SCALE-IT / NIMBioS Workshop, January 2013

Use the following short cuts to jump to a set of resources on this page.

General EMBL/EBI Resources
Module I: Plasmodium Problem Space Resources
Module II: Functional Genomics
Module III: Protein Structure & Visualization
Module IV: Ensembl Resources at EBI
Module V: Proteomic Resource at EBI
Previous SCALE-IT Workshop Web Sites

General EMBL/EBI Resources:

List of Modules – http://www.ebi.ac.uk/training/roadshow/modules.html
Tools / Data

Working with sequence – http://www.ebi.ac.uk/Tools/similarityandanalysis.html
Ensembl – http://useast.ensembl.org/index.html, Ensembl genomes (http://www.ensemblgenomes.org/), ENA (http://www.ebi.ac.uk/ena/)
ATLAS gene expression – http://www.ebi.ac.uk/gxa/, Gene Ontology (http://www.geneontology.org/)
Proteomics resources: Uniprot (http://www.ebi.ac.uk/uniprot/), Intepro (http://www.ebi.ac.uk/interpro/), Intact, Reactome (http://www.reactome.org/)

Plasmodium Problem Space Resources:

Plasmodium Problem Space: http://bit.ly/problemspace

Liu et al (2010) paper that the Plasmodium Problem Space is built from

Robust Phylogenetic Analysis for the Non-specialist: http://www.phylogeny.fr/
Some instructions are available here.

Visualizing malaria: Context for exploring the Plasmodium data

Worldmapper: http://www.worldmapper.org/display.php?selected=2

1. Go to Malaria Cases http://www.worldmapper.org/display.php?selected=229
2. Malaria Deaths http://www.worldmapper.org/display.php?selected=23

Gapminder (prebuilt graph): www.bit.ly/VGrOVZ

1. Run simulation
2. Link Cameroon and run again

Gapminder (Full Tool): http://www.gapminder.org/

1. Select Gapminder World
– Change Y-axis indicator: Malaria cases/100,000
– Run simulation
2. Link Cameroon
– Run simulation in steps: 1990-1994, 1994-1996, 1996-2005, 1995-1996
– Interpret
3. Explore other countries, other indicators
– Share what you’ve learned

Resources for Functional Genomics:

Plasmodium Problem Space: http://bit.ly/problemspace

Resources for Functional Genomics