BIOPHYSICA COMPUTAZIONALE  

A.A. 2017-2018, 6 ECTS.

A course for the Master Program in Physics is given in the 1st semester and is pivotal for the curriculum in biosystems and part of an integrated syllabus together with courses in BIOCHEMISTRY, MOLECULAR BIOLOGY, BIOPHYSICS and THEORETICAL BIOPHYSICS.

The class will meet: mon. 12 -14, tue 8-10 and fri 16-18 in the Careri room (Marconi Building)

Instructor: Andrea Giansanti, room 211 (2nd floor, Marconi Building) tel. 0649914367 Andrea.Giansanti@roma1.infn.it

The course will end on Jan. 12 2018.

Running title: DOING BIOLOGY WITH COMPUTERS AND MODELS: FROM THE BORN-OPPENHEIMER APPROXIMATION TO THE SPACE OF BIOLOGICAL SEQUENCES AND THE INTEGRATIVE MODELLING OF SYSTEMS BIOLOGY

Description/Objectives. This course is intended as an introduction to computational (in silico, as opposed to in vivo/in vitro) Biophysics and Biology in the evolutionary perspective. The course is conceived as a compact (biased) introduction to: i) ARGUMENTS (A) (principles, ideas); ii) METHODS (M) (algorithms and techniques); iii) PERSPECTIVES (What next?) of contemporary computational biology. As far as the bias is concerned: the course will echo under many circumstances topics and themes that prof. Anna Tramontano used to teach, until last year. This 2017-18 course is dedicated to her memory. The style of teaching will be by illustration not by exhaustive demonstration, and requires from the students active participation, through questions, statements, and written essays. Lectures based on detailed demonstration (in the math style) will be limited in number. On the contrary, extensive reference and critical introductions to the literature and to many specialized texts will be offered as a thread for personal study. An effort will be made to locate each topic in a clear scheme to prepare the final exam. The objective of the course is, in a nutshell, to narrow the gap between the institutional level of training and that of research. Guest lecturers will present specialized views and lines of contemporary research of impact and interest to an audience of students enrolled in the biosystems and theoretical curricula.

Requirements. Enrolled students should have taken the basic courses of the BA program. In particular, basic competence in mechanics, thermodynamics, chemical equilibrium and quantum mechanics is required. Basic biological facts will be discussed as needed.

Evaluation: based on written essays, written tests and homeworks and participation to discussions: 40%. Oral exam: 60%.

Topics. The themes of the course will be partitioned into the three tracks: A, M, P, mentioned above.

Recommended texts.

 [HA] PG Higgs, TK Attwood, Bioinformatics and Molecular Evolution, Blckwell, 2006.

[DEKM] R Durbin, Eddy Krogh Michison. Biological Sequence Analysis. CUP, 1999.

[MP] Ron Milo and Rob Phillips, Cell Biology by the numbers, Garland, New York, 2016.

NOTE: STUDY MATERIALS CAN BE FOUND IN SEPARATED FILES AT:

http://server2.phys.uniroma1.it/doc/giansanti/BIOFISICA_COMPUTAZIONALE_2017/

 

SOME OF THE THEMES THAT WILL BE DISCUSSED

 

1.      WHAT IS COMPUTATIONAL BIOPHYSICS

2.      BASIC CELL BIOLOGY BY THE NUMBERS

3.      PROBABILISTIC REASONING (BAYES’THEOREM)

4.      FROM THE SCROEDINGER EQUATION TO MOLECULAR STRUCTURES AND DYNAMICS

5.      EVOLUTIONARY SEQUENCING  OF GENOMES

6.      METHODS OF SEQUENCE ANALYSIS/ BASIC BIOINFORMATICS/ PROGRAMMING

7.      MULTI-VARIATE DATA ANALYSIS (CLUSTERING)

8.      PHILOGENETIC METHODS

9.      MACHINE LEARNING METHODS