Difference between revisions of "Bioinformatics Programming Classes"

From Master Projects
Jump to: navigation, search
Line 48: Line 48:
 
* [[Media:ProgrammingClass5.pdf]]
 
* [[Media:ProgrammingClass5.pdf]]
 
* [[Media:codon_table.txt.zip]]
 
* [[Media:codon_table.txt.zip]]
* Deadline Friday, September 24, please email [mailto:n.bonzanni@vu.nl,a.may@vu.nl Nicola Bonzanni and Ali May]
+
* Deadline Friday, September 26, please email [mailto:n.bonzanni@vu.nl,a.may@vu.nl Nicola Bonzanni and Ali May]
  
  
Line 61: Line 61:
 
* [[Media:ProgrammingClass7.pdf]]
 
* [[Media:ProgrammingClass7.pdf]]
 
* [http://few.vu.nl/~mer500/go.zip go.zip]
 
* [http://few.vu.nl/~mer500/go.zip go.zip]
* Deadline Tuesday, October 8 please email [mailto:n.bonzanni@vu.nl,a.may@vu.nl Nicola Bonzanni and Ali May]
+
* Deadline Tuesday, October 7 please email [mailto:n.bonzanni@vu.nl,a.may@vu.nl Nicola Bonzanni and Ali May]
  
  

Revision as of 13:01, 17 September 2014

Reading

  • Recommended book: Learning Python, Mark Lutz, David Ascher, O'Reilly Media


... after this class ...

If you are thinking of choosing the Bioinformatics profile (even if you're not sure yet) you should already (now) enroll in the course Inleiding programmeren (Python) course ID 401096 via VUnet.


Course Material

Class 1 - intro to linux


Class 2 - python shell: print, operator, types, if exercise: 'calculation' script


Class 3 - lists, for exercise: sum i over n; n!


Class 4 - Functions, scope, namespace, import, while exercise: calculator using functions; interactive calculator with error handling; guessing game


Class 5 - file I/O, dictionaries, string manipulation (e.g., split) exercise: codon table & translation


Class 6 - Regular expressions

* Media:ProgrammingClass6.pdf


Class 7 - Putting everything together exercise: GO parsing


Grading

Only the assignments of Class 5 and Class 7 will be graded (the others you may hand in if you want more detailed feedback). We use the following grading scheme for Class 5 asignment:

Item points comments
Runs 2 does it run without (compilation) errors?
Output 2 produces correct output? is output clear/readable?
Flexibility/parameters 1 are different types of input handled correctly? Are parameters and file names not hard-coded?
Strucure/modularity 1 are functions used? locgical function names? no code before/inbetween function declarations?
Readability 2 logical variable names? Consistent indentation?
Efficient 1 is the implementation logical and efficient?
Extensions 3 about 1 point for each of the possible extensions
Total: 12 (if you do all extensions)

and for Class 7 assignment:

Item points comments
Correctness 3
Efficiency 2
Structure / Readability 2 location of main code, no unnecessary global variables, consistent indentation, useful comments, good function and variable names
Robustness / Error-handling 2 useful error messages, check whether files exist, skipping empty strings, check whether number of arguments is correct
Extension(s) 1
Total 10 (includes extension)

Back to: Fundamentals of Bioinformatics | Introduction to Systems Biology



Back to: Bioinf & Sys Bio Master | Bioinf & Sys Bio Internships | Bioinf & Sys Bio Projects