lang: ITA ENG
 

 
 

AA 2016/2017

Teachers: Alessio Bechini (instructor)

CFU: 6

Code: 688II

Code module 6 CFU in Software Tools for Medicine: 259II
Code for laurea specialistica (6 CFU): II416


COURSE DESCRIPTION
tag cloud of common Bioinformatics terms  

Bioinformatics is an interdisciplinary field where both conceptual and actual tools typical of Computer Science are used to tackle a wide variety of issues in Molecular Biology. In particular, Bioinformatics adopts computational approaches in the management and analysis of biological data.

This class provides an introduction to some topics in Bioinformatics, emphasizing concepts and tools to master the inherent complexity of the target systems. An operative approach is pursued: in problem solving, a combined employment of multiple software applications and a scripting language is proposed. The first part of the class is thus devoted to a thorough teaching of the Python language. Discussed topics include sequence analysis, mutation investigation and molecular evolution, interaction with data banks, molecular modeling, protein structural characterization, and molecular dynamics. Whenever needed, notions of Computers Science and Maths are introduced, e.g. computational complexity and integration schemes.

The course is aimed at properly developing the skills of future Biomedical Engineers in the Computer Science field. Students will acquire the expertise required to participate in design, implementation and integration of heterogeneous software systems in the area of Bioinformatics and Computational Biology.

Prerequisites: knowledge of Computer Science basics, and mastering of at least one programming language; fundamental notions of Physics, Chemistry, and Molecular Biology.

 

NEWS/ALERTS

-   Available only in the italian version.

 

SCHEDULE
First lecture on Wed Sept 28th, 2016

Wed. 10:30-12:30 classroom: B33; Thu. 12:30-15:30 classroom: SI7

Schedule information is available also on a dedicated Google Cal, which can be imported via the following ICS address:
https://www.google.com/calendar/ical/5ub4i6oilcoqcchn649qj2v7oc%40group.calendar.google.com/public/basic.ics


 

SYLLABUS

A detailed description is available via the record of lessons (see aside). Hereafter, a cathegorized list of topics can be interactively explored. 




 

FINAL TEST

Procedure for final test:

a)   preliminary practical test on Python programming (student have to access the dedicated server to check and fix their test files);
b1) - for 259II students - presentation and discussion of a small project (1-2 student teams) on a specific argument, upon agreement with the teacher;
b2) - for 688II students - presentation and discussion of personally assigned homeworks (using the Rosalind system);
c) oral test, with questions on two distinct topics in the class syllabus.

 

CLASS MATERIAL
The main reference material is represented by class notes. Additional useful references are reported here.

Books:
 
  T1 - Title    Python in a Nutshell, 2nd ed.
           Author     Alex Martelli
           Pub.        O'Reilly
           ISBN       0-596-10046-9







Misc:


 L1 - web page with the Python exercises shown in lessons (cured by C. Vallati)

 E1 - Slides with introductory Python exercises

 Seq0 - Sequences: Human mitochondrion DNA (FASTA)

 C0 - Python implementation of the N&W algorithm + examples - allineamento_globale.zip

 M0 - asn.pdb asparagine - gly.pdb glicine - phe.pdb fenilalanine - pro.pdb proline

 M1 - 1hho.pdb hemoglobin (oxi) - 2hhb.pdb hemoglobin (deoxi)

 L2 - web page with basisc of molecular mechanics

 L3 - animation with example of normal modes of molecular vibrations

 S1 - slide on regular expressions in Python (from Dalke Scientific Software)

 T1 - tutorial on matplotlib

 D1 - description of file formats used in NAMD

 G1 - glossary of common terms used in Bioinformatics (ROSALIND portal)



 

LINKS
Python  &      Python(xy) SciPy               NumPy for Matlab users
BioPython moreover: NAMD & tutorial


A list of software tools among the most popular ones in the proteomics field can be found on the ExPASy site.

Open positions for jobs in the field of Bioinformatics and Computational Biology can be found in dedicated pages from BITS, ISBC, and bioinformatics.org

 

Oddities...

Graphical visualization of the Nussinov algorithm (class project, Favale/Vivaldi), .exe version.


  "game" on protein folding, developed at the Baker Lab in Seattle, USA   

 
 
Notes

The picture on the right side of the heading illustrates a particular of protein "lac repressor" (a genic regulator in E.Coli) as it binds to a DNA strand (TCB - Univ. of Illinois at Urbana-Champain)

The background picture represents a portion of an insuline model, as visualized in the VMD application.

The picture in the "description" section represents a "tag-cloud" with popular terms in bioinformatics papers.