headers and publication year are displayed.
All elements can be added to your query, and will thus make sure that your refinement still generates results.
When you are satisfied with the query, you can jump to pubmed and view the results.
Alternative names: PubReMiner, pubmed reminer, pub reminer, pubmed re-miner

2) Chilibot! The smart literature miner…

Find relationships from PubMed abstracts…