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
- Introduction to EMBL & EBI (pdf — LARGE 55MB)
- ArrayExpress and Expression Atlas (pptx — long 7MB)
- ArrayExpress and Expression Atlas (pptx — short 5MB)
- Practical Use of ArrayExpress (docx)
- Practical Use of ArrayExpress (pdf)
- Array Express Quiz (pdf)
- Array Express Quiz solution (pdf)
Resources for Protein Structure
- Protein Structure Interactive Review Using King
- Proteopedia – http://www.proteopedia.org
- Conserf Server – http://consurftest.tau.ac.il/
- Ensembl Tutorial (pdf — 13MB)
- Ensembl Tutorial Answers (pdf)
- UniProt & InterPro (pptx — 3.5MB)
- IntAct Reactome (ppt — 3.5MB)
- Proteomics Exercise (doc — 3.5MB)
- Proteomics Exercise (pdf)