+ indep. WoS citations


Perl programming and Networks
Perl programozás és hálózatok

1.  About the course

  • 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 solution is always listed as the last)

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

2.  Fall 2014

Észak 6.100, Wed 4pm

2014.11.12, 4pm-5.30

2014.11.05, 4pm-5.30, 5.50-7.20

2014.10.22, 4pm-5.30, 5.50-7.20

2014.10.15, 4pm-5.30, 5.50-7.20

2014.09.24, 4pm-5.30

2014.09.17, 4pm-5.30

2014.09.10, 4pm-5.30

2014.09.05

3.  May 23-24-26, 2014 (short course, Debrecen)

Organized by Ferenc Kun at the University of Debrecen

To see the Perl code we wrote during the classes --> Click on the titles of the days

Day 1Perl + ApplicationsData Types, SubroutinesMay 23 Fri10 am - 6 pm with breaks
Day 2Perl + ApplicationsPatterns, ExamplesMay 24 Sat10:15 am - 5:30 pm
Day 3Networks + ApplicationsTheory, Network modelsMay 26 Mon10 am - 5 pm

How to prepare for the course

4.  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

5.  Apr 19-20-22, 2013 (short course, Szeged)

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

6.  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

7.  Jan 3-9, 2012 (short course, ELTE)

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

8.  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

9.  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

10.  Fall 2008