Differenze

Queste sono le differenze tra la revisione selezionata e la versione attuale della pagina.

--- bio:start [07/05/2019 alle 09:54 (5 anni fa)] – Nadia Pisanti
+++ bio:start [07/07/2021 alle 07:30 (3 anni fa)] (versione attuale) – [BIOINFORMATICS] Nadia Pisanti
@@ Linea 1: / Linea 1: @@
-====== BIOINFORMATICS ======
+====== BIOINFORMATICS 2020 ======
-Lecturer: **Nadia Pisanti**
+Lecturer: Prof. **Nadia Pisanti**
 === NEWS ===
-[April 30th] Please be aware that there will be no class on Monday, May 27th due to University cancelling all lectures on that day to allow students to go home and vote for EU elections.
+[February 8th] This page has been created!
-[April 15th] As communicated in the class, on Monday April 29th we will lecture 4 academic hours starting at 14:00 to catch up the classes that were canceled last week.
+===== CLASSES IN COVID-19 TIMES =====
-[April 1st *not a joke*] I recall that next week there will be no classes as comunicated at the beginning of the course. See you on April 15th.
+**Regular live classes are suspended from March 5th, 2020** \\
+Classes will thus take place [[https://meet.google.com/lookup/d2ubhrxcxh | here]]
-[March 26th] Papers have been assigned! __The student Antonio Nuzzo is asked to send an email to prof.Pisanti__ (his email bounced).
+Prof. Pisanti makes office hours on skype or meet upon appointment arranged by mail.\\
-[March 12th] The assignment of papers for the seminar will take place on Monday March 25th.
-[March 5th] From now on, in absence of news, lectures will be on Monday's from 14:00 to 15:30 and on Tuesday's from 9:15 to 10:45. Always in room L1.
-[February 27th] Next week we will have classes on Monday both at 14:00 and at 16:00, and both in room L1.
-[February 12th] The classes of April 8th and April 9th will not take place: we will have to find two slots to catch them up.
-[February 12th] This page has been created!
 === LEARNING GOALS ===
@@ Linea 33: / Linea 25: @@
 //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.
-//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. \\
 //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.\\
@@ Linea 44: / Linea 36: @@
 === STUDY MATERIAL ===
-SUFFIX TREE {{:magistraleinformatica:alg2:tre.pdf|}} \\
+SEQUENCES ALIGNMENTS {{:bio:allineamenti.pdf| Alignments}}\\
-PATTERN MATCHING {{:biotecnologie:informatica:patternmatching1.pdf}} e {{:biotecnologie:informatica:patternmatching2.pdf}} \\
+PATTERN MATCHING {{:biotecnologie:informatica:patternmatching1.pdf | ExactPatternMatching}} e {{:biotecnologie:informatica:patternmatching2.pdf | KnuthMorrisPratt&BoyerMoore}} {{:bio:kr87.pdf| KarpRabin87}} \\
-FRAGMENT ASSEMBLY {{:bio:fragmentassembly.pdf|}}\\
+SUFFIX TREE {{:magistraleinformatica:alg2:tre.pdf| SuffixTrees }} \\
-SEQUENCES ALIGNMENTS {{:bio:allineamenti.pdf|}}\\
+EXACT MOTIFS EXTRACTION  {{:bio:KarpMillerRosenberg.pdf| KarpMillerRosenberg}} \\
-FINDING REPETITIONS: FILTERING {{:bio:amb.pdf|}}\\
+APPROXIMATE MOTIFS EXTRACTION {{:bio:kmrc.pdf| KMRC}} {{:bio:Speller.pdf| Speller}} {{:bio:structured_motifs.pdf| StructuredMotifs}} \\
-NEW GENERATION SEQUENCING {{:bio:illumina-assembly.pdf|}}\\
+FINDING REPETITIONS: FILTERING {{:bio:amb.pdf| TUIUIU}}\\
-OVERVIEW OF SEQUENCING TECNOLOGIES {{:bio:en104-pisanti.pdf}}\\
+FRAGMENT ASSEMBLY {{:bio:fragmentassembly.pdf| FragmentAssembly}}\\
-BUBBLES IN DE BRUIJN GRAPHS (slides) {{bio:Seminar-Bubbles.pdf}}\\
+NEW GENERATION SEQUENCING {{:bio:illumina-assembly.pdf| NewGenerationSequencing}}\\
+OVERVIEW OF SEQUENCING TECNOLOGIES {{:bio:en104-pisanti.pdf | SequencingTechnologies}}\\
+HAPLOTYPE ASSEMBLY {{:bio:jcbwhatshap.pdf | WhatsHap }}\\
+BUBBLES IN DE BRUIJN GRAPHS (slides) {{bio:Seminar-Bubbles.pdf | Bubbles }}\\
 == EXAM ASSIGNMENT ==
-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:
 (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.
@@ Linea 63: / Linea 59: @@
 === SEMINARS SCHEDULE ===
-**MONDAY May 20th**
+TBA
-Marco Cardia: MALVA: genotyping by Mapping-free ALlele detection of known VAriants.\\
-Luca Corbucci: Haplotype-aware graph indexes.\\
-Nicolas Manini: Efficient computation of Sequence Mappability.\\
-Andre' Santos: GenMap: Fast and Exact Computation of Genome Mappability.\\
-**TUESDAY May 21st**
+=== "REGISTRO DELLE LEZIONI" ===
-Shadi Shajari: Simulating the DNA String Graph in Succint Space.\\
-Antonio Nuzzo: Indexing de Bruijn Graphs with minimizers.\\
-Riccardo Manetti: An Efficient, Scalable and Exact representation of High-Dimensional Color Information via de Bruijn Graph Search.\\
-Pouria Faraji: Parallel decompression of gzip-compressed files and random access to DNA sequences.\\
-*TUESDAY May 28th*
+[[https://unimap.unipi.it/registri/dettregistriNEW.php?re=3314294::::&ri=80312|REGISTRO DELLE LEZIONI]]
-Tabriz Hajiyev: Faster queries for longest substring palindrome after block edit.\\
-Newsha Ozgoli: Safe and Complete algorithms for dynamin programming problems, with an application to RNA folding.\\
-Federico Finocchio: CONSENT - Scalable Self-Correction of long reads with multiple sequence alignment.\\
-Paolo Contenti: Efficient Construction of a Complete Index for Pan-Genomics Read Alignments.
+===== WHITEBOARDS AND RECORDING OF LECTURES and MATERIAL =====
+^ Lecture Date ^ Topic ^ Material ^
+| dd/mm/aaaa | bla bla | links and files |
-=== "REGISTRO DELLE LEZIONI" ===
-     * [[https://unimap.unipi.it/registri/dettregistriNEW.php?re=3290064::::&ri=80312|REGISTRO DELLE LEZIONI]]