Tuesday, February 26, 2008

Integrative Bioinformatics 13

[Index of classes ]

February 26 - GUI example 1 / 4 : The Cancer Genome Project

Thursday, February 21, 2008

Integrative Bioinformatics 12

[Index of classes ]

February 21- Standards

Link to the presentation can be found here

Tuesday, February 19, 2008

Integrative Bioinformatics 11

[Index of classes ]

February 19 - Homework review: UCSC data service API

  • Diogo Veiga - using Distributed Annotation System (DAS)

- The reference report was published at http://www.biomedcentral.com/1471-2105/8/333.
Affymetrix Integrated Genome Browser.
- GenBoree at Baylor uses DAS.
- DAS 2 was released in 2007 and supprots both retrieval and submission.
- DAS workshop 2008.

  • Helena Deus - hacking Web 1.0 pages.

The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology


Tuesday, February 12, 2008

Integrative Bioinformatics 10

[Index of classes ]

February 12,14 - S3DB, a distributed semantic DBMS

  1. Why - hurting enough already?
  2. What - simultaneous annotation of usage and content weaved into a permission management model.
  3. How - RESTful API.

Individual accounts will be created in class. You can also download your own at http://www.s3db.org/. Additional documentation can also be found here.

The N3 notation for RDF is VERY instructive, have a look here.

For complete documentation on RDF the right place to go is the source, W3C's reference documentation.

example of public RDF browser: Welkin.

example of commercial RDF browser: Sentient.

Function for building S3QL queries: S3QLSyntax

Tuesday, February 05, 2008

BioDas article for Feb 12 Lab Meeting

Integrative genomics using DAS : http://www.biomedcentral.com/1471-2105/8/333

Integrative Bioinformatics 9

[Index of classes ]

February 7 - more on Graphic User Interfaces

  1. Practice of GUI development in Matlab:
    a) how to find the handles
    b) how to change attribute, value pairs
    c) guihandles and related commands
  2. BIODAS as a tool for integration - Ana's challenge: DILS 2008.