Last updated:
Wednesday, September 29, 2004 15:28
EST huynh@ncbi.nlm.nih.gov
The latest update is available at http://www.bioinfohelpdesk.org/reading/.
A course username/password is required.
Congratulations!!! You have been selected as a course participant in the WHO/TDR sponsored Regional Training Course on Bioinformatics Applied to Tropical Diseases. This is an intensive two week course consisting of both lectures and practicals overviewing many of the basic bioinformatics concepts as they would/could be applied to tropical diseases. We highly suggest you come to the course already pre-reading some of the course materials in the hyperlinks provided below, especially the mandatory pre-course reading assignment. The material will also be provided to you in the course CD after the course. Although many of these concepts will be presented during the course and you will have some time in the evening during the course for some additional offline reading, it is an easier learning experience for you and the instructors, if you have already pre-read as much of the course materials prior to the course as possible. Many of the pre-course readings are "Reviews" from various scientific journals and are of exceptional quality and reading ease.
In general, most of the course participants have a biological science background in infectious disease research with a few rare individuals with a quantitative science background such as computer science or physics. Nevertheless, it is strongly recommended that all students be familiar with basic molecular biology concepts. If you need to review your basic molecular biology knowledge, refer to the NCBI BookShelf for online course books or the MIT OpenCourseWare for online teaching materials. The course will primarily focus on the use of freely available bioinformatics software and operating systems run locally. That is, course participants will for example, look at genome sequence data and analyze it locally on their own local computers. The majority of the course participants have no prior programming experience, however by the end of the course, everyone is expected to be able to write "10" lines of Perl code. In addition, by the end of the course, course participants should be able to setup and maintain a local bioinformatics workstation using an open source operating system and free applications. There are no wet-lab practicals in this bioinformatics course.
See the respective course website for content details and the bioinfohelpdesk.org website.
Note: All resources provided are restricted to resources freely available.
There is ONE mandatory reading assignment:
We strongly encourage all course participants to peruse through the "Recommended Precourse Reading Assignment" section for topics of interest before the course, especially all items with 
. It is strongly recommended that all students be familiar with basic molecular biology concepts. If you need a review of your basic molecular biology knowledge, refer to the NCBI BookShelf or the MIT OpenCourseWare. A good general basic overview of bioinformatics is available on the NCBI: Education website, especially the Science Primer. Both are written with the lay person in mind and assumes the reader has an undergraduate level basic biology education.
Genomics Reviews |
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| Nature Genetics Supplement for Sept 2002 - User's Guide to the Human Genome [Offline] Vol 32, supplement pp1-72 | .
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| World Health Organization: Genomics and World Health: Report of the Advisory Committee on Health Research 2002 | |
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| Mayo Clinic Proceedings: Primer on Medical Genomics: | .
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 Part I:
History of Genetics and Sequencing of the Human Genome |
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Principles and Methods in Molecular Genetics |
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Bioinformatics |
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Genomics and Molecular Genetics in Clinical Practice |
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Evolving Concept of the Gene |
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VIII: Essentials of Medical Genetics for the Practicing Physician |
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IX: Scientific and Clinical Applications of DNA Microarrays- Multiple
Myeloma as a Disease |
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X: Gene Therapy |
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Part XI: Visualizing Human Chromosomes |
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| Part XII: Pharmacogenomics--General Principles With Cancer as a Model |
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| Part XIII: Ethical and Regulatory Issues - May 2004 |
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| Part XIV: Introduction to Systems Biology--A New Approach to Understanding Disease and Treatment - May 2004 |
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| The End of the Beginning - May 2004 |
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| Review: Automation for Genomics, Part One: Preparation for Sequencing | .
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| Review: Automation for Genomics, Part Two: Sequencers, Microarrays, and Future Trends | .
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| Genomics Medicine - A Primer - Guttmacher and Collins N Engl J Med 2002;347(19):1512-1520 | .
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| Science paper - Anopheles gambiae genome project - Freely Available | .
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| Nature paper - Plasmodium falciparum genome project | .
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| The mosquito genome: perspectives and possibilities | .
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| Malaria parasite and vector genomes: partners in crime | .
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| The mosquito genome – a turning point? | .
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| Measuring genome evolution: orthology, synteny, computer analysis, horizontal gene transfer | .
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| Mixed models: getting the best use of parasitological data | .
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| Use of serial analysis of gene expression (SAGE) technology | . |
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| Fulfilling the promise: drug in the post-genomic era | . |
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Database Reviews |
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| Nucleic Acid Database Issue Jan 2004 - Open Access - Freely available | .
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| The Molecular Biology
Database Collection: 2004 update |
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| Database resources of the National Center for Biotechnology Information:
update |
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| UniProt: the Universal Protein knowledgebase |
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| The Pfam protein families database |
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| SMART 4.0: towards genomic data integration |
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| Ensembl 2004 |
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| Nucleic Acid Research Web Server Special Issue - July 2003 - Free Issue | .
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| Nucleic Acid Research Database Issue Jan 2003 - Free Issue (Selected articles) | .
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| The Molecular Biology Database Collection: 2003 update [Compilation
Paper - HTML] [Categories
List - HTML] [Alphabetical
List - HTML] -- Offline |
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| The EMBL Nucleotide Sequence Database: major new developments |
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| GenBank |
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| Database Resources of the National Center for Biotechnology |
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| NCBI Reference Sequence Project: update and current status |
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| Ensembl 2002: accommodating comparative genomics |
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| The European Bioinformatics Institute's data resources |
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| PlasmoDB: the Plasmodium genome resource. A database integrating
experimental and computational data |
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| ToxoDB: accessing the Toxoplasma gondii genome |
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| The InterPro Database, 2003 brings increased coverage and new features
[Supplement] |
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| CDD: a curated Entrez database of conserved domain alignments |
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| MMDB: Entrez's 3D-structure database |
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| The Protein Data Bank and structural genomics |
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| NCBI Handbook [Offline] |
