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bio:start [05/05/2020 alle 09:48 (4 anni fa)]
Nadia Pisanti [RECORDED LECTURES and MATERIAL] |
bio:start [07/07/2021 alle 07:30 (3 anni fa)] (versione attuale)
Nadia Pisanti [BIOINFORMATICS] |
| ====== BIOINFORMATICS ====== | ====== BIOINFORMATICS 2020 ====== |
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| Lecturer: **Nadia Pisanti** | Lecturer: Prof. **Nadia Pisanti** |
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| === NEWS === | === NEWS === |
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| [March 8th] Check all the information below concerning the e-larning procedure. | [February 8th] This page has been created! |
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| [February 17th] The class of February 24th will terminate 15' earlier. | |
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| [February 17th] This page has been created! | |
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| ===== CLASSES IN COVID-19 TIMES ===== | ===== CLASSES IN COVID-19 TIMES ===== |
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| **Regular frontal classes are suspended from March 5th.** \\ | **Regular live classes are suspended from March 5th, 2020** \\ |
| As a consequence, the classes that should have taken place after March 5th will be recorded and made available for download via a google drive linked in this web page. **Exceptions**:\\ | Classes will thus take place [[https://meet.google.com/lookup/d2ubhrxcxh | here]] |
| - Classes of April 20th and April21st (papers assignments for final exams) will take place on-line at the link you will find then in this web page.\\ | |
| - Classes of May 12th, May 18th and May 19th (students' seminars) will also take place on-line. \\ | |
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| Prof. Pisanti makes office hours in the same time slots as those of the classes via Skype provided an appointment is arranged by mail (in order schedule time slots). By email we can exchange Skype names and agree the exact time, so please indicate within your email request the amount of time you expect to need; this will allow to schedule your requests. \\ | Prof. Pisanti makes office hours on skype or meet upon appointment arranged by mail.\\ |
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| //Sequences Alignments//: Dynamic Programming methods for local, global, and semi-local alignments. Computing the Longest Common Subsequences. Multiple Alignments.\\ | //Sequences Alignments//: Dynamic Programming methods for local, global, and semi-local alignments. Computing the Longest Common Subsequences. Multiple Alignments.\\ |
| //Pattern Matching//: Exact Pattern Matching: algorithms (Knuth-)Morris-Pratt, Boyer-Moore, Karp-Rabin with preprocessing of the pattern. Algorithm with preprocessing of the text: use of indexes. | //Pattern Matching//: Exact Pattern Matching: algorithms (Knuth-)Morris-Pratt, Boyer-Moore, Karp-Rabin with preprocessing of the pattern. Algorithm with preprocessing of the text: use of indexes. |
| //Motifs Extraction//: KMR Algorithm for the extracion of exact motifs and its modifications for the inference of approximate motifs.\\ | //Motifs Extraction//: KMR Algorithm for the extraction of exact motifs and its modifications for the inference of approximate motifs.\\ |
| //Finding Repetitions//: Algorithms for the inference of long approximate repetitions. Filters for preprocessing. \\ | //Finding Repetitions//: Algorithms for the inference of long approximate repetitions. Filters for preprocessing. \\ |
| //Fragment Assembly//: Genomes sequencing: some history, scientific opportunities, and practical problems. Some possible approaches for the problem of assembling sequenced fragments. Link with the "Shortest common superstring" problem, the Greedy solution. Data structures for representing and searching sequencing data.\\ | //Fragment Assembly//: Genomes sequencing: some history, scientific opportunities, and practical problems. Some possible approaches for the problem of assembling sequenced fragments. Link with the "Shortest common superstring" problem, the Greedy solution. Data structures for representing and searching sequencing data.\\ |
| == EXAM ASSIGNMENT == | == EXAM ASSIGNMENT == |
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| Each student is assigned a paper that is a very recent scientific work on topics related to those of the course (tipically it is a paper accepted for publication in the proceedings of an international conference that is going to be held in a few weeks/months). The paper is part of a pool of possible papers selected by the lecturer. The paper assignment follows a brief description of all papers in the pool made by the lecturer, and a bidding phase of the students over such papers. | Each student will have to undergo an oral exam over the topics of the classes. |
| | Moreover, each student is assigned a paper that is a very recent scientific work on topics related to those of the course (tipically it is a paper accepted for publication in the proceedings of an international conference that is going to be held in a few weeks/months). The paper is part of a pool of possible papers selected by the lecturer. The paper assignment follows a brief description of all papers in the pool made by the lecturer, and a bidding phase of the students over such papers. |
| Once the student has his/her paper assigned, the task is to prepare and make a presentation of that work that: | Once the student has his/her paper assigned, the task is to prepare and make a presentation of that work that: |
| (1) describes the results presented in that paper, (2) is suited for the actual audience (that will be the course class) as for comprehension opportunity, (3) sticks to the allowed time slot. | (1) describes the results presented in that paper, (2) is suited for the actual audience (that will be the course class) as for comprehension opportunity, (3) sticks to the allowed time slot. |
| === "REGISTRO DELLE LEZIONI" === | === "REGISTRO DELLE LEZIONI" === |
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| [[https://unimap.unipi.it/registri/dettregistriNEW.php?re=3300618::::&ri=80312|REGISTRO DELLE LEZIONI]] | [[https://unimap.unipi.it/registri/dettregistriNEW.php?re=3314294::::&ri=80312|REGISTRO DELLE LEZIONI]] |
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| ===== RECORDED LECTURES and MATERIAL ===== | ===== WHITEBOARDS AND RECORDING OF LECTURES and MATERIAL ===== |
| ^ Lecture Date ^ Topic ^ Material ^ | ^ Lecture Date ^ Topic ^ Material ^ |
| | RECORDED LECTURES | EACH CLASS HAS ONE WHITEBOARD FILE AND TWO VIDEO FILES | Whiteboard is a .pdf and Video* are two (part1 and part2) .mp4 file WHICH YOU **NEED TO DOWNLOAD TO HAVE THE AUDIO** | | | dd/mm/aaaa | bla bla | links and files | |
| | 3/9/2020 | Morris and Pratt Algorithm | {{:biotecnologie:informatica:patternmatching1.pdf | ExactPatternMatching }} \\ {{ https://drive.google.com/file/d/1ilZ1IWVq9J6x_MznAYQZFDe-51POzmPt/view?usp=sharing | Whiteboard }} {{ https://drive.google.com/file/d/1NhPmXWw7cvzX95YxhZCYQIClMoxUwnx2/view?usp=sharing | VideoPart1 }} {{ https://drive.google.com/file/d/1yDhXxHM6s1gdY0olKE5P3f0bUZkrJXGc/view?usp=sharing | VideoPart2 }} | | |
| | 3/10/2020 | Knuth Morris and Pratt Algorithm, Boyer and Moore Algorithm: idea | {{:biotecnologie:informatica:patternmatching2.pdf | KMP&BM}} \\ {{ https://drive.google.com/file/d/1ZXJM7M03dzZMNrWAFD75UcGR09S-kDln/view?usp=sharing | Whiteboard }} {{ https://drive.google.com/file/d/1RUA7xQtbElNuERWniDZ3qOSDSQe7bkyG/view?usp=sharing | VideoPart1 }} {{ https://drive.google.com/file/d/17fw9xrENwvb4L9yTMVRu_2JYJuXaBEfo/view?usp=sharing | VideoPart2 }} | | |
| | 3/16/2020 | Boyer and Moore Algorithm, Karp and Rabin Algorithm. Multiple Patterns or network expression: Aho-Corasick automata. | {{:bio:kr87.pdf| KarpRabin87}} \\ {{ https://drive.google.com/file/d/1UPG4nkBtwYddzItnUG3MjLgUSaPlPAJc/view?usp=sharing | Whiteboard }} {{ https://drive.google.com/file/d/1xtJuCCjYIvMKv6wEl1YMjoGpaYiwW_1U/view?usp=sharing | VideoPart1 }} {{ https://drive.google.com/file/d/1YITXSrV7Isr023a6dOU5jCpAYABTaLhU/view?usp=sharing | VideoPart2 }} | | |
| | 3/17/2020 | Preprocessing the text: Suffix Trees and Suffix Arrays. Approximate Pattern Matching with Hamming Distance, Edit Distance, Don't Care Symbols, Degenerte Alphabets. | {{:magistraleinformatica:alg2:tre.pdf| Suffix Tree}} \\ {{ https://drive.google.com/file/d/1qhVQ8QV7zk6hFIFccghIHmvIiLZfd9XJ/view?usp=sharing | Whiteboard }} {{ https://drive.google.com/file/d/12L4lVLea5DSBaM33hM6yqKUnO4GDF73_/view?usp=sharing | VideoPart1 }} {{ https://drive.google.com/file/d/15KjKSRJv7wZ2GDm_L3uLcS-6llzses4T/view?usp=sharing | VideoPart2 }} | | |
| | 3/23/2020 | Motifs Inference: problem definitions with all its variants and applications in Genomics. Exact Motifs Inference with Suffix Trees: algorithm, complexity, examples. Maximality notions and their characterization on suffix trees. | {{ https://drive.google.com/file/d/1wIMTBSROSeAEP2ZTB3hgmH9XgzAYmAnh/view?usp=sharing | Whiteboard }} {{ https://drive.google.com/file/d/10Ujw5KEFnZMD6AOm2kn6Ysh1_Y4cKclu/view?usp=sharing | VideoPart1 }} {{ https://drive.google.com/file/d/10d6eSUO11NuY4Hu88tN8jQsyraWzxbOH/view?usp=sharing | VideoPart2 }} | | |
| | 3/24/2020 | Exact Motifs Inference with the naming technique: KMR algorithm: description, complexity analysis, examples. Approximate Motifs Extraction: possible notions of approximation, problem definitions, and solutions. | {{:bio:KarpMillerRosenberg.pdf| KarpMillerRosenberg}} \\ {{ https://drive.google.com/file/d/1fOSZQBb-mKa9MdpzIOitGakEqSyGH3HO/view?usp=sharing | Whiteboard }} {{ https://drive.google.com/file/d/1TCkJJeTazzgKZUErioaQkV0y7nIJNh9m/view?usp=sharing | VideoPart1 }} {{ https://drive.google.com/file/d/1rQw-MRLvXlksdedCtaZLLomI0N8qoU58/view?usp=sharing | VideoPart2 }} | | |
| | 3/30/2020 | Approximate Motifs Inference with Suffix Tree: Speller algorithm: description, complexity analysis, examples. Structured Motifs Extraction via Suffix Tree. | {{:bio:Speller.pdf| Speller}} {{:bio:structured_motifs.pdf| StructuredMotifs}} \\ {{ https://drive.google.com/file/d/1IOU3c8NOFVTELCk2zVlVl24qIvcFMDet/view?usp=sharing | Whiteboard }} {{ https://drive.google.com/file/d/1qd40ynbehGmZxm9Sq9X7OFhiz3sJ-kMd/view?usp=sharing | VideoPart1 }} {{ https://drive.google.com/file/d/13Fkc7ZO881zS6fNwFZeR1zBfnNaLig3f/view?usp=sharing | VideoPart2 }} | | |
| | 3/31/2020 | Approximate Motifs Inference with the naming technique: KMRC algorithm: description, complexity analysis, examples. | {{:bio:kmrc.pdf| KMRC}} \\ {{ https://drive.google.com/file/d/1WnWairRZQ_FtCfa7ghW1_0twoYLIkNqg/view?usp=sharing | Whiteboard }} {{ https://drive.google.com/file/d/1NANZKZKGvStMKy-OifSy63VjMPjn41Is/view?usp=sharing | VideoPart1 }} {{ https://drive.google.com/file/d/1362OJMYnRndcnOP5Urk_HWbQR-Gs-1DQ/view?usp=sharing | VideoPart2 }} | | |
| | 4/6/2020 | Finding long repetitions | {{:bio:amb.pdf| Filtering }} \\ {{ https://drive.google.com/file/d/1yRoKoj83ffFyDCLZXvT9KSdZy8mgGzGF/view?usp=sharing | Whiteboard }} {{ https://drive.google.com/file/d/1tI43x5_kNREtpm_bvJttNUrSg0jsucq1/view?usp=sharing | VideoPart1 }} {{ https://drive.google.com/file/d/1Prs9gtsXe1z-3V649X8xYPt_EJqJKT2d/view?usp=sharing | VideoPart2 }} | | |
| | 4/7/2020 | Haplotype Assembly | {{:bio:jcbwhatshap.pdf | WhatsHap }} \\ {{ https://drive.google.com/file/d/1hkZj4JseIbnyK0DLPX_vAbz9Ys89v8fO/view?usp=sharing | Whiteboard }} {{ https://drive.google.com/file/d/1fAs6OE91oqMx0qIb86HWla7-F6fQionH/view?usp=sharing | VideoPart1 }} {{ https://drive.google.com/file/d/1sB7H_W8Mpo3sqvCR1GkwL98joMgm8RqW/view?usp=sharing | VideoPart2 }} | | |
| | 4/20/2020 \\ 14:00-16:00| PAPER ASSIGNMENT 1 | ON-LINE LECTURE at this {{https://meet.google.com/wjo-cezo-xvn | link}} \\ {{:bio:Paperi2020.rtf| List of Papers}} {{:bio:CPM-2020.zip| CPM}}\\ {{:bio:RECOMBa-2020.zip| RECOMBa}} {{:bio:RECOMBb-2020.zip| RECOMBb}} {{:bio:RECOMBc-2020.zip| RECOMBc}}\\ {{:bio:RECOMBd-2020.zip| RECOMBd}} {{:bio:26-RecombCG.pdf | RECOMBe}} \\ {{https://drive.google.com/file/d/1vi_BzpS2aC6uTHa5mDthEFnf6v4UJ9Qa/view?usp=sharing| Recorded Lecture}}| | |
| | 4/21/2020 | PAPER ASSIGNMENT 2 | ON-LINE LECTURE at this {{https://meet.google.com/wjo-cezo-xvn | link}} \\ {{:bio:advises.rtf | ReadMe}} \\ {{ https://drive.google.com/file/d/12ZCKsIdoBl3vHBTjzpJ_vMza-eTDxyJL/view?usp=sharing | Recorded Lecture}} | | |
| | 4/27/2020 | THIS CLASS WILL NOT TAKE PLACE (too many hours in schedule) | | | |
| | 4/28/2020 | Fragment Assembly 1 | {{:bio:fragmentassembly.pdf| Fragment Assembly}} \\ {{ https://drive.google.com/file/d/1zBy24OLU9qJPPv0jRLd1xpXPv34B4F-4/view?usp=sharing | Whiteboard }} {{ https://drive.google.com/file/d/1eZ5gVaXEwES0AWo8YaZFA-mU9Gnt0nQe/view?usp=sharing | VideoPart1 }} {{ https://drive.google.com/file/d/1y9R_248_UD2PGGhsmO3qlOXTd8m9V4BY/view?usp=sharing | VideoPart2 }} | | |
| | 5/4/2020 | Fragment Assembly 2 | {{:bio:fragmentassembly.pdf| Fragment Assembly}} \\ {{ https://drive.google.com/file/d/1nP6q4NVgkI-01o04BHdPAQDnbj7b_wt5/view?usp=sharing | Whiteboard }} {{ https://drive.google.com/file/d/12Ttvnx0gVQFCVTcaYNB4Ekk1cC69WaM7/view?usp=sharing | VideoPart1 }} {{ https://drive.google.com/file/d/1alq0umpn_sffZ4Gonb1iwLyOrfs75eHS/view?usp=sharing | VideoPart2 }} | | | |
| | 5/5/2020 | Bubbles in de Bruin Graphs | {{ XXXX | Whiteboard }} {{ https://drive.google.com/file/d/1c6EnzJ7TS-HZqI3Zd7zVUXaNeWfpt0Kp/view?usp=sharing | VideoPart1 }} {{ https://drive.google.com/file/d/1t7YTrZYz1CK215FXiZaAk04NmiTnWBOE/view?usp=sharing | VideoPart2 }} | | |
| | 5/11/2020 | THIS CLASS WILL NOT TAKE PLACE (too many hours in schedule) | | | |
| | 5/12/2020 | STUDENTS' SEMINARS | ON-LINE LECTURE at this {{https://meet.google.com/wjo-cezo-xvn | link}} | | |
| | 5/18/2020 | STUDENTS' SEMINARS | ON-LINE LECTURE at this {{https://meet.google.com/wjo-cezo-xvn | link}} | | |
| | 5/19/2020 | STUDENTS' SEMINARS | ON-LINE LECTURE at this {{https://meet.google.com/wjo-cezo-xvn | link}} | | |
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