1. Institute of Biomedical Sciences (ICB) Malaria Nucleus Institute of Mathematics and Statistics (IME) BIOINFO-USP Nucleus Latin American Course on Bioinformatics for Tropical Disease Research. University of São Paulo, Brazil Feb 18th – March 2nd - 2002

2. Latin American Course on Bioinformatics for Tropical Disease Research. University of São Paulo, Brazil Workshop Computer Room

3. DB lab (IME) Conference Room (ICB) Latin American Course on Bioinformatics for Tropical Disease Research. University of São Paulo, Brazil

4. Philosophy

5. Join elements of different natures Tropical Diseases + Molecular Biology + Quantitative Techniques Biological Sciences + Mathematical Sciences

6. Organizers w Biological Sciences: 3 (Hernando del Portillo, Arthur Gruber, Bianca Zingales) w Mathematical Sciences: 2 (Alan Durham, Junior Barrera)

7. Students w 10 Biological Sciences (i.e., doctors, biochemists, molecular biologists, etc.) w 5 Mathematical Sciences (i.e., physicians, computer scientists, engineers, statisticians, etc.)

8. Instructors and Invited Speakers w 17 Biological Sciences (i.e., doctors, biochemists, molecular biologists, etc.) w 11 Mathematical Sciences (i.e., physicians, computer scientists, engineers, statisticians, etc.)

9. BIOINFORMATCS Theory + Practice

10. Module 1: Perl + Unix + DB Alan Durham

11. Staff w Alan Durham (perl) w Marco Dimas Gubitoso (Linux) w Joao Eduardo Ferreria (Databases) Marcio,Luciano (DB Workshop)

12. Issues addressed w most biologists have experience using the Microsoft environment but not an Unix one w there are many similarities between Unix (Linux) shell and DOS command line w perl tutorials implicitly assume previous programming knowledge w databases are essencial for handling lots of data but very hard to design w time limitation

13. Considerations w since it is not viable to teach to program we need to convey a basic understanding of the programming activity w it is not possible to teach database design, but we can make students understand database structure w teaching linux should concentrate on similarities with DOS and tools

14. Module objectives w Unix: teach set of Linux command that can enhace researcher productivity teach use of command line for calling programs give basics of emacs w Perl teach basic perl commands teach use of perl for elementary scripts enable student to develop 5-10 line programs give basis for futher studies using tutorials w DataBases understand need of DataBases teach basic understanding of DB structure enable students to make small SQL queries

15. Teaching approach w Style class/workshop: students repeated instructors demonstrations and extra exercises instructors + floaters w Timings: Unix: 4,5 hours Perl: 9,5 hours Databases: 5 hours

16. Quick Analysis w about 40% of students were in the projected profile (except in Databases) w approach proved effective w floaters proved to be essencial w but.... w ideal timing should be increased to 8+ mornings Unix 7 +hours (2 mornings) Perl 14+ hours (4 mornings) Databases 7+ hours (2 mornings) w timeframe (2 weeks) restricts results

17. Building a Bioinformatics Linux Station Alan Durham

18. Staff w Alan Durham w Chuong Huynh

19. Considerations w students are subject to great amount of information in 2 weeks w very little time to think on subject in a global perspective w the notion of what should be used in internet and what should be kept local is important w most people will need eventually to install some software

20. Module objectives w to give students an understanding of how to set up an environment for their research w to think on bioinformatics on thecontext of their own research w understand the advantages and dificulties they will face when going back home w to foster interaction between the students in general and of students of differente backgrounds in particular

21. Teaching approach w Style students separated by interest in particular TDR organisms groups of 3 people, one with more informatics background each group asked to design an Internet page for research in a chosen topic in their organism w Timing: 6 hours (2 hour sessions)

22. Quick Analysis w pages: some groups distracted by the internet page issue w small time available w project need more previous discussion session

23. Analysis Tools Arthur Gruber Latin American Course on Bioinformatics for Tropical Disease Research São Paulo – February 17 th to March 1 st 2002 Faculty of Veterinary Medicine and Zootechny University of São Paulo BRAZIL AG-FMVZ-USP

24. Teaching Strategy w Theoretical introductory lectures - fundamentals of the the different tools available for sequence analysis w Workshops - practical session witth real-life problems w Topics order – lectures and workshops followed the same order that is usually employed for sequence analysis AG-FMVZ-USP

25. Teaching Strategy AG-FMVZ-USP DNA assembly and finishing Similarity searching/ databases Multiple sequence alignment Phylogenetic reconstruction Annotation Gene prediction Genome Comparison

26. w DNA assembly and finishing - Arthur Gruber Phred/Phrap/Consed package, Staden Package, CAP3 w Workshop - Arthur Gruber and Jessica Kissinger Tutorial on Phred/Phrap/Consed using demo files, cosmids and viral genomes AG-FMVZ-USP

27. w Fundamentals of sequence analysis - Cathal Seoighe Fasta, Blast w Workshop - Cathal Seoighe and Jessica Kissinger Tutorial on similarity searching tools: Search33 (Smith-Waterman algorithm, Fasta and Blast Tutorial on PlasmoDB AG-FMVZ-USP

28. w Multiple Sequence Alignment - Cathal Seoighe Fundamentals of sequence alignment, ClustalX w Workshop - Cathal Seoighe Tutorial on ClustalX AG-FMVZ-USP

29. w Phylogenetic Reconstruction - Cathal Seoighe Parsimony, Maximum likelihood, etc. w Workshop - Cathal Seoighe Tutorial on Phylogenetic Reconstruction using ClustalX/Phylip AG-FMVZ-USP

30. w Artemis and gene prediction software - Neil Hall Genome annotation, public databases, Pfam, Artemis w Workshop - Neil Hall Tutorial on Artemis I AG-FMVZ-USP

31. w Gene Finding - Neil Hall Gene finding, protein domains, annotation pipeline w Workshop - Neil Hall Tutorial on Artemis II AG-FMVZ-USP

32. w Comparative Genomics - Neil Hall Artemis Comparison Tool w Workshop - Neil Hall Tutorial on Artemis Comparison Tool AG-FMVZ-USP

33. Tropical Disease Scientists 10. Computer Scientists 5.

38. TDR/USP Bioinformatics Course Group Picture