Virtual Bioinformatics

1. Martti Tolvanen & Bairong Shen University of Tampere Virtual Bioinformatics

2. Methods to analyse, store, search, retrieve and represent biological data by computers /in computers massive amounts of data: databases extracting information and knowledge from "raw" data for most bioscientists, all they need in bioinformatics = sequence analysis What is bioinformatics?

4. Bioinformatics applications • comparison and analysis of nucleotide and protein sequences • comparison and analysis of molecular structures (especially proteins) • results of comparisons can be used in evolutionary and phylogenetic studies • data mining of genomic data (large-scale gene expression results etc.)

5. Bioinformatics virtual learning • web courses at U of Tampere • from anywhere, (almost) any time • Introduction to Bioinformatics (3 cp) • Bioinformatics in Functional Genomics (4 cp) • http://bioinf.uta.fi/courses/

6. Web tutoring • we have several bioinformatics researchers acting as tutors in our virtual courses • each student will have one tutor as their main instructor • you can interact with your tutor using various tools inside in the course, by e-mail, and by MSN Messenger chat

7. Starting the web courses • fill in the application, click a first confirmation • you receive a confirmation request by e-mail to verify your e-mail address • visit the confirmation link (web address in e-mail) • take care of payment details as instructed • you will get the course ID and password on the date you requested

8. Course overview University of Tampere Introduction to Bioinformatics

9. Main goals • introduction to biological databases • good knowledge of major databases • an overview of the large variety of minor databases • learning to use tools at major database sites • GenBank/NCBI, UniProt/SwissProt, PDB

10. Bioinformatics databases • nucleotide and protein sequences • protein structures • all sorts of functional data related to genes, proteins and their regulation, interactions etc. • curated and non-curated databases

11. Main goals (2) • introduction to sequence searching and sequence alignments • the tools with most practical "everyday" usability • the course teaches you some theoretical background and things to beware to make you a confident user of these programs

12. Minor goals • looking at properties that can be analyzed/predicted from sequence data • overview, not profound learning • protein structures and their analysis • structural classification • visualisation of macromolecules

13. How the course works • you have 8 weeks of time, starting from the date of your choice • small assignments inside the course material while you read • study at your own pace, ask questions if needed - approx. one week of full time • final project, to put your newly learned skills into real use (a few days to one week of full-time work)

14. Final project • a series of analyses on one protein sequence • can be your favourite protein, or one of our choice • includes homologue searching, multiple alignment and some other basic tasks • you can make a suggestion to have specific analyses of your own interest to be included in your project

15. Course certificate • at the end of your course, when your project has been approved, you will receive a printed and signed certificate • to transfer it to formal credits in your home institute, you need to follow the procedures of registering any course modules which originate from outside your school • this does not apply to our degree students or those of Helsinki biochemistry, who get a direct registration