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Bioinformatics

• Vakcode BW02K
• Admin. code FDBA
• Studielast 12 ( EC)
• Ingangseis Deze cursus is alleen toegankelijk voor 3e jaars studenten.
• Periode(n) Semester 2 ( blok 4 1-2-2010 t/m 26-3-2010)
• Onderwijsinstituut College of Science domein Levens- en Aardwetenschappen
• Verzorgd door Swammerdam Instituut voor Levenswetenschappen (SILS)
• Docent(en) dr. ir. H.C.J. Hoefsloot (coördinator), prof. dr. A.H.C. van Kampen, drs. J. Rauwerda en dr. G. Zwanenburg
• Inlichtingen dr. ir. H.C.J. Hoefsloot
• Nieuwe Achtergracht 166 kamer C.707
• +31 20 5255867
• Onderdeel van
  • Bachelor Bio-medische wetenschappen
  • Bachelor Biologie

• See also Studiegids

Book: Introduction to computational genomics, a case study approach, Nello Cristianini and Matthew W. Hahn, ISBN 0 521 67191-4 (Cambridge University Press).

Course material

Here you find all material related to the topics presented by prof. dr. A.H.C. van Kampen (Antoine)

Topics:

• Chapter 5 (pptx). Are Neanderthals among us? Variation within and between species.
• Chapter 6 (pptx). Fighting the Human Immunodeficiency Virus (HIV)Natural selection at the molecular level.
  • Background information: History of HIV by David Hall, 2006.
• Chapter 7 (pptx). Severe Acute Respiratory Syndrome (SARS). A post-genomic epidemic. Phylogenetic analysis.
  • Background information: Four point condition (additive distances; pdf) by L. Ridgway Scott.
• Scores (ppt). The basics of score matrices and their statistical evaluation.
  • Exercises Score Matrices (doc)
  • Teacher Notes Exercies (doc)
  • Exercise.xls
  • Exercise+Answers.xls
  • PAM_Exercise.xls
  • PAM_Exercise+Answers.xls
  • Generation of PAM matrices

Mini project

In this part of the module you will learn to use bioinformatics methods and databases to address a biological problem. You will:

• Perform a full literature research
• Perform a simple programming exercise
• Write a report

Please, carefully read the instructions:

• Instructions mini project

Papers and links transcriptome maps:

• miniproject_transcriptomemap.zip

Login to computer server of the Bioinformatics Laboratory

For some of the mini projects you need access to the computer server of the Bioinformatics Laboratory. To get access you need to install Putty and Xming. The instructions are given below.

• Binary for PuTTY can be found at: http://www.chiark.greenend.org.uk/~sgtatham/putty/
• In order to display Linux X11 output on a Windows machine, you can use Xming

Configuration PuTTY

Session:

• Host = amc-app1.amc.sara.nl
• Port = 22
• Protocol = SSH

Connection

• Sending of null packets to keep session active: 3600

Connection → SSH → Tunnels:

• Enable X11 forwarding = on
• X display location = localhost:0

Session:

• → Save

Start the connection

Just startup Xming and PuTTY. Xming is used as X-server. When PuTTY is started you'll get a terminal where you can enter your username and password.

Contact

Antoine van Kampen (a.h.vankampen@amc.uva.nl / 020-5667096 / 06-41768067)