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

• Short description in English  |  Course notes -- jegyzetek  |  A tárgy leírása  |  Óraterv, ajánlott irodalom
• Notes from previous years (mainly in Hungarian) -- régebbi jegyzetek (nagyrészt magyarul)

1.  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 below nickname "FI" or "water")

2.  Recommended reading

• Learning Perl (O'Reilly book) -- ask me for an electronic copy
• http://perldoc.perl.org
• Watts, Strogatz. Collective dynamics of 'small-world' networks. PDF
• Albert, Jeong, Barabási. Internet: Diameter of the World-Wide Web. PDF
• Barabási, Albert, Jeong. Mean-field theory for scale-free random networks. PDF
• Newman. The Structure and Function of Complex Networks. PDF

3.  Fall 2013

We will start on the week of Sep 9.

4.  Spring 2013

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

Perl code	Perl code we wrote during the classes
Day 1	Perl	Data Types, Subroutines, Patterns	Apr 19 Fri	11-12.30, 1.30-3, 3.15-4.45, 5-6.30
Day 2	Networks	Quantities, Models, Examples	Apr 20 Sat	9-10.30, 11-12.30, 2-3.30, 4-5.30
Day 3	Clustering	Properties, Methods, Examples	Apr 22 Mon	9-10.30, 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

5.  Fall 2012

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

• Homework: Compare clustering coefficient: measured network vs. two models
• Class notes: Discussing previous homework | Generating a Scale-Free network

2012.nov.07

• Homework: Compare largest degrees of a measured and an Erdos-Renyi network
• Class notes: Generate a Small-World graph | Patterns: Parentheses, Precedence

2012.oct.24

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

2012.oct.17

• Homework: Read/Write human protein sequences
• Class notes: References, functions

2012.oct.10

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

2012.oct.3

• Homework: Most frequently used AA sequences in human proteins
• Class notes: For, while, do-while | Hashes: definitions, usage with list operators

2012.sep.26

• Homework: Which are the 10 longest proteins?
• Class notes: List definitions | List operators: pop, push, shift, unshift, map, grep

2012.sep.19

• Homework: How long are the 10 longest human proteins?
• Class notes: Scalar operators | Lists: Definition and the sort command

2012.sep.12

• Homework: GC content of human chromosome 1
• Class notes: Use linux/mac or win+cygwin | Resources | Use Perl from the command line | Why and when to use Perl | Scalars in a nutshell

6.  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

• class notes: networks (ER), bioinf (examples: seq motif search, ODEsys solution & analysis)

Jan 5

• class notes: perl I/O, team work, 2d data structures (HoH, AoA, AoH), networks (basic, motifs, modules)

Jan 4

• class notes: perl: hashes, patterns & usage, references, functions, file I/O

Jan 3

• class notes: resources · why/when to use: perl & networks · perl operators & variables

Top

7.  Fall, 2010

2010.dec.08

• assignment: number of FFL and FBL subgraphs in a network
• class notes: Network motifs. Network models/1: Erdos-Renyi model.

2010.dec.01

• assignment: number of nodes with degree=1 in an Erdős-Rényi graph
• class notes: previous assignment, networks (purpose of modeling, basic quantities)

2010.nov.24

• assignment: Co-authorship network of authors in a selected field of research
• class notes: Regular expressions/3: greedy matching vs. parsimony, parentheses, modifiers. Using regular expressions: match, substitute.

2010.nov.10

• assignment: read the list of yeast protein-protein interactions from IntAct and write this list
• class notes: Regular expressions/2: character classes, quantifiers, greedy matching vs. parsimony.

2010.nov.03

• assignment: find restriction enzyme sites
• class notes: Last assignment with patterns (regular expressions). Reg.exps./1: sequence, alternation, character classes.

2010.oct.20

• assignment: read/write mapping: UniProtKB AC -> UniProtKB primary AC
• class notes: functions, 2d data structures

2010.oct.13

• assignment: read key-value pairs with a subroutine and write them
• class notes: homework from sep/29, functions, passing by reference, examples

2010.sep.29

• assignment: frequencies of 4-base subsequences
• class notes: hashes, keys/values, defined, examples

2010.sep.22

• assignment: transcribe DNA to RNA, count occurrences of CG and CU
• class notes: array operators / 2 (map/grep, sort, join/split, shift/unshift/pop/push)

2010.sep.15

• assignment: count A, C, T, Gs in a file
• class notes: arrays, array operators / 1

2010.sep.08

• assignment: print radius, circumference and area of a circle
• class notes: intro, scalars in a nutshell

2010.sep.07 (preparatory meeting)

• Use Perl from the command line

Top

8.  Spring, 2009

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

• class notes: (1) array of arrays, hash of hashes (2) network models
• project: Google vs. AltaVista hits for a word
• project: analyze parts of a sequence of numbers

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

• assignments:
  • beginner: convert a fixed list of IDs to upper case
  • intermediate: histogram of the sizes of human protein-protein interactions listed by IntAct
• class notes: (1) patterns: precedence, usage; references, subroutines; program: key-2-value replacement (2) network models

2009.apr.15. short

• class notes: discussed homework from apr/01

2009.apr.01.

• assignments:
  • beginner: cellular component of first 10 genes from a GEO file
  • intermediate: UniProt ID mappings
• class notes: patterns (multipliers, parentheses, precedence)

2009.mar.25.

• assignments:
  • beginner: number of data (not comment) lines in a file
  • intermediate: repeated subsequences in DNA
• class notes: patterns (character classes, anchors)

2009.mar.18.

• assignments:
  • beginner: reverse a hash
  • intermediate: nucleotide usage by position in miRNA sequences
• class notes: patterns (sequence, alternation, character classes)

2009.mar.11.

• assignments:
  • beginner: read text, print word usage histogram
  • intermediate: histogram of 2-base units (AA, AT, ...) in a DNA sequence

• class notes: file I/O, hashes

2009.mar.04.

• assignments:
  • beginner: download protein txt info file from Uniprot, print first line
  • intermediate: component size distribution of a graph
• class notes: for-while-do/while, I/O, map-grep-slice

2009.feb.25.

• assignments:
  • beginner: print bases of an RNA sequence in groups of 3
  • intermediate: find the "loop subgraph" of a graph (the smallest subgraph containing all nontrivial loops)
• class notes: pop-push-shift-unshift, split-join, sort

2009.feb.18.

• assignments:
  • beginner: translate a DNA sequence
  • intermediate: for each base: how many times is it used in a DNA sequence?
• class notes: resources, cygwin, scalar operators, decisions, loops (for, do, while)

2009.feb.11.

• assignments:
  • beginner: try ++$a and $a++
  • intermediate: print the sum of integers from 1 to 500
• class notes: admin, resources, mol. bio. background, cygwin, perl intro, scalars

2009.feb.09. (preparatory meeting)

• Install cygwin and/or read Ch.1 of Alberts et.al
• ActivePerl, NotePad++ (thanks for suggesting these)

Top

9.  Fall, 2008

• 2008.dec.09
  • class notes (Lee/Marcotte 2004 - gene association network)
  • final assignments
• 2008.dec.02
  • class notes
• 2008.nov.25
  • assignments
    • Erdos-Renyi network: Highest degrees (beginner)
    • E-R network: Clustering coefficient (intermediate)
  • class notes
• 2008.nov.18
  • assignments
    • Length distribution of W tracts in S.cerevisiae Chr IV (intermediate)
  • class notes
• 2008.nov.4
  • assignments
    • Human DNA: count bases, find rnd sequence, find repeats (beginner)
  • class notes
• 2008.oct.21
  • assignments
    • Number to name substitution, sort miRNA sequences by their seeds (beginner)
  • class notes
• 2008.oct.14
  • assignments
    • Name length, average length of names (beginner)
    • Print lines starting with DR from a UniProt record (intermediate)
  • class notes
• 2008.oct.07
  • assignments: beginner | advanced | project
  • class notes
• 2008.sep.30
  • assignments: beginner | intermediate | advanced
  • class notes
• 2008.sep.23
  • assignments: beginner | intermediate | advanced
  • class notes
• 2008.sep.16
  • assignments: beginner (kezdő) | advanced (haladó)
  • class notes: 10am class | 6pm class
• 2008.sep.09
  • How to use Linux on your Windows computer
    --> Install Cygwin on your Windows computer