intro to bioinformatics by HC120213083330


									Virtual Bioinformatics

    Martti Tolvanen & Bairong Shen

    University of Tampere
What is bioinformatics?
   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
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.)
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)
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
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-
   take care of payment details as instructed
   you will get the course ID and password on
    the date you requested
Introduction to Bioinformatics
 Course overview

        University of Tampere
Main goals
   introduction to biological databases
       good knowledge of major databases
       an overview of the large variety of minor
   learning to use tools at major database
       GenBank/NCBI, UniProt/SwissProt, PDB
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
Main goals (2)
   introduction to sequence searching and
    sequence alignments
       the tools with most practical "everyday"
       the course teaches you some theoretical
        background and things to beware to make
        you a confident user of these programs
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
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)
Final project
   a series of analyses on one protein
       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
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

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