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http://creativecommons.org/licenses/by-sa/2.0/. Bioinformatics. Prof:Rui Alves [email protected] 973702406 Dept Ciencies Mediques Basiques , 1st Floor , Room 1.08 Website:http :// web.udl.es / usuaris /pg193845/ testsite /

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bioinformatics

Bioinformatics

Prof:Rui Alves

[email protected]

973702406

DeptCiencies Mediques Basiques,

1st Floor, Room 1.08

Website:http://web.udl.es/usuaris/pg193845/testsite/

CourseWebsite: http://web.udl.es/usuaris/pg193845/Courses/Bioinfo_Biotech_2011/

language of the course
Language of the course
  • Mine: English
  • Slides: English
  • Webpage: English
  • Yours: Whichever you choose as long as I understand it. ALWAYS ASK WHEN YOU DON’T UNDERSTAND SOMETHING!!
web page of the course
Web Page of the course

http://web.udl.es/usuaris/pg193845/Bioinfo_Biotech_2011/

  • There, youwillfindalltheinformationaboutyourtasks, links tobioinformaticsresources, and thelecture.
  • Itwillbe up fromtomorrowonwards.
goals of this course
Goals of this course
  • Give you an integrated view of how to use computers and informatics to gain a systemic understanding of biological systems at the molecular level.
  • Integrate bioinformatics, mathematical modelling and other areas of computational biology to save lab work and address problems that can not yet be solved at the lab.
what this course will be
Whatthiscoursewillbe
  • A coursetoteachyouhowtothinkaboutproblem, not a coursetoteachyouhowto use programs.
course plan
Course Plan
  • Firstpart of thecourse (2-3 weeks): Broadintroductiontobioinformatics and computationalbiology in molecular biology.
  • Secondpart of thecourse: Problemsforyoutosolve in group at home, + in-depthlecturesaboutthedifferentsubjectsyouneedtosolvetheproblems.
evaluation plan
Evaluation Plan
  • 5 tasks in groups of four. At the end of each task you deliver a paper as a group. (overall, all tasks will account for 70% of final grade).
  • Final exam (with two sections) where a problem will be posed to each of you and you will have to outline how you would solve it (20%).
  • My discretion (10%).
  • CAUTION: YOU NEED TO HAVE AT LEAST 6 IN EACH TASK, AND IN EACH SECTION OF THE FINAL EXAM.
index
Index
  • Why bioinformatics?
  • Ontologies & Classification schemes
  • Databases and servers
slide10

Why Bioinformatics?OrThings to do when it is raining and you want to have an integrated view about biological systems…

Prof:Rui Alves

[email protected]

973702406

DeptCiencies Mediques Basiques,

1st Floor, Room 1.08

Website:http://web.udl.es/usuaris/pg193845/

CourseWebsite: http://web.udl.es/usuaris/pg193845/Courses/Bioinfo_Biomed_2011/

what obvious problems do large scale sets create
What obvious problems do large scale sets create?
  • Imagine the 6 500 000 000 human beings born within the last 130 years and still alive.
  • By and large a majority of them has had and education.
  • What problems need solving to ensure that education?

1 – Organize Knowledge

2 – Organize its transmission

Knowledge

first problem organizing knowledge
First problem: organizing knowledge
  • We do not need to know all there is to know in order to be productive in society.
  • Furthermore we can not learn everything at the same time.
  • Problem: How to organize knowledge into bite-sized packages that can be consecutively parceled out, and from which one can build upon?
organizing knowledge
Organizing knowledge

Communication

(Read, write, count)

Humanities

Sciences

second problem organizing the transmission of knowledge
Second problem: organizing the transmission of knowledge
  • The school system is a way in which the most people can be trained with the least societal effort

Not effective

school and books are the servers and databases of educating people
School and Books are the servers and databases of educating people

Database

New Server:

You

Server

Users

understanding biological systems
Understanding biological systems

You’re WRONG!!!!!

I need more data!!! How do I plan whatto do now?

Hey, it’sraining!!! Whydon’twe try and figure outhowallthelittle molecular pieces in a cellworktogether?!?!?!

the omics revolution in molecular biology
The “omics” revolution in molecular biology
  • Over many decades, a huge amount of biological data has accumulated.
  • Unlike the “KNOWLEDGE” we discussed before, this data is not well organized and the connections between the different parcels of data are obscure.
  • The omics revolution has compounded this problem 1000 fold because data now accumulates faster than ever.
what is the omics revolution in molecular biology
What is the “omics” revolution in molecular biology?
  • The omics revolution is a period of about ten years in which several different technologies that can be applied to study the complement molecular landscape of cells!!!
    • Genomics
    • Proteomics
    • Metabolomics
    • Et caeteromics
understanding biological systems1
Understanding biological systems

I need more data!!! Whydon’ttheygiveitto me

the omics revolution in molecular biology1
The “omics” revolution in molecular biology
  • (We!!) Biologists want the data to make sense and they (we) want it now!!!
comparison between the two problems
Comparison between the two problems

PeopleorganizedtheKnowledgetransmissionsystem and itsconnectionsovermilenia of trial and error.

Itisimpossibleforpeopletoorganizethebiologicalknowledgebroughtaboutbyomics in the20 yearsthathavepassedsincethebeginning of theomics era.

slide22
Why?
  • Data is not well classified.
  • Data is not well connected.
  • Data is not well understood.
  • Not enough people to do it in a short amount of time.
new types of servers and databases are required for very fast organization and data mining
New types of servers and databases are required for very fast organization and data mining

Database

Server

Users

BIOINFORMATICS!!

what is bioinformatics
What is Bioinformatics?
  • Development and application of computational/informatic tools to the solution of biological problems
  • The Standard of internet Bioinformatics:

LAM P

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X

P

A

C

H

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Q

L

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P

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T

H

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Operating system

Programing

language(s)

Internet server

Database server

the standards are changing
The standards are changing
  • JAVA facilitates that the servers launch a smaller number of processes by using the client’s machines for calculus and allowing for a larger number of simultaneous connections.
  • TOMCAT “talks” very well with JAVA.

LTM J

A

V

A

I

N

U

X

O

M

C

A

T

Y

S

Q

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Operating system

Programing

language(s)

Internet server

Database server

what does a computer need to be effective
What does a computer need to be effective?
  • Well classified data
    • Ontologies, Classification schemes
  • Well organized data
    • Databases, servers
  • Good users
index1
Index
  • Why bioinformatics?
  • Ontologies & Classification schemes
  • Databases and servers
ontologies and classification schemes for data

Ontologies and classification schemes for data

Prof:Rui Alves

[email protected]

973702406

Dept Ciencies Mediques Basiques,

1st Floor, Room 1.08

Website:http://web.udl.es/usuaris/pg193845/testsite/

biological classification schemes
Biological Classification Schemes
  • What is an Ontology (in the Biological sense)?

A set of definitions of controlled vocabularies with hierarchical relationships to one another, that can easily be dealt with by computers

what are bio ontologies
What are Bio-Ontologies?

Biological Ontologies (Bio-ontologies) can be defined as a complex hierarchical structure in which biological concepts are described by their meanings (definitions) and relationships to each other.

There are many Bio-Ontologies available and in use by databases. The Plant Ontology, along with other ontologies such as the Gene Ontology, are included in the open source Open Biological Ontologies project at Sourceforge.

http://obofoundry.org/

the gene ontology
The Gene Ontology

The most well-known example of a bio-ontology is the Gene Ontology (GO; http://www.geneontology.org) which describes three biological domains: cellular component (where the gene product locates), molecular function (what the gene product does) and biological process (the cellular, developmental or physiological events the gene product is involved in).

GO are used to describe gene products. Because these descriptions are independent of species-specific nomenclature and uniformly applied, it is possible to make meaningful and efficient comparisons of genes across diverse taxa.

three super categories of go
Three “Super Categories of GO
  • Molecular Function (what)
    • Tasks performed at the molecular level
  • Biological Process (why)
    • How it pertains to the organism
  • Cellular Component (where)
    • Its location
example
Example
  • Gene Name: BRCA1
  • Molecular Function: protein binding
  • Biological Process: DNA Replication and Chromosome Cycle
  • Cellular Component: nucleus
structure of go
Structure of GO
  • How to define the relationship between concepts?
  • Example: How to relate the terms: “cell” “nucleus” “membrane”
how is go annotated
How is GO Annotated?
  • Manual
    • Humans sifting through primary literature
  • Electronic
    • Assign GO Terms using already existing information in databases.
evidence code for go annotation
Evidence Code for GO Annotation

IEA Inferred from Electronic Annotation

ISS Inferred from Sequence Similarity

IEP Inferred from Expression Pattern

IMP Inferred from Mutant Phenotype

IGI Inferred from Genetic Interaction

IPI Inferred from Physical Interaction

IDA Inferred from Direct Assay

RCA Inferred from Reviewed Computational Analysis

TAS Traceable Author Statement

NAS Non-traceable Author Statement

IC Inferred by Curator

ND No biological Data available

Detailed info available from: http://www.geneontology.org/doc/GO.evidence.html

how to use go in data analysis
How to use GO in data analysis
  • Simple Queries
  • Find over-represented GO categories in a list of genes
    • Search Biological “Themes”
  • Binning
    • Obtain a broad view of the distribution of major GO terms in a list of genes.
  • Clustering Genes on GO terms
    • Group together functionally related genes based on GO terms.
go tools
GO Tools
  • NetFlix – Get GO Annotation
  • AmiGO – Browser and Simple Queries
  • GoTermMapper – Binning(Go Slim)
  • GeneToolBox –
    • Finding over-represented GO categories
    • Clustering based on similar GO terms
    • Query for Gene with Similar Function.
go is not very good
GO is not very good
  • EC numbers
  • Protein classification schemes
  • TF classification schemes
  • Transport proteins classification schemes
  • Etc.
the transport proteins classification database
The transport proteins classification database

All these classifications are reminiscente of the Dewey classification system for books!!!! (Remember public libraries?)

how close are we to have good comprehensive universally used classifications
How close are we to have good, comprehensive & universally used classifications?
  • Far!!!!!
  • BMC Bioinformatics + Bioinformatics publish papers with proposals for new ontologies and classifications almost every month in one are or another of molecular biology.
  • Wet lab molecular biologists still not won to the cause of single name for single entity…
  • There is hope! The situation is much better than 5 years ago!!!
what does a computer need to be effective1
What does a computer need to be effective?
  • Well classified data
    • Ontologies, Classification schemes
  • Well organized data
    • Databases, servers
index2
Index
  • Why bioinformatics?
  • Ontologies & Classification schemes
  • Databases and servers
databases servers

Databases & Servers

Prof:Rui Alves

[email protected]

973702406

Dept Ciencies Mediques Basiques,

1st Floor, Room 1.08

Website:http://web.udl.es/usuaris/pg193845/testsite/

what is a database
What is a Database?
  • A database is a collection of data organized in such a way that it is easy to store in a computer and to mine by appropriate software
  • A database is usually organized as a set of tables in which information about an object is stored
  • The tables are related to each other in different ways.
what does database technology allow
What does database technology allow?
  • Making information useful
  • Avoiding "accidental disorganisation”
  • Making information easily accessible and integrated with the rest of our work
s tructured q uery l anguange
S(tructured)Q(uery)L(anguange)
  • ANSI (American National Standards Institute) standard computer language for accessing and manipulating database systems.
  • SQL statements are used to retrieve and update data in a database.
  • Includes:
    • Data Manipulation Language (DML)
    • Data Definition Language (DDL)
web databases
Web Databases
  • Data is accessible through Internet
  • Have different underlying database models
  • Example: biological databases
    • Molecular data: NCBI, Swissprot, PDB, KEGG, GO
    • Protein interaction : DIP , BIND
    • Organism specific: Mouse , Worm, Yeast
    • Literature: Pubmed
    • Disease: OMIM
how to make databases useful
How to make databases useful
  • Attach it to a server
  • Let people use to mine for knowledge
an example of wamp
An example of WAMP
  • A simple bioinformatics class server
an example of wamp1
An example of WAMP
  • A simple bioinformatics class server
an example of wamp2
An example of WAMP
  • A simple bioinformatics class server
an example of wamp3
An example of WAMP
  • A simple bioinformatics class server

Wireless

an example of wamp4
An example of WAMP
  • The bioinformatics class server

Wireless

how close are we to have good comprehensive universally used data repositories
How close are we to have good, comprehensive & universally used data repositories?
  • Not far at all!!!!!
  • NCBI, KEGG, Protein databank, SGD, Uniprot,….
  • Problems:
    • Redundant data over many databases…
    • Conflicting information due to the use of different data sources, standards, and classifications
a glimpse at a useful present
A glimpse at a useful present

Relationaltools

Online analyticalprocessingtools

Data

warehouse

Applications

Data Sources

the future
The future
  • Cloud computing
  • Distributed computation
  • Artificial inteligence methods to facilitate data search, analysis and mining
summary
Summary
  • Why bioinformatics:
    • Because there is simply too much data out there for human being to deal with without computer assistance.
    • Because many of the calculations to extract knowledge from the data would take too long without computers.
  • How to do bioinformatics:
    • Organize data well using appropriate classification systems.
    • Use databases and server technology.
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