+ indep. WoS citations


University of Debrecen -- May 23-24-26, 2014
Perl programming and Networks in Physics and Biology

Day 1PerlData Types, Subroutines, PatternsMay 23 Fri10-11.30, 12.30-2, 2.15-3.45, 4-5.30
Day 2NetworksQuantities, Models, ExamplesMay 24 Sat9-10.30, 11-12.30, 2-3.30, 4-5.30
Day 3ApplicationsNumerical simulations, Clustering,
Sequence analysis
May 26 Mon9-10.30, 11-12.30, 1.30-3, 3.30-5
Perl codePerl code written during the classes

How to prepare for the course



Perl programming and Networks in Computational Biology
Perl programozás és hálózatok a bioinformatikában

Evaluation, Questions

  • Grades: 50% Based on weekly assignments, 50% Exam or project.
  • If there's anything that is not clear, please tell me, thanks
  • Click on the assignments to see the problems + solutions (suggested: see nickname "FI" or "water")

Recommended reading

  • Albert, Jeong, Barabási. Internet: Diameter of the World-Wide Web. PDF
  • Newman. The Structure and Function of Complex Networks. PDF

1.  Fall, 2013

2013.12.04

2013.11.27

2013.11.13

2013.10.16

2013.10.09

2013.10.02

2013.09.25

2013.09.18

2013.09.13

2013.09.11

2013.09.06, Preparatory meeting

2.  Apr 19-22, 2013

Course for the Papp lab at the Biological Research Center (Szeged) and students from the University of Szeged

Perl codePerl code we wrote during the classes
Day 1PerlData Types, Subroutines, PatternsApr 19 Fri11-12.30, 1.30-3, 3.15-4.45, 5-6.30
Day 2NetworksQuantities, Models, ExamplesApr 20 Sat9-10.30, 11-12.30, 2-3.30, 4-5.30
Day 3ClusteringProperties, Methods, ExamplesApr 22 Mon9-10.30, 11-12.30, 1.30-3, 3.30-5

Reading
D'haeseleer. How does gene expression clustering work? PDF
"Computational Biology Primer" articles in Nature Biotechnology and PLoS Computational Biology

Preparatory steps for beginners
feb.22: Read these sections of the book "Learning Perl" and **ask**
feb.08: How many lines of a given sequence file contain N
jan.22: Use linux or install CygWin/MinGW on your Win computer and start the "hello world" program

3.  Fall 2012

ideas

  • have a look at the pattern match program again
  • compute the Z score of a value using randomization

2013.jan.03 (1pm-6pm)

  • Class notes: The goal(s) of modeling | Network properties | Network models: ER, SW, SF | Network motifs | Data clustering | Perl data structures

2012.nov.14

2012.nov.07

2012.oct.24

  • Homework: Compare largest node degree
  • Class notes: Previous homework | Generate an Erdos-Renyi graph | Patterns: Character classes, Counters

2012.oct.17

2012.oct.10

  • Homework: Replace keys
  • Class notes: Usage of hashes and arrays | File I/O

2012.oct.3

2012.sep.26

2012.sep.19

2012.sep.12

4.  Jan 3-9, 2012

Jan 9

  • class notes: discussion of final projects
  • final projects:
    • ODE system solution with multiple parameter sets
    • data processing, many 7z input files
    • SQL read/write

Jan 6

Jan 5

Jan 4

Jan 3

Top

5.  Fall, 2010

2010.dec.08

2010.dec.01

2010.nov.24

2010.nov.10

2010.nov.03

2010.oct.20

2010.oct.13

2010.sep.29

2010.sep.22

2010.sep.15

2010.sep.08

2010.sep.07 (preparatory meeting)

Top

6.  Spring, 2009

2009.apr.29. 08:30-11:45

2009.apr.22. 08:30-11:45

2009.apr.15. short

  • class notes: discussed homework from apr/01

2009.apr.01.

2009.mar.25.

2009.mar.18.

2009.mar.11.

2009.mar.04.

2009.feb.25.

2009.feb.18.

2009.feb.11.

2009.feb.09. (preparatory meeting)

Top

7.  Fall, 2008