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Welcome to the Bioinformatics.org.za wiki

This wiki hopefully provides an online forum for Bioinformatics in South Africa. The idea is that everyone who has an interest, whether a student or practitioner, or anyone with a need for bioinformatics will use this site to give and take according to ability.

This is an initiative of Cape Biotech and has been set up and initial text supplied by Inus Scheepers. The site is currently hosted at Hetzner in Johannesburg, South Africa.

Nomenclature

The terms bioinformatics and computational biology are often used interchangeably. However bioinformatics more properly refers to the creation and advancement of algorithms, computational and statistical techniques, and theory to solve formal and practical problems arising from the management and analysis of biological data. The term bioinformatics was coined by Paulien Hogeweg in 1979. [1]

Computational biology, on the other hand, refers to hypothesis-driven investigation of a specific biological problem using computers, carried out with experimental or simulated data, with the primary goal of discovery and the advancement of biological knowledge.

Put more simply, bioinformatics is concerned with the information while computational biology is concerned with the hypotheses.

A similar distinction is made by National Institutes of Health in their working definitions of Bioinformatics and Computational Biology, where it is further emphasized that there is a tight coupling of developments and knowledge between the more hypothesis-driven research in computational biology and technique-driven research in bioinformatics. Bioinformatics is also often specified as an applied subfield of the more general discipline of Biomedical informatics.

Definitions

The NIH Biomedical Information Science and Technology Initiative Consortium agreed on the following definitions of bioinformatics and computational biology recognizing that no definition could completely eliminate overlap with other activities or preclude variations in interpretation by different individuals and organizations.

Bioinformatics

Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data.

Computational Biology

The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems.

Genomics

Genomics is the term established by Fred Sanger when he first sequenced the complete genomes of a virus and a mitochondrion. His group established techniques of sequencing, genome mapping, data storage, and bioinformatics analyses in the 1970-1980s.

A major branch of genomics is still concerned with sequencing the genomes of various organisms, but the knowledge of full genomes has created the possibility for the field of functional genomics, mainly concerned with patterns of gene expression during various conditions.

The most important tools here are microarrays and bioinformatics.

Functional genomics

Functional genomics includes function-related aspects of the genome itself such as

  • mutation and polymorphism (such as SNP) analysis,
  • measurement of molecular activities.

The latter comprise a number of "-omics" such as

  • transcriptomics (gene expression),
  • proteomics (protein expression),
    • phosphoproteomics (a subset of proteomics) and
  • metabolomics.

Together these measurement modalities quantifies the various biological processes and powers the understanding of gene and protein functions and interactions.

Functional genomics uses mostly high-throughput techniques to characterize the abundance gene products such as mRNA and proteins. Some typical technology platforms are:

  • DNA microarrays and SAGE for mRNA
  • two-dimensional gel electrophoresis and mass spectrometry for protein

Because of the large quantity of data produced by these techniques and the desire to find biologically meaningful patterns, bioinformatics is crucial to this type of analysis. Examples of techniques in this class are

  • data clustering or
  • principal component analysis for unsupervised machine learning (class detection) as well as
  • artificial neural networks or
  • support vector machines for supervised machine learning (class prediction, classification).


Molecular biology

is the study of biology at a molecular level. The field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis and learning how these interactions are regulated.

Where can I study Bioinformatics?

SA Universities

Abroad

  • Canada: CIHR/MSFHR : A bioinformatics training program that operates as a scholarship program

for a select number of students who are undertaking a Bioinformatics M.Sc. or Ph.D. degree at either the University of British Columbia or Simon Fraser University [2]

Cape Biotech Short Courses

Cape Biotech offers intensive Short Courses for postgraduate students and biotech professionals that need to acquire bioinformatics skills for their projects. The first course for 2009 was held at Stellenbosch from February to March, and more than 20 people from all over the country attended. The 2010 Introduction to Bioinformatics Course will be held at the CHPC from 15 Feb 2010 to 1 April 2010.

Specialty Courses for Biotech professionals

if enough persons are interested, courses can be arranged to meet this demand. Contact mailto:tim.newman@capebiotech.co.za with your requests.

Bioinformatics Research

IIDMM -- The Institute of Infectious Disease and Molecular Medicine at the University of Cape Town: http://www.iidmm.uct.ac.za/

Funding Opportunities for Bioinformatics Students

Sponsorships are available for South African students to attend internship programs in Bioinformatics.


Anyone interested should contact Dr Timothy K. Newman mailto:tim.newman@capebiotech.co.za.


Specific information on past internships are available below:

  • See http://www.stats.ox.ac.uk/research/genome/projects for projects and reports to give students a feel for what is done. A student can propose an interesting project if they have something in particular they'd like to work on. The student may also join other Summer students as part of a bigger project.
  • Dr Quin Wills, together with a colleague, is working on best practice trends in genetical genomics (eQTLs). Genetical genomic approaches are still fairly ad hoc, and they believe that a review on where the successes are, and how genetical genomics should be done, is timely. The student will be reviewing literature, testing methods etc. This will probably need to be a more mature student who can hit the ground running as a co-author on the paper.


Government Support for Biotechnology

Details of government policy and support is in Government Support for Biotechnology

Bioinformatics Institutes

SANBI: The South African National Bioinformatics Institute

SANBI is located at the University of the Western Cape: http://www.sanbi.ac.za/

International Centre for Genetic Engineering and Biotechnology (ICGEB)

Located in Cape Town, this was launched by the president on 10 September 2007. Among other benefits, hosting the multimillion rand ICGEB component provides the country's researchers with access to a world class research laboratory in order to conduct health related research, as well as participation in projects that are aimed at the sustainable application of biotechnology in agriculture. http://www.icgeb.org/home-ct.html

Which South African companies use or provide bioinformatics services?

On-Line University Resources for Bioinformatics


Bioinformatics Resources List

Tools and Databases

Open-source Software Resources

Online Workbench Sites

Online Courses

NCBI Mini-courses

http://www.ncbi.nlm.nih.gov/Class/minicourses/#bioinformatics : Twelve on-line mini-courses ranging from introductory to the use of NCBI Entrez and Blast resources

Bioinformatics Journals

Bioinformatics Societies

  • ASBCB: African Society for Bioinformatics and Computational Biology http://asbcb.org/

Bioinformatics Conferences

  • Joint ISCB Africa & ASBCB Conference on Bioinformatics of African Pathogens, Hosts and Vectors (November 30 - December 2, 2009)

For more information visit: http://www.iscb.org/iscb-africa

Freely Available Software for Bioinformatics

See the Software page.

Websites related to Bioinformatics and Biotechnology

South Africa

International


Genome Projects

Bioinformatics Resources

Funding Organisations

  • Industrial Development Corporation:
    • Special Programme for industrial Innovation (SPII) http://www.spii.co.za/
      • Matching schemes: Grant up to 75% of up to R1.5M
      • Partnership scheme: >R1.5M repayable through royalties
      • Product process scheme: Grant < R500k
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