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http://creativecommons.org/licenses/by-sa/2.0/


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


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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.


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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:

LAMP

E

R

L

I

N

U

X

P

A

C

H

E

Y

S

Q

L

H

P

Y

T

H

O

N

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.

LTMJ

A

V

A

I

N

U

X

O

M

C

A

T

Y

S

Q

L

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

IEAInferred from Electronic Annotation

ISSInferred from Sequence Similarity

IEPInferred from Expression Pattern

IMPInferred from Mutant Phenotype

IGIInferred from Genetic Interaction

IPIInferred from Physical Interaction

IDAInferred from Direct Assay

RCAInferred from Reviewed Computational Analysis

TASTraceable Author Statement

NASNon-traceable Author Statement

ICInferred by Curator

NDNo 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 ec number database

The EC number database


The brenda database

The BRENDA database


The tf classification database

The TF classification database


The signal transduction classification database

The signal transduction classification database


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?)


A general protein classification database

A general protein classification database


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


A glimpse of a useful present

A glimpse of a useful present


A glimpse of possible futures

A glimpse of possible futures


A glimpse of possible futures1

A glimpse of possible futures


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.


A glimpse at a useful present1

A glimpse at a useful present


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