Bioinformatics - 6 CFU - a.a. 2016-2017
Bioinformatics page on DISIM Web Site
Friday 10:00 - 11:30 a.m. - email for appointment
office: Building A. Turing, second Floor
email address: email@example.com
Exam: homeworks; project and its discussion.
- Biological definitions and concepts (DNA, RNA, microRNA, Central dogma, mutations,…)
- Main biological on-line DB. Data extraction from such systems.
- Alignment algorithms and substitution matrix. Suffix Tree.
- Phylogenetic analysis. Algorithms to build Phylogenetic trees. Test and accuracy.
- Computation models for biological systems modeling. Petri Nets and Hidden Markov Model
- Technologies and languages: Python, Bio-Python e NEO4J
- An introduction to bioinformtics algorithms. N.C. Jones and P.A. Pevzner. (Capitoli 3,6,9)
- Scientific papers, slides and other material
- If not done, send me an email with name and course (e.g., master in Computer Science, etc)
- the lesson of today, March 30th is canceled. See you tomorrow
Slides and teaching material
- [March 2nd 2017] - Introduction to the course and to Bioinformatics. Cell Structure and Functions [slides]
- [March 3rd 2017] - Central Dogma. On-line DB.[slides]
- [March 9h 2017] - On-line DB: NCBI and flat-file format.[slides]
- [March 10h 2017] - Single Alignement, Substitution Matrix, PAM.[slides]
- [March 16h 2017] - BLOSUM, score schema for gap,exahustive and heuristic algoritm, first homework.[slides]
- [March 17h 2017] - FASTA, Dynamic Programming [slides]
- [March 24h 2017] - BLAST [slides]
- [March 25h 2017] - Multiple Alignment, CLUSTAL [slides]
- [March 31h 2017] - Edit Distance[slides]
- [April 07h 2017] - Phylogenetic Analysis[slides]
- [April 20th 2017] - Second Homework assignment: assay on one of the presented algorithm or a report on the allignment of two proteins with 4 configuration using FASTA. Send an email to communicate the type of homework to develop and to have details on the second type. Deadline on 15th of May.
- [April 27th-28th 2017] - Neo4J DB, Cypher query language [slides]
- [May 4th 2017] - Project Presentation [pdf], [slide], [MirNA-HCC], [article], [Report].
- [May 5th 2017] - EduDay
- [May 11th 2017] - Introduction to Python [links]
- [May 12th 2017] - Laboratory: DIANA DB, Cypher Queries, Excercise.
- [May 18th, 25th and June 8th 2017] - Introduction to Petri Net and modeling exercises. [paper]. Pathways modeling using Petri Nets[slides].
- [May 19th, 26th and June 1sr and 9th 2017] - Project reviews and implementation. Documentation: [slides on visualization frameworks].