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1DLoadBalancingConceptualDraft
Parallelism In The SeqAn Library: 1D Load Balancing: Conceptual Draft Open issues * Providing N algorithm states to the forall method instead of just one introduces ...
454genfusionen
Page 454genfusionen This page is a collection of ideas concerning 454 RNA sequencing data analysis. TODOs 25.3.: General Questions * which reference sequence ...
AProtLec8MaterialsWS14
Learning units Learning unit 8A/B to De novo peptide identification and algorithmic concepts Learning unit 8C to De novo ID with Antilope Learning unit 8D to Complementary ...
r3 - 02 Feb 2015 - 10:09 by jpfeuffer
AdapterRemoval
template void remove(StringSet seq, StringSet qual, StringSet const adapter) { Align, ArrayGaps align; resize(rows(align), 2); for ...
AdvancedAlgorithms
Page AdvancedAlgorithms This is the Wiki for a project oriented version of P4. Here you can find a StudentList Direct links to topics $ Algorithmic problems in ...
AdvancedAlgorithms11
Page AdvancedAlgorithms11 Welcome to the Wiki of the Lecture Advanced Algorithms in Bioinformatics (P4). News * 28.09. (Weese): The second examination (Nachklausur ...
AdvancedAlgorithms11_GenomeRNAComparison
Genome Comparison and RNA Analysis Lectures Date Lecture* *Materials Genome Comparison 03.06.2011 Segment Match Refinement script 12 MatchRefinement ...
AdvancedAlgorithms11_Indices
Index Data Structures Lectures Date Lecture* *Materials (Enhanced) Suffix Array 09.05.2011 Suffix Array Construction and Searching script 07 ...
AdvancedAlgorithms11_Searching
Online String Searching and Filtering Lectures Date Lecture* *Materials Online Searching 11.04.2011 Introduction, Horspool, Wu Manber script ...
AdvancedAlgorithms12
Page AdvancedAlgorithms12 Welcome to the Wiki of the Lecture Advanced Algorithms in Bioinformatics (P4). News * (18.1.13) The results of the second exam can ...
AlDaBiWS10
Page AlDaBiWS10 Willkommen im Wiki der Vorlesung "Algorithmen und Datenstrukturen für Bioinformatik" Nachrichten * 17.09.2010 (Reinert): Das Semester beginnt ...
AlDaBiWS10CodeReview
Page AlDaBiWS10CodeReview Tragen Sie sich zu einem der beiden Termine für den Code Review 1 ein. Zurück zur Veranstaltungsseite. Dienstag, 14.12., Arnimallee 6 ...
AlDaBiWS10CodeReview2
Page AlDaBiWS10CodeReview2 Tragen Sie sich zu einem der beiden Termine für den Code Review 2 ein. Zurück zur Veranstaltungsseite. Dienstag, 08.02., Arnimallee 6 ...
r27 - 22 Feb 2011 - 21:28 by agebel
AlDaBiWS10Groups
Page AlDaBiWS10Groups Tragen Sie hier ihre Gruppe mit deren Teilnehmern (voller Name) ein. Zurück zur Veranstaltungsseite. Gruppen Gruppennr. Teilnehmer 1 ...
AlDaBiWS10PResults
Page AlDaBiWS10PResults ((short description what this page is about)) Section 1 ((content)) Section 2 ((content)) Comments * Punktestand.pdf: Punktestand.pdf ...
AlDaBiWS10Praktikum
Praktikumsvorlesung Hier finden Sie die Termine und Folien der P VL. Zurück zur Veranstaltungsseite. 1. Vorlesung, 22.10. #AnchorVL1 $ Thema: Einführung, Subversion ...
AlDaBiWS10Tutorium
Page AlDaBiWS10Tutorium Tragen Sie bei Bedarf hier für ein Dienstagstutorium ein. Der Termin 14 16 Uhr ist als Backup gedacht, wenn zum Termin 12 14 Uhr kein Platz ...
AlDaBiWS11
Page AlDaBiWS11 Willkommen im Wiki der Vorlesung "Algorithmen und Datenstrukturen für Bioinformatik" Nachrichten * 16.4.2012 (Reinert): Die Ergbnisse der zweiten ...
AlDaBiWS11CodeReview
Die Code Review findet am 13.12.2011 im PC Pool statt. Tragen Sie ihre Gruppe in die Tabelle ein. Zurück zur Veranstaltungsseite. Gruppen Zeit Gruppennr. ...
r26 - 13 Dec 2011 - 12:46 by chrkle
AlDaBiWS11Groups
Tragen Sie hier ihre Gruppe mit deren Teilnehmern (voller Name) ein. Zurück zur Veranstaltungsseite. Gruppen Gruppennr. Teilnehmer 1 Teilnehmer 2 Teilnehmer ...
AlDaBiWS11Praktikum
Praktikumsvorlesung Hier finden Sie die Termine und Folien der P VL. Zurück zur Veranstaltungsseite. 1. Vorlesung, 20.10. #AnchorVL1 $ Thema: Einführung, Subversion ...
AlDaBiWS11Tutorium
Page AlDaBiWS11Tutorium Tragen Sie bei Bedarf hier für ein Dienstagstutorium ein. Der Termin 14 16 Uhr ist als Backup gedacht, wenn zum Termin 12 14 Uhr kein Platz ...
AlDaBiWS12
Page AlDaBiWS12 Willkommen im Wiki der Vorlesung "Algorithmen und Datenstrukturen für Bioinformatik" Nachrichten * 16.04.2013: Die Klausurergebnisse der 2. Klausur ...
AlDaBiWS12CodeReview
Die Code Review findet am 11.12.2012 im PC Pool statt. Tragen Sie ihre Gruppe in die Tabelle ein. Zurück zur Veranstaltungsseite. Gruppen Gruppe 1 9 ...
r19 - 10 Dec 2012 - 21:04 by pratik
AlDaBiWS12CodeReview2
Die Code Review findet am 25.01.2013 im Raum 018 für die Gruppen 1 9 und im Raum 010 für die Gruppen 10 18 statt. Tragen Sie ihre Gruppe in die Tabelle ein. ...
r17 - 24 Jan 2013 - 14:34 by monarams
AlDaBiWS12Groups
Tragen Sie hier ihre Gruppe mit deren Teilnehmern (voller Name) ein. Zurück zur Veranstaltungsseite. Gruppen Gruppennr. Teilnehmer 1 Teilnehmer 2 Teilnehmer ...
AlDaBiWS12Praktikum
Praktikumsvorlesung Hier finden Sie die Termine und Folien der P VL. Zurück zur Veranstaltungsseite. 1. Vorlesung, 18.10. #AnchorVL1 $ Thema: Einführung, C ...
AlDaBiWS12Tutorium
Page AlDaBiWS12Tutorium Tragen Sie bei Bedarf hier für ein Dienstagstutorium ein. Der Termin 14 16 Uhr ist als Backup gedacht, wenn zum Termin 12 14 Uhr kein Platz ...
r21 - 19 Nov 2012 - 10:39 by nordos
AlDaBiWS13
Page AlDaBiWS13 Willkommen im Wiki der Vorlesung Algorithmen und Datenstrukturen für Bioinformatik (19700) Die Vorlesung hat 12 credits, davon zählen 6 credits auf ...
AlDaBiWS13CodeReview
Page AlDaBiWS13CodeReview Tragen Sie hier Ihre Gruppe für einen Time Slot des Code Reviews ein. Stellen Sie sich darauf ein, den Code den ihre Gruppe abgegeben hat ...
r22 - 03 Feb 2014 - 21:32 by jdf
AlDaBiWS13Groups
Tragen Sie hier ihre Gruppe mit deren Teilnehmern (voller Name) ein. Zurück zum Praktikum oder zur Veranstaltungsseite. Gruppen Gruppennr. Teilnehmer 1 Teilnehmer ...
r35 - 14 Oct 2014 - 09:55 by celine4
AlDaBiWS13Praktikum
AlDaBiWS13Praktikum Diese Seite behandelt das Praktikum zu Algorithmen und Datenstrukturen WS13 (hier geht es zur Vorlesungsseite). Übersicht Das Praktikum besteht ...
r31 - 04 Mar 2014 - 10:29 by mauli87
AlDaBiWS13Tutorium
Page AlDaBiWS13Tutorium Tragen Sie bei Bedarf hier für ein Praktikumstutorium ein. Der Termin 14 16 Uhr ist als Backup gedacht, wenn zum Termin 12 14 Uhr kein Platz ...
r27 - 20 Dec 2013 - 20:49 by hayko1991
AlDaBiWS14
AlDaBi (WiSe 2014) Willkommen im Wiki der Vorlesung Algorithmen und Datenstrukturen für Bioinformatik (LV Nr. siehe Orte und Zeiten) Die Vorlesung hat 12 credits ...
AlDaBiWS14CodeReview
Page AlDaBiWS14CodeReview Tragen Sie hier Ihre Gruppe für einen Time Slot des Code Reviews ein. Es gibt 2 parallele Time slots. Jede Gruppe trägt sich nur in eine ...
AlDaBiWS14Groups
Tragen Sie hier ihre Gruppe mit deren Teilnehmern (voller Name) ein. Zurück zum Praktikum oder zur Veranstaltungsseite. Gruppen Gruppennr. Teilnehmer 1 Teilnehmer ...
r33 - 18 Jan 2015 - 19:52 by damazein
AlDaBiWS14Praktikum
AlDaBiWS14Praktikum Diese Seite behandelt das Praktikum zu Algorithmen und Datenstrukturen WS14 (hier geht es zur Vorlesungsseite). Übersicht Das Praktikum besteht ...
AlDaBiWS14Tutorium
Page AlDaBiWS14Tutorium Tragen Sie bei Bedarf hier für ein Praktikumstutorium ein. Der Termin 14 16 Uhr ist als Backup gedacht, wenn zum Termin 12 14 Uhr kein Platz ...
r39 - 28 Oct 2014 - 08:36 by danielseeler
AlDaBiWS15
AlDaBiWS15 ((short description what this page is about)) Section 1 ((content)) Section 2 ((content)) Comments
NEW - 12 Oct 2015 - 13:52 by sandra48
AlDaBiWS15Groups
Tragen Sie hier ihr Paar mit deren Teilnehmern (voller Name) ein. Zurück zum Praktikum oder zur Veranstaltungsseite. Paare Paarnr. Teilnehmer 1 Teilnehmer ...
r44 - 13 Mar 2016 - 00:33 by rrezart
AlDaBiWS15Praktikum
AlDaBiWS15Praktikum Diese Seite behandelt das Praktikum zu Algorithmen und Datenstrukturen WS15. Übersicht Das Praktikum besteht aus: * Praktikumsvorlesung ...
r27 - 01 Feb 2016 - 14:55 by kjk
AlDaBiWS15Tutorium
Page AlDaBiWS15Tutorium Tragen Sie sich bei Bedarf jeweils in der Woche vor dem Prakikumstutorium hier für ein Praktikumstutorium ein. Der Haupttermin für das Tutorium ...
r68 - 17 Jan 2016 - 17:42 by nilsj24
AlgBioWS11
Page AlgBioWS11 Willkommen im Wiki der Vorlesung Algorithmische Bioinformatik! News Die Einsicht in die Nachklausur findet am Donnerstag den * 3. Mai um 14:00 ...
r28 - 02 May 2012 - 10:08 by jpp
AlgLecture10Materials
Here is all the material for the lecture unit 3, lecture 6/6 * Download the script
AlgLecture10MaterialsWS13
Here is all the material for the lecture unit 3, lecture 5 * Download the lecture notes
AlgLecture10MaterialsWS14
Here is all the material for the third block (lectures 10 and 11). * Download the lecture notes
AlgLecture11Materials
Here is all the material for the lecture 12 * Download the slides
AlgLecture12Materials
Here is all the material for the lecture 12 * Download the slides * Video on Alan Turing at Youtube * Additional material: Characterizing r.e. sets by generators ...
AlgLecture12MaterialsWS14
Here is all the material for the lecture 12 * Download the slides * Video on Alan Turing
AlgLecture13Materials
Here is all the material for the lecture 13 * Download the slides * Additional material: Turing machine codes and a non r.e. language
AlgLecture13MaterialsWS13
Here is all the material for turing machines pt. 1. * Download the lecture notes
NEW - 25 Nov 2013 - 10:41 by anduryl
AlgLecture13MaterialsWS14
Here is all the material for the lecture 13 * Download the slides * Additional material 1 : Turing machines as enumerators * Additional material 2 : Undecidable ...
AlgLecture14Materials
Here is all the material for the lecture 14 * Download the slides
AlgLecture14MaterialsWS13
Here are the materials for turing machines pt. 2 definition of run time analysis. * Download the lecture notes
NEW - 03 Dec 2013 - 15:36 by anduryl
AlgLecture14MaterialsWS14
Here is all the material for the lecture 14 * Download the slides
AlgLecture15Materials
Here is all the material for the lecture 15 * Download the slides
AlgLecture15MaterialsWS13
Here are the notes about polynomial reductions, NP, NP completeness and some examples. * Download the lecture notes
NEW - 03 Dec 2013 - 15:37 by anduryl
AlgLecture15MaterialsWS14
Here is all the material for the lecture 15 * Download the slides
AlgLecture16Materials
Here is all the material for the lecture 16 * Download the slides
AlgLecture1Materials
Here is all the material for the lecture unit 1, lecture 1 * Download the script
AlgLecture1MaterialsWS13
Here is all the material for the lecture unit 1, lecture 1 * Download the script
r4 - 11 Oct 2013 - 14:52 by anduryl
AlgLecture1MaterialsWS14
Here is all the material for the first block (lectures 1 and 2). * Download the lecture notes * Chapter of Motwani book * Review paper by Karp: Randomized ...
AlgLecture2Materials
Here is all the material for the lecture unit 1, lecture 2 * Download the script
AlgLecture2MaterialsWS13
Here is all the material for the lecture unit 1, lecture 2 * Download the lecture notes
NEW - 17 Oct 2013 - 06:08 by anduryl
AlgLecture2MaterialsWS14
For the script see lecture 1.
AlgLecture3Materials
Here is all the material for Lecture 3 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.1.1 1.3)
AlgLecture3MaterialsWS13
Here is all the material for the lecture unit 1, lecture 3 * Download the lecture notes
NEW - 21 Oct 2013 - 14:20 by anduryl
AlgLecture3MaterialsWS14
Here is all the material for Lecture 3 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.1.1 1.3)
AlgLecture4Materials
Here is all the material for Lecture 4 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.4.2 4.4)
AlgLecture4MaterialsWS13
Here is all the material for the lecture unit 2, lecture 1 * Download the lecture notes
AlgLecture4MaterialsWS14
Here is all the material for Lecture 4 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.4.2 4.4) * Some history
AlgLecture5Materials
Here is all the material for Lecture 5 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.3.1,3.2,3.4)
AlgLecture5MaterialsWS13
Here is all the material for the lecture unit 2, lecture 2\ For script see previous lecture.
AlgLecture5MaterialsWS14
Here is all the material for Lecture 5 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.3.1,3.2,3.4)
AlgLecture6Materials
Here is all the material for the lecture unit 2, lecture 4/5 * Download the script
AlgLecture6MaterialsWS13
Here is all the material for the lecture unit 3, lecture 1 * Download the lecture notes
AlgLecture6MaterialsWS14
Here is all the material for the third block (lectures 6 and 7). * Download the lecture notes
AlgLecture7Materials
Here is all the material for the lecture unit 2, lecture 4/5 * Download the script
AlgLecture7MaterialsWS14
AlgLecture7MaterialsWS14 ((short description what this page is about)) Section 1 ((content)) Section 2 ((content)) Comments
AlgLecture8Materials
Here is all the material for the lecture unit 3, lecture 3/4 * Download the script
AlgLecture8MaterialsWS13
Here is all the material for the lecture unit 3, lecture 3 * Download the lecture notes
AlgLecture8MaterialsWS14
Here is all the material for the third block (lectures 8 and 9). * Download the lecture notes
AlgLecture9Materials
Here is all the material for the lecture unit 3, lecture 3/4 * Download the script
AlgorithmsProgrammingCodeReview
The code review takes place on the 28th of November in room 020 in the Takustraße 9. Please, fill in the group number into your desired time slot. Back to programming ...
r10 - 24 Nov 2014 - 19:15 by ziska
AlgorithmsProgrammingExerciseWS14
Please, fill in the names of your group members (given name and surname). Back to programming wiki or to lecture wiki. Gruppen Group No. Member 1 Member 2 ...
AlgorithmsWS12
Page AlgorithmsWS12 Welcome to the Wiki of the MSc lectures Algorithms News 27.03.2013: The second exam will be on Monday, April 15th (12 14, Arnimallee 6, SR032 ...
AlgorithmsWS13
Page AlgorithmsWS13 Welcome to the Wiki of the MSc lectures Algorithms (19712) News Klausureinsicht 2. Prüfung : 30 April 2014, 9 10h, T9, R012 Nachklausur ...
AlgorithmsWS14
Algorithms (WiSe 2014) Welcome to the Wiki of the MSc lectures Algorithms (VL: 19400501, UE: 19400502) News * The results of the second exam are online ...
AlignmentHeuristics
Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * chaining.pdf * filtering.pdf Übungen: Inhalt Datei Material 6. Übung ...
AlignmentHeuristicsWS11
Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * filtering.pdf * blast filtering.pdf Übungen: Inhalt Datei Material 7. ...
r6 - 03 Jan 2012 - 20:51 by hartnamn
AlignmentHeuristicsWS12
Page AlignmentHeuristicsWS12 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * fasta.pdf * blast filtering.pdf * quasar.pdf Videos ...
AlignmentHeuristicsWS13
Page AlignmentHeuristicsWS13 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * fasta.pdf * blast.pdf * quasar.pdf Videos: * Vorlesungsvideo ...
r6 - 15 Jan 2014 - 12:07 by thwelln31416
AlignmentHeuristicsWS14
Page AlignmentHeuristicsWS14 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * fasta * blast * quasar Videos: Hier das Vorlesungsvideo ...
r6 - 04 Dec 2014 - 13:19 by denisethiel
AnalysisMethods
Analysis Methods and algorithm design Lectures Date Lecture* *Materials 19.10.2010 Run time analysis I runtime.pdf 21.10.2010 Run time analysis ...
AnalysisMethodsWS11
Analysis Methods and algorithm design Lectures Date Lecture* *Materials 18.10.2011 Run time analysis I runtime.pdf 20.10.2011 Run time analysis ...
AsperaDownloads
AsperaDownloads Aspera is a company that provides the fasp protocol which uses UDP for file transfer and is much faster than FTP over TCP. The protocol is proprietary ...
AssemblyComparison
Original goal: 1. Download the reads from a fairly well finished genome Human chr.21 2. and assemble it using two or more standard assemblers e.g. Celera ...
AssignmentWeek1
General information for programming exercises * Each group gets access to a svn directory at https://svn.mi.fu berlin.de/agbio/advancedAlgo/SS12/GroupX (Groups ...
AssignmentWeek2
Sign up at ProgrammingGroupList for one of the exercises on Tuesday 15th and Wednesday 16th Exercise 2 Read mapping with QUASAR Deadline: 23.05.2012 9:00 a.m. Implement ...
AssignmentWeek3
Sign up at ProgrammingGroupList for one of the exercises on Tuesday 12th and Wednesday 14th Exercise 3 Compression with BWT Deadline: 24.06.2012 6:00 p.m. Implement ...
BScBlastInSeqAn
BScBlastInSeqAn A study comparing the classic NCBI BLAST implementation with a straightforward implementation in SeqAn. * Project Page Background BLAST 1 is ...
r3 - 25 Jun 2013 - 11:26 by annkatrin
BScBlastInSeqAnProject
Eine vergleichende Studie von BLAST Algorithmen Aufgabenstellung BLAST (Basic Local Alignment Tool) ist das bekannteste Programm zur Identifizierung von lokalen Alignments ...
r3 - 14 Jul 2013 - 21:16 by annkatrin
BScDataStructureSV
BScDataStructureSV SNP efficient Journal Strings Einleitung In den letzten 10 Jahren hat sich die Technologie zur Sequenzierung der DNS von Organismen kolossal verbessert ...
BScEfficientExactMotifDiscovery
BScEfficientExactMotifDiscovery Implementation of an existing motif discovery algorithm in SeqAn. Background The goal of motif finding is the detection of novel ...
BScGenAlignGraphs
BScGenAlignGraphs Comparing graphs for genome alignment of multiple sequences under the presence of large structural events. Schedule Moritz Finishing Date ...
r9 - 19 Sep 2013 - 13:22 by kiekemo
BScParallelBamIO
BScParallelBamIO Implementation of parallel de /compression of BAM files. * Parallel Bam I/O Schedule/Report Background BAM 1 files are used for storing alignments ...
BScParallelBamIOScheduleProject
BScParallelBamIOScheduleProject Implementation of parallel de /compression of BAM files Project Schedule Tasks 1) Extract the compression and decompression into ...
r8 - 05 Feb 2014 - 06:16 by olfrik
BScReadRealignment
BScReadRealignment Comparing short read realignment algorithms. Background Read alignment is a crucial step for the analysis of Next Generation Sequencing (NGS) data ...
BeamerCalendars
OUTDATED! Go to: https://wikis.fu berlin.de/display/abi/Beamer Beamer Calendars * Beamer Calendar General (beamer for lending/public use, if need be) * Beamer ...
BetterEnglish
Polish Up Your English * Oxford Dictionaries: Better Writing * Oxford Dictionaries: Grammar * Oxford Dictionaries: Punctuation
BeverageOrder
OUTDATED! Do not use. Page BeverageOrder We plan to regularly order beverages and others from https://www.durstexpress.de Please fill in your orders and give the ...
BiBWTApps
MSc Thesis The birectional BWT and its applications Topic TODO Journal * 2014 09 15: I read up on templates, forked the official seqan repository, set Eclipse ...
BlastX
BlastX Diese Seite stellt das Wiki zur BlastX Implementierung von Hannes Hauswedel dar. Zusammenfassung BLASTX ist ein Programm zum Finden von Nucleotid Sequenzen ...
BoSSADraft
Page BoSSADraft This page describes the current draft of a Benchmark of Seeds for Sequence Analysis. Sources of inspiration are Rabema, PAPI and Pizza Chili Corpus ...
BowtieBwaComparison
Ich habe mir schon einmal ein paar Gedanken zu meinem Projekt gemacht und würde gerne einen Vergleich von bwa Burrows Wheeler Alignment Tool und dem Bowtie anstellen ...
BscImprovementsOfGraphBasedRealignment
BscImprovementsOfGraphBasedRealignment Improving the Graph Based Realignment in SeqAn. Background The SeqAn library contains a powerful method for realignment and ...
BscKmerBinCounting
Implementing and evaluating different strategies to assign the set of k mers in a NGS sample to genomic bins Background For metagenomics read mapping it becomes more ...
BscPlagiarismApp
Implementation of an IOS app to compare documents and visualize common paragraphs using a local alignment software. Background The goal of this thesis is to adapt ...
BscRawSeqJournaling
BscRawSeqJournaling BSc Thesis: Journaling raw sequences. Weekly Progress Introduction Nowadays sequencing technologies lead to a tremendous number of available ...
BscRegionFilter
BscRegionFilter Possible Project for a BSc Thesis in Bioinformatics or Computer Science Introduction "Many nucleotide and amino acid sequences are highly repetitive ...
BscSeqAn010Seeds
Implementing 01*0 seed search strategy using the bidirectional FM index in SeqAn Background Approximate string matching is an important subtask in many bioinformatic ...
BscSeqAnAlphabetReduction
BscSeqAnAlphabetReduction ((short description what this page is about)) introduction "Research on the functional redundancy of amino acids dates back to ...
BscSeqAnAppInBrowser
BscSeqAnAppInBrowser Possible Project for a BSc Thesis in Bioinformatics or Computer Science Introduction Since modern web browsers are used for all kinds of tasks ...
BscSeqAnOpenMSPeptideIndexer
Peptide Indexer using SeqAn and OpenMS Background In Proteomics one subtask for Peptide ID is to search peptide sequences in protein databases. This thesis shall ...
BscTreeBasedMapAlignment
BscTreeBasedMapAlignment B.Sc. topic proposal in high throughput proteomics Focus * Programming: ** * Math: ** * Biology: * Introduction LC MS data is ...
CalendarOrders
OUTDATED! Please use calendar orders at https://www.mi.fu berlin.de/w/Orga/CalendarOrders. Calendar Order Table Name DIN A 4, card board, 6 months on each side ...
CalenderOrders
Page CalendarOrders Calendar Order Table Name DIN A 4, card board, 6 months on each side large sized paper calendar, one year on one sheet (fits on door: 86x61 ...
CaptureCompoundMS
Devising read mapping strategies in KNIME Area Proteomics, label free quantitation, data bases Topic tbd. Timeline tbd References tbd.
Carsonella_reanotation
Page Reanotation of the genome of Carsonella Ruddii using non collinear methods Description will follow shortly Layout of project * Identification of a set of ...
r13 - 08 Jul 2010 - 22:35 by ivankel
ChipSeq
ChIP Seq Motivanalyse Konzept Bei der ChIP Seq Analyse werden die genomweiten Bindungsstellen von Transkriptionsfaktoren dadurch identifiziert, dass man die Transkriptionsfaktoren ...
ChipSeqAnalysis
MSc Thesis #8211; Analysis of protein DNA interactions from ChIP seq data Remark This thesis will be a joint project of the Algorithmische Bioinformatik group at ...
ChipSeqProfiles
Übersicht ChIP Seq ist eine Methode zur genomweiten Untersuchung von Protein DNA Interaktion 1 . Mit Hilfe von Antikörpern werden die Proteine von Interesse gemeinsam ...
ClinicalDegradomics
ClinicalDegradomics Background: Recent scientific advances, including sequencing of the genome and new approaches to modeling complex biological systems may ultimately ...
CodingTutorial
Page CodingTutorial Dieses Tutorial sollte euch an die OpenMS library heranführen damit ihr die Funktionalität und Konzepte kennenlernt. Am besten nutzt ihr folgende ...
CoffeeCoffeeCoffee
Page CoffeeCoffeeCoffee This page is world readable but can only be changed by .AgabiGroup, .AgseGroup. Kaffee Gedicht Kaffee, Kaffee, Kaffee, Kaffee, Kaffee, Kaffee ...
CombinatorialOptimization
Combinatorial Optimization Lectures Date Lecture* * Lecture Material Additional Material 20.1.2011 Constraint Programming ConstrProg.pdf ...
CombinatorialOptimizationWS11
Combinatorial Optimization Lectures Date Lecture* * Lecture Material Additional Material 19.01.2012 Constraint Programming ConstrProg.pdf Survey ...
CompMethodsWS11
Page CompMethodsWS11 In this seminar, we will focus on two different kinds of high throughput technologies: * second generation DNA sequencing * liquid chromatography ...
ComplexityAnalysis
Page ComplexityAnalysis Complexity analysis of algorithm sgip Algorithm sgip The major of our work focus on the generation of a family of distinguishing sets (some ...
ComputabilityComplexity
Date Lecture* * Lecture Material Additional Material 3.2.2011 Turing machines Comput1.pdf AdditionalMaterial 8.2.2011 Undecidable problems Comput2 ...
ComputabilityComplexityWS11
Computability and Complexity Theory Lectures Date Lecture* * Lecture Material Additional Material 02.02.2012 Turing machines Comput1.pdf 07.02.2012 ...
ConsultationsP4
Page ConsultationsP4 Bitte tragt euch hier einen Termin (~60 Minuten) in einem der angebotenen Zeitfenster ein. Bringt zu diesem Termin auch die schriftliche Ausarbeitung ...
r24 - 30 Jul 2009 - 14:28 by drefahl
CppAdvancedSS11
Fortgeschrittenenkurs C SS2011 Auf dieser Seite wird die Kurs Kommunikation stattfinden. Ebenso werden Skripte und Übungsaufgaben hier verfügbar gemacht. Skripte ...
CppAdvancedSS12
Fortgeschrittenenkurs C SS2012 Auf dieser Seite wird die Kurs Kommunikation stattfinden. Ebenso werden Skripte und Übungsaufgaben hier verfügbar gemacht. ...
CppIntroWS10
Page CppIntroWS10 Material zum C Kurs * sample.cpp: sample.cpp * Monday.pdf: Slides und Aufgaben für Montag * Tuesday.pdf: Slides und Aufgaben für Dienstag ...
CppIntroWS11
Page CppIntroWS11 Auf dieser Seite werden die Seminarfolien und Übungsaufgaben (letzte Seite im Skript) bereitgestellt Montag Skript, sample.cpp Dienstag ...
CppIntroWS12
Page CppIntroWS12 Auf dieser Seite werden die Seminarfolien und Übungsaufgaben (letzte Seite im Skript) bereitgestellt * Script_Montag.pdf * Script_Dienstag ...
CppLinks
Page CppLinks ((short description what this page is about)) * http://blog.knatten.org/2012/11/30/how to avoid includes in headers/ * http://visualstudiomagazine ...
DCLoadBalancingConceptualDraft
Parallelism In The SeqAn Library: 1D Load Balancing With Divide Conquer: Conceptual Draft Related to 1DLoadBalancingConceptualDraft . This part looks at the divide ...
DCStaticLoadBalancing
Parallelism In The SeqAn Library: 1D Load Balancing: Conceptual Draft forall(AlgorithmState state, DataSpec spec) if spec is a leaf then process(state ...
DeepCoffee
Extending SeqAn::TCoffe for deep alignments Area Mulitple Sequence Alignment Topic tbd. Timeline References 1. Rausch, T, Sergey Koren, Gennady Denisov, David ...
DfgWorkPackages
Page DfgWorkPackages This is the list of work packages from the DFG project. Design and verification of a suitable model for cross species genome compari son (3 ...
DiscretMathWS10
Page DiscretMathWS10 Welcome to the Wiki of the Lecture Discrete Mathematics News 23.3.2011 (Andreotti): Termin Nachklausur 15.4.2011, 12 14, SR006 Takustr. 9 1 ...
DiscretMathWS11
Page DiscretMathWS11 Welcome to the Wiki of the Lecture Discrete Mathematics News 6.7.2012 (Reinert): The results of the second exam are online. 29.3.2012 (Reinert ...
DraftS
Drafts * Rabema * RazerS2 * RazerS2Revision * Read Mapper Benchmarks * Fiona * Stellar * SearchJoin
EclipsePluging
BSc Thesis: Developing an Eclipse plugin for SeqAn Motivation SeqAn is an open source C library of efficient algorithms and data structures for the analysis of sequences ...
EventLocations
Event Locations A selection of full service locations for meetings, conferences, retreats, and of places to go for lunch/dinner or special events. For the organization ...
ExactMatching
Page ExactMatching Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: exact.pdf Übungen: Inhalt Datei Material Vorbereitende Übung ...
ExactMatchingWS11
Page ExactMatchingWS11 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: exact.pdf Übungen: Inhalt Datei Material Vorbereitende ...
ExactMatchingWS12
Page ExactMatchingWS12 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: exact.pdf Video: Hier das Vorlesungsvideo 1 Hier das Vorlesungsvideo ...
ExactMatchingWS13
Page ExactMatchingWS13 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: exact.pdf Video: Hier das Vorlesungsvideo 1 aus 2012. Hier das Vorlesungsvideo ...
ExactMatchingWS14
Page ExactMatchingWS14 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: exact.pdf Video: Hier das Vorlesungsvideo 1 aus 2012. Hier das Vorlesungsvideo ...
r9 - 23 Oct 2014 - 10:16 by denisethiel
ExamList
Time slots for oral examinations: Time Candidate 14:00 Hesse 14:20 Phieler 14:40 Schmoldt 15:00 Martens 15:20 Eckert 15:40 ...
ExamPreparation
Page ExamPreparation Rooms: 14:00 16:00 Arnimallee 6 SR 031 16:00 18:00 Takustr. 9 R 006 Questions and topics Please put your questions or things you want to ...
r6 - 09 Feb 2012 - 19:12 by elamrani
ExerciseStore
Page ExerciseStore This page is supposed to be the upload area for the solutions you worked out in groups. Please also check solutions of other groups and test whether ...
r6 - 09 May 2012 - 08:44 by secutor
Expose
Page Expose An expose for the Master's Thesis: "Journal Set: A container for utilizing Incremental Index Structures". Abstract In this Master's Thesis the concepts ...
FMIndex
Page FMIndex TITLE TITLE Student Jochen Singer Academic Advisor Prof. Dr. Knut Reinert, David Weese Expose Recent developments in the field of DNA ...
FMIndexThesis
FM Index in Seqan
FMTree
Improving Location Algorithms in FM indices Implementation of FMtrees A recently published paper improves the location time (retrieving positions in the text) for ...
Flexbar
Flexbar Flexbar (flexible barcode and adapter removal) ist eine Software für das Postprocessing von Next Generation Sequencing Reads. Sie Umfasst die Funktionen ...
r13 - 16 Sep 2013 - 12:43 by serosko
FormalLanguages
Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * languages.pdf Literatur: Übungen: Inhalt Datei Material 12. Übung ...
FormalLanguagesWS11
Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * languages.pdf Übungen: Inhalt Datei Material 11. Übung A11.pdf ...
FormalLanguagesWS12
Page FormalLanguagesWS12 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * languages.pdf Videos: * Vorlesungsvideo Formale Sprachen ...
FormalLanguagesWS13
Page FormalLanguagesWS13 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * languages.pdf Videos: * Vorlesungsvideo Formale Sprachen ...
r2 - 23 Jan 2014 - 12:43 by thwelln31416
FormalLanguagesWS14
Page FormalLanguagesWS14 Vorlesung Skript: script Videos: Hier das Vorlesungsvideo aus 2012. Inhalt Datei Material zehnte Übung A10.pdf elfte ...
r3 - 15 Jan 2015 - 13:38 by denisethiel
ForumSpace
Page ForumSpace Thsi page will be the discussion forum. Lecture 1 REINERT (30.4): Hier könnte eine ausgearbeitetere Version der Vorlesungsabfolge stehen. Oder ...
ForumSpaceP2
Page ForumSpaceP2 This page will be the discussion forum. Comments to the proposal talk on April 21 Here are some additional comments that haven't been made in the ...
r5 - 07 May 2010 - 07:40 by FelixHeeger
GeneExpression
Gene expression Vorlesungen Date Lecture* *Materials 2.1.2012 Gene expression technology microarrays.pdf 4.1.2012 Normalization and differential ...
r4 - 24 Jan 2012 - 21:22 by rokrause
GeneMotif
Genefinding and motif search Vorlesungen Date Lecture* *Materials 09.11.2011 Genefinding genefinding.pdf 14.11.2011 Motif seach I (discrete methods ...
r7 - 22 Nov 2011 - 08:58 by rokrause
GenomeAssembly
Genome assembly Vorlesungen Date Lecture* *Materials 05.12.2011 WGA 1 assembly.pdf 07.12.2011 WGA 2 12.12.2011 WGA 3 14.12.2011 ...
r3 - 02 Jan 2012 - 12:21 by jpp
GenomeComparisonGroup
GenomeComparisonGroup: TWiki access control group for Genome Comparison Research log * Set GROUP = Main.BirteKehr, Main.KnutReinert, Main.DavidWeese, Main.ManuelHoltgrewe ...
GenomeComparisonP4
Page GenomeComparisonP4 This is the project page of the Genome Comparison group. Students Mail an alle Gruppenmitglieder: AA2010SS GenComp bei lists.spline.de Name ...
r39 - 19 Jul 2010 - 16:50 by homilius
GenomeEvolutionSimulator
MSc Thesis: Simulation of Genomes and Genome Evolution Also see the attached PDF file with figures. Motivation The explosion of the availability of genomic data over ...
Genomics12
Page Genomics12 Welcome to the Wiki of the MSc lecture Genomics. News The 2nd exam will be on May 13th (Monday), 10 12h, room 049 / Takustr. 9 Bonus Review: There ...
Genomics13
Page Genomics13 Welcome to the Wiki of the MSc lecture Genomics (19711 CUB848/CUB849). News Nachklausur: : The 2nd exam will be oral. It will be on April 1st ...
Genomics14
Genomics (WiSe 2014) Welcome to the Wiki of the MSc lecture Genomics (CUB848/CUB849). News * (...) General Information SWS: 2 2 ECTS: Lecturer: Peter Robinson ...
GenomicsLecture10Materials
Page GenomicsLecture10Materials Download lecture slides: structural variation.pdf
NEW - 27 Dec 2012 - 18:39 by probins
GenomicsLecture10MaterialsWS13
GenomicsLecture10MaterialsWS13 ((short description what this page is about)) Section 1 ((content)) Section 2 ((content)) Comments
NEW - 11 Jan 2014 - 13:32 by hamid24
GenomicsLecture12Materials
* rnaseq1.pdf: rnaseq1.pdf
NEW - 15 Jan 2013 - 10:13 by probins
GenomicsLecture13Materials
Lecture slides: * rnaseq2.pdf: rnaseq2.pdf
NEW - 22 Jan 2013 - 11:34 by probins
GenomicsLecture14Materials
Page GenomicsLecture14Materials ((short description what this page is about)) * chipseq.pdf: chipseq.pdf
NEW - 30 Jan 2013 - 12:46 by probins
GenomicsLecture15Materials
Page GenomicsLecture15Materials ((short description what this page is about)) * chipseq2.pdf: chipseq2.pdf
NEW - 06 Feb 2013 - 12:11 by probins
GenomicsLecture1Materials
Here is all the material for the lecture unit 1, lecture 1 The lecture introduces you to the basic sequencing techniques used in genomics analysis. * Download Script ...
r3 - 21 Oct 2012 - 17:14 by dim
GenomicsLecture1MaterialsWS13
GenomicsLecture1MaterialsWS13 ((short description what this page is about)) Section 1 ((content)) Section 2 ((content)) Comments
NEW - 20 Oct 2015 - 10:44 by wangxuesong
GenomicsLecture2Materials
Here is all the material for the lecture unit 1, lecture 2 * Download the script
GenomicsLecture2MaterialsWS13
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GenomicsLecture3Materials
Here is all the material for the lecture unit 1, lecture 3 * Watch a previous lecture as a video: HD (about 0.5 GB or in lower res. * Download the script ...
GenomicsLecture3MaterialsWS13
Here is all the material for the lecture unit 1, lecture 3 * Watch a previous lecture as a video: HD (about 0.5 GB or in lower res. * Download the script
GenomicsLecture4Materials
Here is all the material for the lecture unit 1, lecture 4 * Watch a previous lecture as a video: HD or in lower res * Download the script * Download the Exercises ...
GenomicsLecture4MaterialsWS13
Here is all the material for the lecture unit 1, lecture 4 * Watch a previous lecture as a video: HD or in lower res * Download the script
GenomicsLecture5Materials
Here is all the material for the lecture unit 1, lecture 5 * Watch a previous lecture as a video: HD or in lower res * Download the script * Download the Exercises ...
GenomicsLecture5MaterialsWS13
Here is all the material for the lecture unit 1, lecture 5 * Watch a previous lecture as a video: HD or in lower res * Download the script
GenomicsLecture6Materials
Here is all the material for the lecture unit 2, lecture 1 * Download the script * Exercises are in the lecture unit 2, lecture 2
r2 - 30 Nov 2012 - 19:14 by dim
GenomicsLecture6MaterialsWS13
Here is all the material for the lecture * Download the script
GenomicsLecture7Materials
Here is all the material for the lecture unit 2, lecture 2 * Download the script * Genomics Exercise 6.pdf: 6th Exercise sheet
r2 - 30 Nov 2012 - 19:15 by dim
GenomicsLecture7MaterialsWS13
Slides for Variant Calling 21: available from https://compbio.charite.de/contao/index.php/genomics.html
r2 - 29 Nov 2013 - 14:22 by probins
GenomicsLecture8Materials
Page GenomicsLecture8Materials Here is all the material for lecture 8, variant calling * Download the script * Download the Exercises ((short description what ...
r2 - 14 Dec 2012 - 11:17 by probins
GenomicsLecture8MaterialsWS13
Slides for Variant Calling 1: * varcall 2013 A.pdf: varcall 2013 A.pdf * Genomics Exercise VarCall 1.pdf: Genomics Exercise VarCall 1.pdf
GenomicsLecture9Materials
Page GenomicsLecture9Materials The script (lecture notes) for lectures 8/9 can be found on the wikipage for lecture 8. In that lecture, additional material about ML ...
GraphAlgorithms
Graph algorithms Lectures Date Lecture* * Lecture Material Additional Material 16.11.2010 Shortest paths ShortestPaths.pdf L. Schrijver, Combinatorial ...
GraphAlgorithmsWS11
Graph algorithms Lectures Date Lecture* * Lecture Material Additional Material 15.11.2011 Shortest paths ShortestPaths.pdf L. Schrijver, Combinatorial ...
GroupList
Page GroupList Enter the account names of your group into one of the two tables for the practical exercises in the first programming exercise week. Form groups of ...
GuineaPigAnnotation
Timeline: * Week one: Preparation of the data (Matepairs, Illumina) for mapping, plus evaluation of the Matepair library quality. Choose suitable mapping programs ...
Here
Weekly Report Weekly reports about this master thesis. Week 1 (24.05.2010 30.05.2010) Comments
HiddenMarkovModels
Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * hmms.pdf Literatur: Übungen: Inhalt Datei Material 14. Übung A14.pdf ...
HiddenMarkovModelsWS11
Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * hmms.pdf Übungen: Inhalt Datei Material 13. Übung A13.pdf
HiddenMarkovModelsWS12
Page HiddenMarkovModelsWS12 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * hmms.pdf Videos: * Vorlesungsvideo HMMs I * Vorlesungsvideo ...
HiddenMarkovModelsWS13
Page HiddenMarkovModelsWS13 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * script.pdf: script.pdf Übungen: Inhalt Datei Material ...
r2 - 30 Jan 2014 - 15:03 by thwelln31416
HiddenMarkovModelsWS14
Page HiddenMarkovModelsWS14 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * script.pdf: script.pdf * slides.pdf: slides.pdf Inhalt ...
r3 - 29 Jan 2015 - 13:08 by denisethiel
HmmEm
HMMs Vorlesungen Date Lecture* *Materials 02.11.2011 HMMs I hmms em.pdf 07.11.2011 HMMs II 09.11.2011 HMMs III: see above Übungen ...
HowToImproveYourWriting
How To Improve Your Slides, Articles etc. This document aims to help to circumvent some pitfalls in data presentation and creating scientific articles and slides. ...
InitialSetup
Content according to Studienordnung Es werden vertieft Themen aus folgenden Gebieten behandelt: * Verfahren für exaktes und approximatives Suchen in Strings, Filter ...
IntegerLinearOptimization
Lectures Date Lecture* *Materials 16.12.2010 Branch and Cut Intro b and c.pdf, Webpage http://www2.iwr.uni heidelberg.de/groups/comopt/software/PORTA ...
IntegerLinearOptimizationWS11
Combinatorial optimization and integer linear programming Lectures Date Lecture* *Materials 15.12.2011 Combinatorial Optimization ILP Introduction ...
JMatch
In diesem Praktikum geht es um die Erstellung von Software, um die Bindungsstellen von Transkriptionsfaktoren in DNA Sequenzen zu identifizieren und die Auswirkung ...
JournalClubS15
Journal Club, SoSe 2015 (19401311) Welcome to the Wiki of the Journal Club In this seminar we will present original work in Computational biology as well as progress ...
JournalClubS16
Journal Club, SoSe 2016 (19402911, vormals 19401311) Welcome to the Wiki of the Journal Club In this seminar we will present original work in Computational biology ...
JournalClubSS11
Page JournalClubSS11 Welcome to the Wiki of the Journal Club In this seminar we will present original work in Computational biology as well as progress reports from ...
JournalClubSS12
Page JournalClubSS12 Welcome to the Wiki of the Journal Club In this seminar we will present original work in Computational biology as well as progress reports from ...
JournalClubSS13
Page JournalClubSS13 Welcome to the Wiki of the Journal Club In this seminar we will present original work in Computational biology as well as progress reports from ...
r24 - 10 Jul 2013 - 13:15 by mauli87
JournalClubSS14
Journal Club, SoSe 2014 (19576b) Welcome to the Wiki of the Journal Club In this seminar we will present original work in Computational biology as well as progress ...
JournalClubW15
Journal Club (WiSe 2015) Welcome to the Wiki of the Journal Club (19402911) In this seminar we will present original work in Computational biology as well as progress ...
JournalClubWS10
Page JournalClubWS10 Welcome to the Wiki of the Journal Club In this seminar we will present original work in Computational biology as well as progress reports from ...
JournalClubWS11
Page JournalClubWS11 Welcome to the Wiki of the Journal Club In this seminar we will present original work in Computational biology as well as progress reports from ...
JournalClubWS12
Page JournalClubWS12 Welcome to the Wiki of the Journal Club In this seminar we will present original work in Computational biology as well as progress reports from ...
r20 - 18 Feb 2013 - 09:58 by lecram87
JournalClubWS13
Page JournalClubWS13 Welcome to the Wiki of the Journal Club (19576b) In this seminar we will present original work in Computational biology as well as progress reports ...
r22 - 07 Feb 2014 - 12:50 by TemesgenDadi
JournalClubWS14
Journal Club (WiSe 2014) Welcome to the Wiki of the Journal Club (19401311) In this seminar we will present original work in Computational biology as well as progress ...
Knime
https://www.mi.fu berlin.de/w/ABI/Knime
KnimeSec
General info n this part of the Practical course sequence analysis you will be confronted with the situation of integrating several NGS analysis programs (which you ...
KrakauReport
Page KrakauReport Mai week 1 * Worked my way into Mason * Developed draft of bs read simulator based on Mason week 2 * Implementing simulator June ...
KrakauWeeklyReport
Page KrakauWeeklyReport Mai June July Comments
LaganHome
LaganHome Projektplanung und Umsetzung zur Implementierung von LAGAN Projektplan und Aufteilung 1. Start: Einlesen von FastA Dateien (Moritz) 2. Diese soll stellar ...
r11 - 16 May 2013 - 16:20 by kiekemo
LaganSeqan2018
LArge Genome AligNer (LAGAN) Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntnisse ...
NEW - 13 Apr 2018 - 11:26 by jwinkler
LastImplementation
Implementation of LAST with gapped seeds and applications to read mapping and local alignment Area Substring Indices, read mapping, local alignment Topic The goal ...
LeckerSchmecker
Restaurant Recommendations A collection of restaurant recommendations. You are welcome to add more recommendations. * See also: Restaurants Cafés in Event Locations ...
Lecture10Materials
Here is all the material for the lecture unit 3, lecture 4 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * For the script see previous ...
Lecture10MaterialsOptWS12
Below you find material for the lecture: * script : lagrange.pdf
Lecture10MaterialsOptWS13
Below you find material for the lecture: * script : rna_lagrange,lara2.pdf.gz
Lecture10MaterialsOptWS14
Below you find material for the lecture: * script : rna_lagrange,lara2.pdf.gz
Lecture11Materials
Here is all the material for the lecture unit 3, lecture 5 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * For the script see here ...
Lecture11MaterialsOptWS12
Here is all the material for the lecture 11 * Download the slides * Recommended reading: article by Lustig/Puget (2001)
Lecture11MaterialsOptWS13
Below you find material for the lecture: * script : CP1.pdf:
NEW - 30 Jan 2014 - 15:43 by anduryl
Lecture11MaterialsOptWS14
Here is all the material for the lecture 11 * Download the slides * Recommended reading: article by Lustig/Puget (2001)
Lecture12Materials
Here is all the material for the lecture unit 4, lecture 1 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * For the script see here ...
Lecture12MaterialsOptWS12
Here is all the material for the lecture 12 * Download the slides * Recommended survey article: Sect.2.4 2.5, Sect.3
Lecture12MaterialsOptWS13
Below you find material for the lecture: * script : CP2.pdf:
NEW - 30 Jan 2014 - 15:43 by anduryl
Lecture12MaterialsOptWS14
Here is all the material for the lecture 12 * Download the slides
Lecture13Materials
Here is all the material for the lecture unit 5, lecture 2 * Watch lecture as a video: Watch lecture as a video: here * For the script see here
Lecture13MaterialsOptWS12
Here is all the material for the lecture 13 * Download the slides * Recommended survey article: Sect.2
Lecture13MaterialsOptWS13
Below you find material for the lecture: * script : CP IP.pdf:
NEW - 30 Jan 2014 - 15:44 by anduryl
Lecture13MaterialsOptWS14
Here is all the material for the lecture 13 * Download the slides * Recommended survey article
Lecture14Materials
Here is all the material for the lecture unit 5, lecture 3 * For the script see here
Lecture14MaterialsOptWS12
Here is all the material for the lecture 14 * Download the slides * Recommended survey article
Lecture14MaterialsOptWS14
Here is all the material for the lecture 14 * Download the slides * Recommended survey article
Lecture15Materials
Here is all the material for the lecture unit 5, lecture 4 * For the script see here
Lecture15MaterialsOptWS12
Here is all the material for the lecture 15 * Download the slides * Additional material: Article Data
Lecture15MaterialsOptWS14
Here is all the material for the lecture 15 * Download the slides * Additional material: Article Data
Lecture16Materials
Here is all the material for the lecture unit 4, lecture 2 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * For the script see here ...
Lecture17Materials
Here is all the material for the lecture unit 5, lecture 1 * Watch lecture as a video: The video file was unfortunately corrupted. * For the script see here ...
Lecture1Materials
Here is all the material for the lecture 1 * Download the slides
Lecture1MaterialsOptWS12
Here is all the material for the lecture 1 * Download the slides * Additional material: Kolman/Beck, Linear programming, Chap.1.3 1.4 (click on pdf)
Lecture1MaterialsOptWS13
Here is all the material for the lecture unit 1, lecture 1 * Download the script
NEW - 09 Dec 2013 - 15:48 by anduryl
Lecture1MaterialsOptWS14
Here is all the material for the lecture 1 * Download the slides * Additional material: Kolman/Beck, Linear programming, Chap.1.3 1.4 (click on pdf)
Lecture2Materials
Here is all the material for the lecture unit 1, lecture 2 * Watch lecture as a video: HD (about 0.5 GB or in lower res. * Download the script * Download ...
Lecture2MaterialsOptWS12
Here is all the material for the lecture 2 * Download the slides
Lecture2MaterialsOptWS13
Lecture2MaterialsOptWS13 ((short description what this page is about)) Section 1 ((content)) Section 2 ((content)) Comments Hafiz Muhammad Hamid Main.hamid24 ...
NEW - 18 Dec 2013 - 18:36 by hamid24
Lecture2MaterialsOptWS14
Here is all the material for the lecture 2 * Download the slides
Lecture3Materials
Here is all the material for Lecture 3 * Download script (see Lecture 2). * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.1.1 1.3)
Lecture3MaterialsOptWS12
Here is all the material for the lecture 3 * Download the slides
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Lecture4Materials
Here is all the material for Lecture 4 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.4.2 4.4)
Lecture4MaterialsOptWS12
Here is all the material for the lecture 4 * Download the slides
Lecture4MaterialsOptWS14
Here is all the material for the lecture 4 * Download the slides
Lecture5Materials
Here is all the material for Lecture 5 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.3.1,3.2,3.4)
Lecture5MaterialsOptWS12
Below you find material for the lecture: * script : comb_opt.pdf
Lecture5MaterialsOptWS13
Below you find material for the lecture: * script : combopt.pdf:
Lecture5MaterialsOptWS14
Below you find material for the lecture: * script : combopt.pdf
Lecture6Materials
Here is all the material for the lecture unit 2, lecture 3 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * Download the script ...
Lecture6MaterialsOptWS12
Below you find material for the lecture: * script : see Lecture 1
Lecture6MaterialsOptWS13
Below you find material for the lecture: * script : siehe lecture 1
Lecture6MaterialsOptWS14
for the script see lecture 5.
Lecture7Materials
Here is all the material for the lecture unit 3, lecture 1 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * Download the script
Lecture7MaterialsOptWS12
Below you find material for the lecture: * script : see Lecture 1
Lecture7MaterialsOptWS13
Below you find material for the lecture: * script : siehe lecture 1
Lecture7MaterialsOptWS14
for the script see lecture 5.
Lecture8Materials
Here is all the material for the lecture unit 3, lecture 2 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * Download the script
Lecture8MaterialsOptWS12
Below you find material for the lecture: * script : see Lecture 1
Lecture8MaterialsOptWS13
Below you find material for the lecture: * script : siehe lecture 1
Lecture8MaterialsOptWS14
for the script see lecture 5.
Lecture9Materials
Here is all the material for the lecture unit 3, lecture 3 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * Download the script
Lecture9MaterialsOptWS12
Below you find material for the lecture: * script : lagrange.pdf
Lecture9MaterialsOptWS13
Below you find material for the lecture: * script : lagrange.pdf * chapter_lagrange.pdf
Lecture9MaterialsOptWS14
Below you find material for the lecture: * script : lagrange.pdf * chapter_lagrange.pdf
LectureSchedule
Week/session Date Content People in charge 1/1 2010/04/12 Project A: Proposal of project by students Team, Instructors A 1/2 Project A: Proposal ...
LectureWiki
OUT OF USE! Go to: https://kvv.imp.fu berlin.de/portal/ * SS 2018 * PMSB SeqAn * SS 2017 * PMSB SeqAn * SS 2016 * Journal Club * Sequence ...
LinearOptimization
Linear optimization Lectures Date Lecture* * Lecture Material Additional Material 30.11.2010 Optimization problems OptProbl.pdf AdditionalMaterial ...
LinearOptimizationWS11
Linear Optimization Lectures Date Lecture* * Lecture Material Additional Material 29.11.2010 Optimization problems Optprobl.pdf Additional Material ...
ListOfStudents
Name email laptop Kersten Döring kdoering #64;zedat.fu berlin.de YES Christoph Standfuß christoph.standfuss #64;inf.fu berlin.de YES Max ...
MCRazerToDo
MCRazerToDo 1 For Herrn Kleffe: * script to parallelize by reads with normal version * don't do all reads at a time: go over contig with some read ...
r11 - 17 Mar 2010 - 08:37 by mriese
May2011
Page May2011 Progress report Accomplishments in the last six months: General: * CNV detection in exome sequencing developed R/C HMM script for finding windows ...
MethylationMapping
Multi Split Mapping of NGS reads for variant detection Student Sabrina Krakau Academic Advisor Prof. Dr. Knut Reinert, Anne Katrin Emde Expose The goal of ...
ModifiedTrypticMasses
Computing masses of modified peptides (Email Hartmut Schlüter) Das Tool soll in der Lage sein die Massen von tryptischen Peptiden zu berechnen, die definierte Modifizierungen ...
MultiReadAssignment
Solving the Multi read assignment problem Description This thesis should provide new ideas to solve the problem of multi read assignment for NGS data. Based on ...
r7 - 06 Jul 2011 - 12:16 by SvenLeonKuchenbecker
MultiReadAssignments
Page MultiReadAssignments This project will check the quality of mapper(s) concerning the multi reads assignment. Schedule * Generate random sequence OR get an ...
r2 - 16 Jun 2010 - 12:42 by dangad
MultiSplitMappingNGS
Multi Split Mapping of NGS reads for variant detection Student Kathrin Trappe Academic Advisor Prof. Dr. Knut Reinert, Anne Katrin Emde Expose The goal of ...
MultipleAlignment
Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * multipleAlignment.pdf Literatur: * Sequence Comparison Kapitel 5 * Sequence Comparison ...
MultipleAlignmentWS11
Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * multal.pdf
r2 - 05 Jan 2012 - 13:41 by hartnamn
MultipleAlignmentWS12
Page MultipleAlignmentWS12 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * multal.pdf * tcoffee.pdf Videos: * Vorlesungsvideo ...
r6 - 07 Jan 2013 - 15:38 by Krannich479
MultipleAlignmentWS13
Page MultipleAlignmentWS13 Vorlesung Skript: * multal1.pdf: multal1.pdf * multal2.pdf: multal2.pdf Videos: Übungen: Inhalt Datei Material Achter ...
r6 - 16 Jan 2014 - 10:16 by thwelln31416
MultipleAlignmentWS14
Page MultipleAlignmentWS14 Vorlesung Skript: * script Videos: Hier das Vorlesungsvideo aus 2012 zu TCoffee. Inhalt Datei Material achte Übung A8 ...
r3 - 18 Dec 2014 - 14:22 by denisethiel
NewHMMLearningAlgorithms
MSc Thesis: Faster HMM Learning with Indexing Structures Motivation Hidden Markov Models (HMMs) are among the most prominent methods in Bioinformatics. They are routinely ...
NonTrypticPeptides
Analysis of Non Tryptic peptides (Email Hartmut Schlüter) Im Plasma kommen viele Peptide vor, die "nicht tryptisch" sind, d.h. diese Peptide wurden von anderen Proteasen ...
NormEditDist
PISB SeqAn Projekt Normalised Edit Distance Hintergrund: Normalisierte Edit Distanz Die Edit Distanz ist ein Standarddistanzmaß für Sequenzalignments, Mappings ...
OfficeChairs
Office Furniture Hardware / Büroeinrichtung Technik Office Chairs / Bürostühle Room No. total number of chairs how many are flawed/need replacement ...
OfficeEquipment
OUTDATED! Do not use. Office Furniture Hardware / Büroeinrichtung Technik Office Chairs / Bürostühle Room No. total number of chairs *how many are flawed ...
OldContent
Online String Searching and Filtering 11.04. 06.05. Index Data Structures 09.05. 30.05. Review 1 11.05. Genome Comparison and RNA Analysis 03.06 ...
OptimizationWS12
Page OptimizationWS12 Welcome to the Wiki of the MSc lecture Optimization. News (27.3.2013)The 2nd exam (together with Discrete Mathematics for Bioinformatics ...
OptimizationWS13
Page OptimizationWS13 Welcome to the Wiki of the MSc lecture Optimization (19182). News Update Klausurnoten Klausureinsicht 2. Prüfung : 30 April 2014, 9 ...
r38 - 09 Dec 2015 - 16:02 by AnnikaRoehl
OptimizationWS14
Optimization (WiSe 2014) Welcome to the Wiki of the MSc lecture Optimization (VL: 19400701, UE: 19400702) News * Results of 2nd exam are online General Information ...
r41 - 19 Jan 2017 - 11:02 by AnnikaRoehl
P4Projects
Page P4Projects Material Please download the template cmake project and use it for four project. In the Readme file you should find all the information you need to ...
PMSB_OpenMS_2011
Projektmanagement im Softwarebereich OpenMS 2011 Wiki Seite zum Praktikum Projektmanagement im Softwarebereich OpenMS 2011. Zeitplan 01.04.2011 (10.00 Uhr) ...
PMSB_OpenMS_2012
Projektmanagement im Softwarebereich OpenMS 2012 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich OpenMS. Projektgruppen ...
PMSB_Seqan_2010
Projektmanagement im Softwarebereich Seqan 2010 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich Seqan. Aufteilung auf die ...
PMSB_Seqan_2011
Projektmanagement im Softwarebereich Seqan 2011 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich Seqan. Aufteilung auf die ...
PMSB_Seqan_2012
Projektmanagement im Softwarebereich SeqAn 2012 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich SeqAn. Teilnehmer Name ...
PMSB_Seqan_2013
Projektmanagement im Softwarebereich SeqAn 2013 Dies ist die Wiki Seite zum Praktikum Projektmanagement im Softwarebereich SeqAn. Alle Zeiten sind s.t. also wie ...
r47 - 11 May 2015 - 08:43 by kiekemo
PMSB_Seqan_2014
Projektmanagement im Softwarebereich, SoSe 2014 (19588a und 19588b) * Einführung in Software Engineering am Freitag entfällt leider! Dies ist die Wiki Seite ...
PMSB_Seqan_2015
Projektmanagement im Softwarebereich, SoSe 2015 (19401511 (S) und 19401513 (P)) Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" SeqAn ...
PMSB_Seqan_2016
Projektmanagement im Softwarebereich, SoSe 2016 (19401511 (S) und 19401513 (P)) Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" SeqAn ...
PMSB_Seqan_2017
Projektmanagement im Softwarebereich, SoSe 2017 (19401511 (S) und 19401513 (P)) Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" SeqAn ...
PMSB_Seqan_2018
Projektmanagement im Softwarebereich, SoSe 2018 Dies ist die Wiki Seite zum Praktikum "Projektmanagement im Softwarebereich" SeqAn für BSc Studenten. Alle Zeiten ...
PSMB_Seqan_2013_BlastX
Page PSMB_Seqan_2013_BlastX Hintergrund: NGS Daten in Proteindatenbanken Next Generation Sequencing (NGS) Daten werden heute für unterschiedlichste Aufgaben verwendet ...
PSMB_Seqan_2013_Lagan
Page PSMB_Seqan_2013_Lagan Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntnisse ...
PSMB_Seqan_2013_NGS_Data_Cleansing
NGS Data Postprocessing Hintergrund Als Next Generation Sequencing (NGS) oder auch High Througput Sequencing (HTS) bezeichnet man Sequenzierverfahren, die in vergleichsweise ...
r2 - 12 Apr 2013 - 09:14 by SvenLeonKuchenbecker
PSMB_Seqan_2013_NGS_Data_Cleansing_New
NGS Data Postprocessing Hintergrund Als Next Generation Sequencing (NGS) oder auch High Througput Sequencing (HTS) bezeichnet man Sequenzierverfahren, die in vergleichsweise ...
r2 - 12 Apr 2013 - 08:27 by SvenLeonKuchenbecker
PSMB_Seqan_2013_NGS_Data_Cleansing_Progress
Progress "NGS Data Postprocessing" Projektplan Datum Wer Ziel erreicht 29.04. Sebastian Input / Parsing X 29.04. Benjamin Read Trimming ...
r10 - 22 May 2013 - 08:26 by serosko
PSMB_Seqan_2013_NGS_Quality_Control
Page PSMB_Seqan_2013_NGS_Quality_Control Hintegrund: NGS Quality Control Als Next Generation Sequencing (NGS) oder auch High Througput Sequencing (HTS) bezeichnet ...
r6 - 19 Apr 2013 - 04:59 by olfrik
PSMB_Seqan_2013_NGS_Quality_Control_Details_Features
PSMB_Seqan_2013_NGS_Quality_Control_Details_Features Our application will read fastq files and collect statistical data about its content. The input itself will not ...
r3 - 25 Apr 2013 - 10:00 by dkersting
PSMB_Seqan_2013_PEMer
Page PSMB_Seqan_2013_PEMer PEMer overview, Figure 1 from (Korbel et al., 2009). Hintergrund: Paired End Signaturen und Strukturvarianten Als Strukturvarianten bezeichnet ...
r7 - 07 May 2013 - 10:32 by zer
PSMB_Seqan_2013_Suboptimal_Alignments
Page PSMB_Seqan_2013_Suboptimal_Alignments Hintergrund: Suboptimale Alignments Lokale Alignments sind eine mächtige Methode um Sequenzhomologien zwischen zwei Sequenzen ...
PSMB_Seqan_2013_UBlast
Schnelle Blastsuche durch Datenbank Clustering Hintergrund: Der Vergleich von Next Generation Sequencing (NGS) Daten gegen DNA oder Proteindatenbanken gehoert mittlerweile ...
r3 - 12 Apr 2013 - 12:13 by SvenLeonKuchenbecker
PSMB_Seqan_2013_UBlast_Progress
Progress "Schnelle Blastsuche durch Datenbank Clustering" Projektplan Datum Wer Ziel erreicht 01.05. Hannes GScore mit LocalAlignEnum für cluster ...
PSMB_Seqan_2014_SNP_caller
PSMB_Seqan_2014_SNP_caller Hintergrund Die häufigste und kleinste mögliche genomische Variation ist der Single Nucleotide Polymorphism. Nach dem Mapping von Reads ...
PSMB_Seqan_2014_large_insertd
PSMB_Seqan_2014_large_insertd Hintergrund Lange Sequenzstücke, die im Donor aber nicht in der Referenz enthalten sind, lassen sich nur schwer mit einzelnen Reads ...
r6 - 12 May 2014 - 06:59 by jobau
PSMB_Seqan_2014_mapper
PSMB_Seqan_2014_mapper Hintergrund Der erste Schritt ein einer Pipeline zur Analyse von Genomvarianten ist das Read Mapping. Dabei soll für jeden NGS Read eigentlich ...
PSMB_Seqan_2014_overview
PSMB_Seqan_2014_overview Im PSMB SeqAn 2014 geht es darum, eine einfach Pipeline zur Variantenanalyse aufzubauen. Hintergrund Insbesondere für das menschliche Genom ...
PSMB_Seqan_2014_small_indels
PSMB_Seqan_2014_small_indels Hintergrund Neben SNPs sind kleine Insertionen und Deletionen (indels) eine Klasse wichtiger genomischer Varianten. Für die Suche solcher ...
PSMB_Seqan_2015_p2
Page PSMB_Seqan_2015_p2 Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntnisse bez ...
PSMB_Seqan_2015_p3
PSMB_Seqan_2015_p3 Einleitung Eines der bekanntesten und meist genutzten Programme im Kontext der Bioinformatik ist NCBI Blast. Blast ist ein heuristisches Tool zum ...
PSMB_Seqan_2015_p4
PSMB_Seqan_2015_p4 Introduction Trypsin is a serine protease found in the digestive system of many vertebrates, where it hydrolyses proteins. It cleaves peptide chains ...
PSMB_Seqan_2015_p5
PSMB_Seqan_2015_p5 Introduction The q gram(k mer) Index in seqan allows looking up k mers over the index in constant time. However it has two limitations. The first ...
r12 - 26 Mar 2015 - 18:34 by cxpan
PSMB_Seqan_2015_palign
PSMB_Seqan_2015_palign Einleitung Paarweise Sequenzalignments liefern wertvolle biologische Informationen über die Identität zweier Sequenzen. Entsprechend ...
PSMB_Seqan_2016_p1
PSMB_Seqan_2016_p1 PMSB Project with possible Bachelor Project. Some experience with Javascript is required, some experience with C or C is recommended. Introduction ...
PSMB_Seqan_2016_p2
Assessment of off target effects of non coding RNAs Bioinformatics or computational biology is one of the fast growing and most exciting fields in science. Through ...
r3 - 27 Jan 2016 - 18:16 by kjk
PSMB_Seqan_2016_p3
PSMB_Seqan_2016_p3 Hintergrund Der erste Schritt ein einer Pipeline zur Analyse von Genomvarianten ist das Read Mapping. Dabei soll für jeden NGS Read eigentlich ...
PSMB_Seqan_2016_p4
PSMB_Seqan_2016_p4 In this project you will implement the typical Needleman Wunsch Algorithm, but with a few twists that will hopefully allow "auto vectorization" ...
PSMB_Seqan_2016_p5
Add BAM support to SeqAn SequenceFile In this project you will be asked to write an interface that will help the Sequence IO of SeqAn to seamlessly read SAM/BAM files ...
r2 - 28 Jan 2016 - 16:35 by TemesgenDadi
PSMB_Seqan_2016_p6
LArge Genome AligNer (LAGAN) Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntnisse ...
PSMB_Seqan_2017_p1
Assessment of off target effects of non coding RNAs Bioinformatics or computational biology is one of the fast growing and most exciting fields in science. Through ...
NEW - 08 Feb 2017 - 10:28 by kjk
PSMB_Seqan_2017_webassembly
PSMB_Seqan_2017_webassembly PMSB Project at the intersection of C , High performance computing and modern web technologies. Has the possibility to be continued as ...
PSMB_Seqan_IBF
Auswertugn von Binning directories mit Hilfe von Interleaved Bloom filters Hintergrund: Filtern von NGS reads in bins In dem projekt soll (zufällig generierte) ...
PSMB_Seqan_MF
In this project a simple motif discovery algorithm should be implemented in SeqAn. Background The goal of motif finding is the detection of novel, unknown signals ...
PSMB_Seqan_fft
Detection of homologous regions with FFT Given a set of sequences your task is to compute homologous segments for all pairs of the input set. The detection of homologous ...
r2 - 13 Feb 2018 - 15:00 by troja
ParallelSuffixArray
Parallel Suffix Array Construction Area Substring Indices Topic Das Suffix Array speichert die Anfänge aller Suffixe eines (oder mehrerer) Texte in lexikographischer ...
PhylogeneticAnalsysis
Phylogenie News Skript wird nach der Vorlesung aktualisiert. Abweichungen zwischen Material der Vorlesung und aktuellem Skript halten sich in Grenzen. Vorlesungen ...
r12 - 01 Nov 2011 - 10:59 by rokrause
Phylogeny
Vorlesungen Phylogenetische Analyse Date Lecture* *Materials 16.12.2010 Branch and Cut Intro b and c.pdf, Webpage http://www2.iwr.uni heidelberg.de ...
PiSWS10
Projektmanagement im Softwarebereich (WS 10/11) An fünf Terminen im Wintersemester finden jeweils 14 Uhr Veranstaltungen als Vorbereitung auf das eigentliche Softwarepraktikum ...
Praktikum
Praktikum Das Blockpraktikum findet vom 5.12. bis 16.12.2011 statt. Der Bericht ist bis zum 23.12.2011 per Mail an rokrause #64;fu berlin.de einzureichen Zuteilung ...
r9 - 07 Dec 2011 - 21:20 by rokrause
ProgrammingExerciseOptiWS12
General information for programming exercises * We will continue working in the repository from the Algorithms lecture. To discriminate the exercise files we append ...
r12 - 10 Dec 2013 - 13:35 by AnnikaRoehl
ProgrammingExerciseOptiWS13
Short Overview The practical exercises for the lecture Optimization won't be programming exercises. Mostly you have to get familiar with an LP Solver, try to solve ...
r11 - 17 Dec 2015 - 10:47 by AnnikaRoehl
ProgrammingExercises
General information for programming exercises * Each group gets access to a svn directory at https://svn.imp.fu berlin.de/agbio/AlgorithmsWS12/GroupX (Enter your ...
ProgrammingExercisesWS13
General information for programming exercises * Each group gets access to a svn directory at https://svn.imp.fu berlin.de/agbio/AlgorithmsWS13/GroupX * The ...
ProgrammingExercisesWS14
General information for programming exercises * Please note, that there will be an optional C crash course on Friday during the exercises. * Please, fill ...
r9 - 17 Dec 2015 - 17:08 by AnnikaRoehl
ProgrammingGroupList
Page ProgrammingGroupList Enter the account names and your group id into one of the two tables for the practical exercises in the second programming exercise week ...
r82 - 12 Jun 2012 - 06:23 by mauli87
ProgressAicheFall2010
Progress report Stephan Aiche fall 2010 OpenMS * generic labeling framework for MSSimulator is finished * OpenMS 1.7 released * parallel implementation of ...
ProgressAicheSpring2010
Progress report Stephan Aiche fall 2010 OpenMS * new Model for Elution profiles in MSSimulator * started implementation of generic labeling framework (local ...
ProgressAicheSpring2011
Progress report Stephan Aiche sprint 2011 Protease Kinetics * MSSimulator Paper published in JPR * prepared thesis outline AicheOutlineDraft * implemented ...
ProgressAndreotti2010
Progress report Sandro Andreotti fall 2010 Work performed last 6 months * Several programming tasks were performed for the major revision of the ANTILOPE paper ...
ProgressReportEmde-04-2010
Page ProgressReportEmde 04 2010 Progress report Accomplishments in the last six months: General: * Read many papers on variant detection, notes taken here. ...
ProgressReportEmde-05-2011
Page ProgressReportEmde 05 2011 Progress Report (under construction) Accomplishments in the last six months: SplazerS: * redid single end read simulation (compared ...
ProgressReportEmde-10-2010
Page ProgressReportEmde 10 2010 Progress Report Accomplishments in the last six months: Split read mapping: * Finished implementation of splitRazers, poster ...
ProgressReportHu
Page ProgressReportHu The purpose of this page is to make a schedule for my research progress and work plan for the next six months or more. Research progress and ...
ProgressReportHu-05-2011
Page ProgressReportHu 05 2011 The purpose of this page is to make a schedule for my research progress and work plan for the next six months or more. Work performed ...
ProgressReportHu-10-2012
Page ProgressReportHu 10 2012 The purpose of this page is to make a schedule for my research progress and work plan for the next six months or more. Work performed ...
ProgressReportSiragusaFall2010
Page ProgressReportSiragusaFall2010 This is the progress report of Enrico Siragusa for the Fall 2010. Accomplishments up to the Fall 2010 * Familiarized with SeqAn ...
ProgressReportSiragusaSpring2011
Page ProgressReportSiragusaSpring2011 This is the progress report of Enrico Siragusa for the Spring 2011. Accomplishments up to the Fall 2010 Literature Seeds Literature ...
Projektseminar_Advanced_Sequence_Analysis_2013
Praxismodule Applied Sequence Analysis Welcome to the Wiki of the Praxisseminar Applied Sequence Analysis News Times and rooms Rooms and timings Event Day ...
ProtLec0MaterialsWS14
Learning units No learning units for the introductory lecture. Please see the materials for Lecture 1 for the first units. Lectures 00_CPM_WS14_Introduction 00_CPM ...
r7 - 21 Oct 2014 - 13:14 by jpfeuffer
ProtLec10MaterialsWS14
Learning units Learning unit 10A to Protein post translational modifications Learning unit 10B to Exptl. techniques for phosphoproteomics Learning unit 10C to Algorithms ...
ProtLec11MaterialsWS14
Learning units Learning unit 11A to Metabolomics and Metabolites Learning unit 11B to Metabolite Databases Learning unit 11C to Metabolite ID via Spectral Matching ...
ProtLec12MaterialsWS14
Learning units Lecture slides Lecture slides (PPT) Lecture slides (PDF) Exercises Videos
ProtLec1MaterialsWS14
Learning units Learning unit 1A to Introduction to Proteomics and Metabolomics Learning unit 1B to Overview of separation techniques Learning unit 1C to Introduction ...
r9 - 24 Oct 2014 - 13:27 by XiaoLiang
ProtLec2MaterialsWS14
Learning units Learning unit 2A to Chromatography (updated) Learning unit 2B to Mass spectrometry Lecture slides Lecture slides Exercises Exercises about separation ...
r6 - 06 Nov 2014 - 11:40 by jpfeuffer
ProtLec3MaterialsWS14
Learning units Learning unit 3A to Basic Statistics Learning unit 3B to Mixture Models and EM Algorithm Lecture slides Lecture slides (PPT) Lecture slides (PDF ...
r5 - 11 Nov 2014 - 15:24 by XiaoLiang
ProtLec4MaterialsWS14
Learning units Learning unit 4A to Basic Analytical Chemistry Learning unit 4B to Quantification strategies (SWATH, TMT, MRM/AQUA, ... ) Learning unit 4C to Isobaric ...
r3 - 19 Nov 2014 - 19:16 by jpfeuffer
ProtLec5MaterialsWS14
Learning units Learning unit 5A to Label free quantification Learning unit 5B to Map alignment Learning unit 5C to SILAC quantification Lecture slides Lecture slides ...
r5 - 26 Nov 2014 - 11:15 by XiaoLiang
ProtLec6MaterialsWS14
Learning units Learning unit 6A to SRM/MRM Learning unit 6B to MRM and Skyline (Tool) Learning unit 6C to SWATH and OpenSWATH (Tool) Lecture slides Lecture slides ...
r5 - 10 Dec 2014 - 14:15 by XiaoLiang
ProtLec7MaterialsWS14
Learning units Learning unit 7A to Peptide database search Learning unit 7B to Tools for database earch (Tool) Learning unit 7C to FDR estimation Learning unit 7D ...
r5 - 10 Dec 2014 - 15:13 by XiaoLiang
ProtLec9MaterialsWS14
Learning units Learning unit 9A to Protein inference problem Learning unit 9B to ProteinProphet Learning unit 9C to Protein FDR estimates Lecture slides Lecture ...
r5 - 12 Jan 2015 - 15:24 by XiaoLiang
ProteinID
Page ProteinID Progress reports Progress report fall 2010 Section 2 ((content)) Comments MajorRevisionAntilope MyTodos
ProteinStructure
Proteinstrukturen Vorlesungen Date Lecture* *Materials 30.1.2012 Elemente der Strukturbiologie (Krause) Structural Biology 1.2.2012 Review ...
r4 - 09 Feb 2012 - 13:58 by rokrause
ProteomeAnalysis
Proteomics Vorlesungen Date Lecture* *Materials 18.1.2012 Einführung HPLC/MS Intro 23.1.2012 Quantitative Proteomics CPM_WS11_05_Quant_I.pdf ...
r6 - 31 Jan 2012 - 11:23 by rokrause
ProteomicS_SS14
Proteomics, SoSe 2014 (19577) Welcome to the Wiki of the MSc seminar Proteomics. In this seminar we will discuss original articles that deal with the analysis of HPLC ...
ProteomicsVL_WS14
Forschungsmodul: Proteomics VL UE (WiSe 2014) Welcome to the Wiki of the MSc lecture Proteomics (VL: 19400901, UE: 19400902) In this lecture we will cover the basics ...
r17 - 03 Feb 2015 - 15:53 by jpfeuffer
QualityTrim
// ================================================================ // quality_trimmer // =================================== ...
QuantProtP4
Page QuantProtP4 This is the project page of the quantitative proteomics group. Students Mail an alle Gruppenmitglieder: AA2010SS QuantProt bei lists.spline.de ...
QuantProtP4_AMS
AMS 3.0 predicting post translational modification sites Material Paper http://www.biomedcentral.com/1471 2105/11/210/abstract OpenMS docu: http://www bs2.informatik ...
QuantProtP4_Elution
Page QuantProtP4_Elution Project Planning for QuantProtP4 Elution Profile comparison Status Stefan * implement a C code (Main.C, see attachment) to determine ...
QuantProtP4_Fingerprint
Page QuantProtP4_Fingerprint Project Planning for QuantProtP4 Mass fingerprinting (1) Digestion of protein sequences Naive tryptic digestion (split after every ...
r9 - 19 Jul 2010 - 18:35 by cstandfu
QuantProtP4_emPAI
Page QuantProtP4_emPAI Exponentially Modified Protein Abundance Index (emPAI) for Estimation of Absolute Protein Amount in Proteomics by the Number of Sequenced Peptides ...
r3 - 05 Jul 2010 - 13:57 by annakriv
RNAAligner
Area Computational RNA analysis Topic Extending structural RNA alignment algorithm to find regulatory motifs in mRNAs The project builds on work on structural ...
RNA_Bioinformatics
RNA Bioinformatics (S) (19401111), SoSe 2016 Welcome to the Wiki of the seminar RNA Bioinformatics. PLEASE NOTE THAT WE WILL USE THE NEW KVV SYSTEM. CLICK HERE to ...
Raw_results
Page Raw_results Raw results of benchmark Dataset I Runs completed: Error Rate 5 10 Sample 0.1 1 0.1 1 RazerS done done done done ...
Razers2Revision
Page Razers2Revision General Points TODO: Wait for evaluation of Hobbes on human, execute class, update tables. Manuel : Section S5 was updated to reflect the usage ...
ReadLengthSplicing
Mich hat es interessiert zu wissen wie viele exons wir tatsächlich verlieren, wenn wir nicht auf die spliced reads achten würden. Bzw wie sich diese verteilung ...
r11 - 02 Sep 2010 - 02:56 by balcazar
ReadMapper
Devising read mapping strategies in KNIME Area Read mapping quality, Mappability, KNIME Topic The main goal of this thesis is to devise strategies to compute a) ...
r5 - 26 Aug 2013 - 10:07 by kys
ReadMappingBWT
Read mapping Vorlesungen Date Lecture* *Materials 21.11.2011 Read mapping overview and the BWT Read mapping survey, Read mapping benchmark 23.11 ...
Reads
reads.fastq This page contains the read.fastq file
ReinertAppointment
OUTDATED! Go to: http://www.mi.fu berlin.de/en/inf/groups/abi/teaching/office hours/ if (window.location.search == "") document.write(' back'); else { var date ...
RepeatMasking
Repeat Masking Repeats in DNA Sequenzen sind ein häufig beobachtetes Phänomen. Insbesondere in den ersten Schritten der Genome Analyse verursachen sie Probleme, ...
ResearchCooperations
Research Cooperations The Reinert group at FU Berlin maintains research cooperations with German and international research groups. Note that this list here is not ...
ResearchLogAlessandroMammana
Page ResearchLogAlessandroMammana ((short description what this page is about)) Section 1 ((content)) Section 2 ((content)) Comments
ResearchLogOliverStolpe
ResearchLogOliverStolpe ((short description what this page is about)) Section 1 ((content)) Section 2 ((content)) Comments
NEW - 28 Jan 2014 - 14:45 by OliverStolpe
ResearchLogReneMaerker
Algorithm Engineering for High Throughput Sequencing Data Summary During the last five years modern sequencing technologies have brought a super exponential growth ...
ResearchLogTemesgenDadi
Metagenomics. Background Metagenomics is the study of genetic material (metagenome) recovered directly from environmental samples. In these environmental samples ...
r3 - 20 Mar 2014 - 08:12 by TemesgenDadi
ResearchLogTemesgenDadi18032014
Meeting/Consultation minute 18 03 2014 Discussed Topics: * Genovo: Genovo is written in C . * Other metagenomic assemblers: Metavelvet, an extension of ...
NEW - 20 Mar 2014 - 08:12 by TemesgenDadi
ResearchLogXintianYOU
ResearchLogXintianYOU Developing tools for high throughput sequencing technology Section 1 ((content)) Section 2 ((content)) Comments
ResearchLogs
Research Logs * Genome Comparison (Birte Kehr, Manuel Holtgrewe) * Precursor Selection (Alexandra Zerck) * Indices and Applications (David Weese) * BWTIndex ...
r8 - 20 Oct 2014 - 14:16 by cxpan
RnaAnalysis
RNA analysis Vorlesungen Date Lecture* *Materials 11.1.2012 RNA folding rna.pdf 16.1.2012 RNA alignment rna2.pdf Übungen Content Exercise ...
r4 - 16 Jan 2012 - 23:14 by rokrause
RnaSeqMSplazers
PISB SeqAn Projekt RNA Seq: Mapping von RNA reads mit MSplazer Hintergrund: Mapping von RNA reads Im Gegensatz zum Whole Genome Sequencing, wo ein kompletter ...
RnaSeqP4
Page RnaSeqP4 This is the project page of the RNA Seq group. Students Mail an alle Gruppenmitglieder: AA2010SS RNASeq bei lists.spline.de Name email Corinna ...
r51 - 22 Jul 2010 - 14:30 by cblasse
RnaSeqReadSimulator
PISB SeqAn RNA Seq Read Simulator Hintergrund: RNA Seq Simulation Simulierte Daten leisten wichtige Dienste bei der Entwicklung, Fehlersuche und Bewertung von Software ...
SIMDDpAlgo
SIMDDpAlgo SIMD extension of the standard DP algorithms in SeqAn Introduction Newer processors are shipped with 16 registers having an extended width of 128 bit ...
SS13Lecture10Materials
Here is all the material for the lecture 10 * Download the script
SS13Lecture11Materials
Here is all the material for the lecture 11 * Download the script
SS13Lecture12Materials
The lecture on Thursday 4.7.2013 will start 10:30 Here is all the material for the lecture 9 * Download the script
SS13Lecture13Materials
Here is all the material for the lecture 11 * Download the script
SS13Lecture1Materials
Here is all the material for the lecture 1 * Download the script.pdf
SS13Lecture2Materials
Here is all the material for the lecture 1 * See lecture 1
SS13Lecture3Materials
Here is all the material for the lecture 3 * Download the script.pdf * Watch a previous lecture as a video lower res or high res
SS13Lecture4Materials
Here is all the material for the lecture 4 * Download the script * exercise_4.pdf
SS13Lecture5Materials
Here is all the material for the lecture 5 and 6 * Download the script
SS13Lecture6Materials
Here is all the material for the lecture 6 * Download the script
SS13Lecture7Materials
Here is all the material for the lecture 6 * Download the script
SS13Lecture8Materials
Here is all the material for the lecture 6 * See last script
SS13Lecture9Materials
Here is all the material for the lecture 9 * Download the script
SS14Lecture11Materials
Here is all the material for the lecture 7 and 8 * Download the script:
SS15Lecture10Materials
Here is all the material for the lecture 12 * Download the script
SS15Lecture9Materials
Here is all the material for the lecture 12 * Download the script
Scan
Page Scan Scanning scanning scanning... How to scan * Using Network ScanGear Software * Install the scanner driver by following the instructions in the Orgaweb ...
SearchJoinTodo
Page SearchJoinTodo ((short description what this page is about)) TODO * Put FileReader/FileWriter into extras DONE * Optimize global Myers DONE * Backtracking ...
SeedDesign
Page SeedDesign This page contains an essay on the state of the art of seed design. The goal of this essay is to give an unifying view on seed design. Most relevant ...
SeedingStrategies
Implementation and evaluation of index based seeding strategies in SeqAn Area Substring Indices, read mapping, local alignment, q mer indices Topic The goal of this ...
SegementAligner
PISB SeqAn Teilprojekte Segment Aligner Hintergrund: Hierarchisches Genomalignment Um das Alignment ganzer Genome zu ermöglichen, werden in der Regel zunächst ...
SeqAn
General info n this part of the Practical course sequence analysis you will be confronted with the situation of prototyping NGS analysis programs with an available ...
SeqAnRetreat2010
Information about the SeqAn retreat Please keep checking for updates! Schedule The meeting begins on Monday, 04 Oct 2010 at 10 a.m. and ends on Friday, 08 Oct 2010 ...
SeqAnRetreat2011
Information about the SeqAn workshop 2011 The SeqAn BioStore website is up. Please find information here.
SeqAnRetreat2012
Guidelines for the Organization of Meetings Technical Factors * find/reserve a room SeqAn Retreat March 2012 with Illumina: T9/053 * look into technical ...
SeqAnRetreatInternal
Page SeqAnRetreatInternal Confirmed Participants Social Event Options Fernsehturm ...
SequenceAlignment
Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Der letzte Abschnitt, "Banded alignment", wird nicht relevant für die Klausur sein. Skript: pairwise ...
SequenceAlignmentWS11
Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: alignment.pdf Übungen: Inhalt Datei Material 4. Übung A4.pdf 5. Übung ...
r10 - 23 Nov 2011 - 16:17 by mauli87
SequenceAlignmentWS12
Page SequenceAlignmentWS12 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * alignment.pdf Videos: * Vorlesungsvideo Alignment1 ...
r12 - 05 Dec 2012 - 04:31 by tmasar
SequenceAlignmentWS13
Page SequenceAlignmentWS13 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * alignment.pdf Videos: * Vorlesungsvideo Alignment1 ...
r5 - 19 Nov 2013 - 01:20 by thwelln31416
SequenceAlignmentWS14
Page SequenceAlignmentWS14 Vorlesung Bitte lesen Sie das Skript vor der Vorlesung durch. Skript: * alignment.pdf Videos: Video 3 ist defekt. Hier das Vorlesungsvideo ...
Sequence_analysi_2013
Sequence Analysis SS 2013 Welcome to the Wiki of the Lecture Sequence Analysis. This module consists of 2 hours lecture, 2 hours exercise and 2 hours seminar. The ...
Sequence_analysis_2013
THIS IS STILL OLD Times and rooms Rooms and timings Event Day Time Address Room Lecture Tue 10 12 Takustr. 9 005 Lecture Thu 10 ...
Sequence_analysis_2014
Sequence Analysis, SoSe 2014 (LV Nr. 19716, 19716a, 19716b) Welcome to the Wiki of Sequence Analysis. This module consists of 2 hours lecture, 2 hours exercise ...
Sequence_analysis_2015
Sequence Analysis, SoSe 2015 (LV Nr. 19401601 (V), 19401602 (Ü), 19401611 (S)) Welcome to the Wiki of Sequence Analysis. This module consists of 2 hours lecture ...
Sequence_analysis_2016
Sequence Analysis, SoSe 2016 *(LV Nr. 19401601 (V), 19401602 (Ü), 19401611 (S)) Welcome to the Wiki of Sequence Analysis. Dear Students. We will use for the lecture ...
ShortPaperPresentations
Page ShortPaperPresentations Groups and papers List of groups together with the papers to be presented during the lecture on January 18. Details are presented on ...
r4 - 15 Jan 2011 - 01:13 by penzla
SimpleBowtie
Simple Bowtie Bowtie ist ein "ultrafast and memory efficient" Read Mapper 1 der auf der Burrows Wheeler Transformation (BWT) basiert. Die BWT eines Textes T ist ...
SlaganSupermap
SLAGAN Input: two genomic dna sequences in FASTA file(s) Generation of local alignments (Svenja) SLAGAN uses the CHAOS aligner for this phase: * finding seeds ...
r11 - 12 Jul 2010 - 11:57 by FelixHeeger
SnippetsAnneKatrin
Page SnippetsAnneKatrin This is where I write my weekly goals. all time todos: * make splitRazers project page * add link in seqanswers forum srp thread ...
SnpStore
Page SnpStore Short overview of SnpStore implementation. General structure Here is a general pseduocode like outline of how SnpStore proceeds. The functionality ...
Sol
Lösungen zu Übung 1 Solution for Exercise 2 only so far. Excercise 2 Find all occurrences! t = ACACTCCCCCGACAACC p = ACAACC occurs only at position 6 (startposition ...
NEW - 16 Apr 2012 - 10:26 by cellar
SpaceEfficientBWTConstruction
SpaceEfficientBWTConstruction Implementation of a fast and memory efficient BWT construction algorithm. Background The Burrows Wheehler Transform transforms a text ...
r7 - 11 Jul 2013 - 14:19 by zer
SpecificationsAR
Write a SeqAn program that: * reads in....
StellarMotifFinder
Topic Motif finding using the STELLAR engine and SeqAn::TCoffee The project builds on work on exact local alignment by Kehr, Rausch, Emde and Reinert 1,2 . STELLAR ...
StellarMotifFinderWeeklyReports
Page StellarMotifFinderWeeklyReports These are brief weekly reports about the status of the BSc Thesis StellarMotifFinder. Week 1 (25.07.2012 31.07.2012) * Tutorial ...
r4 - 31 Aug 2012 - 07:46 by shalini6
StellarTuning
Page StellarTuning export CPUPROFILE=stellar.prof LD_PRELOAD="/usr/lib/libprofiler.so.0" ./stellar d hs_ref_chr10.fa q contig_0000aa.fa.2000 l 30 k 16 e 0.03 ...
StructuralAndCopyNumberVariationV1
Page StructuralAndCopyNumberVariationV1 Method using read depth from genome resequencing without case/control pairs. Implemented in pipeline at MPI MG for Stefan Haas ...
StundenPlan
StundenPlan Reinert / Piro / Marsico SoSe 2017 time: Monday Tuesday Wednesday Thursday Friday 8 10 10 12 SeqAnalys (VL) 051/t9 ...
SuffixArrayConstruction
Implementation of Suffix Array Construction Algorithms The SDSL (Succinct Data Structure Library) has various implementations of string indices based on suffix arrays ...
TeilnehmerIn
TeilnehmerIn ((short description what this page is about)) Section 1 ((content)) Section 2 ((content)) Comments
NEW - 26 Oct 2015 - 11:37 by coombercel
ThesesHome
Theses Page OUTDATED! Go to: https://kvv.imp.fu berlin.de/x/8RK4cp Available topics * If you are interested in doing your thesis in algorithmic bioinformatics ...
ThesisAnnoAlign
Page ThesisAnnoAlign Brief overview Next generation sequencing methods have given rise to a whole new set of algorithmic problems. Using the principles of huge amounts ...
r3 - 16 Nov 2009 - 17:06 by mheuser
ThesisAnnoAlignReports
Page ThesisAnnoAlignReports Back to ThesisAnnoAlign. Week 0 (21.10.2009 25.10.2009) * First meeting with David and Marcel * Recieved topic and short introduction ...
r6 - 19 Jan 2010 - 23:44 by maheuser
ThesisApproxHammingMatch
Approximate String Matching (Hamming Distance) This Bachelor thesis gets you in touch with current research for string matching, modern implementation in C /SeqAn ...
ThesisBScMyriMatch
Implementation and Evaluation of a Myrimatch Adapter Student Dimitri Schachmann Academic Advisor Prof. Dr. Knut Reinert, Chris Bielow Expose The goal of ...
r5 - 20 Apr 2012 - 12:58 by schachma
ThesisCNVs
Page ThesisCNVs Detektion von Copy Number Variationen in Sequenzierdaten $ Student: Kerstin Neubert $ Betreuer: Anne Katrin Emde, Prof. Dr. Knut Reinert Zusammenfassung ...
r20 - 29 Jul 2010 - 22:35 by neubertk
ThesisGPGPUSeqan
Page ThesisGPGPUSeqan Myers Bit Vector Algorithm on GPU for Seqan Massiv parallelization of Myers Fast Bit Vector Algorithm for Approximate String Matchinsg using ...
r28 - 22 Mar 2011 - 21:35 by llangner
ThesisGenomesPerMail
Page ThesisGenomesPerMail ((short description what this page is about)) Expose Rene, please write an expose for the thesis here with the following tasks. Tasks ...
ThesisIncrementalIndices
Page ThesisIncrementalIndices ((short description what this page is about)) Currently working On Performance tests and improvement of Journal String Class Section ...
NEW - 30 Sep 2009 - 12:47 by pyl
ThesisMCRazer
ThesisMCRazer Check, whether abstract, description, and literature are in CMS Parallelization of RazerS $ Student: Martin Riese $ Academic Advisor: David Weese ...
r4 - 03 Feb 2010 - 08:03 by mriese
ThesisMCRazerInOfficialMain
Page ThesisMCRazerInOfficialMain * Weekly reports * TODO * Parallel Options * Results * Versions
r3 - 15 Mar 2010 - 08:20 by mriese
ThesisMCRazerMcSpeedDifferentNumberOfCores
Page ThesisMCRazerMcSpeedDifferentNumberOfCores * Auf Tanne * Reference: chr22.fa * Reads: SRR006387.fastq_1.00000 (100,000) cores real time *cpu ...
NEW - 22 Mar 2010 - 21:38 by mriese
ThesisMCRazerMcWindowBlock
Page ThesisMCRazerMcWindowBlock * Auf Tanne * Reference: chr22.fa * Reads: SRR006387.fastq_1.00000 * Used real part of time out put due to the lack of ...
r2 - 17 Mar 2010 - 16:24 by mriese
ThesisMCRazerParallelOptions
Page ThesisMCRazerParallelOptions Option Details and Options Pro Contra TBB? Parallelize by Genome /RazerS Piktogram Parallel by Genome ...
r3 - 14 Feb 2010 - 19:21 by mriese
ThesisMCRazerQgrams
Page ThesisMCRazerQgrams * 5 Millionen Reads von Yuruba auf Chromosom 22 (ca. 2x35Mb) * id i 98 nc 8 bt 1 ws 50000 * razerMC 1.3 * Matches beinhalten ...
r6 - 15 Apr 2010 - 14:05 by mriese
ThesisMCRazerResults
Page ThesisMCRazerResults * Open addressing * speed test * size * higher Q's * speed test 1 * window * parallel by reads * speed ...
r5 - 29 Mar 2010 - 06:58 by mriese
ThesisMCRazerSizeOA
Page ThesisMCRazerSizeOA * 7,000,000 reads * Yoruba * q length sa length dir size normal (Mb) size open addressing (Mb) * 11 626700240 9937467 ...
NEW - 29 Mar 2010 - 07:00 by mriese
ThesisMCRazerSpeedOA
Page ThesisMCRazerSpeedOA what was the used q here? Can you make for a first estimate q =10, q=14, q=22 (f course only in open adressing?) Next question would be, ...
r7 - 14 Mar 2010 - 18:18 by mriese
ThesisMCRazerVersions
Page ThesisMCRazerVersions Version of Parallel RazerS: Number Revision Remarks 1.0 5414 With smaller critical reagion, Option to set the number of threads ...
r7 - 19 Jun 2010 - 19:57 by mriese
ThesisMCRazerWeeklyReports
Page ThesisMCRazerWeeklyReports Week 1 (25.1.) * Q gram index with open hashing Week 2 (1.2.) * Adapt mapRead functions to parallelism * Overview over parallelization ...
r13 - 22 Mar 2010 - 21:39 by mriese
ThesisMCRazerWorkPlan
ThesisMCRazerWorkPlan * Implementieren des Open hashing Q gram index * Paralleles filtern der Referenz in über kürzere Abschnitte dann parallel verifizieren ...
r3 - 26 Jan 2010 - 19:03 by mriese
ThesisMeganRazers
Page ThesisMeganRazers brief overview * continue/finish implementation of RazerBlastS, an adaptation of RazerS, aimed at providing BLAST like options and compatible ...
r3 - 15 Sep 2009 - 13:28 by hauswede
ThesisMeganRazersReports
Page ThesisMeganRazersReports Weekly Reports for the Bachelor Thesis "Comparative Genomics with MEGAN and RazerS" by Hannes Hauswedell Week 1 (2009 07 11..2009 07 ...
r9 - 29 Sep 2009 - 19:55 by hauswede
ThesisNGSOverlap
Overlap Module for NGS Pipeline Summary The overlap module merges the information retained by read mapping to a genome with annotation information (for example genes ...
r4 - 16 Aug 2009 - 19:30 by krakau
ThesisNgsCleaning
NGS Data Cleaning TODO: Manuel Note that we can shift the focus of the thesis much stronger towards programming/implementation if you want to program! Next Generation ...
ThesisPalindromes
Complemented palindromes Zusammenfassung Implementierung und Vergleich drei verschiedener Ansätze zum Finden von maximalen, komplementären Palindromen einer signifikanten ...
r3 - 10 Sep 2009 - 09:40 by fheeger
ThesisPalindromesBerichte
Wochenberichte Woche 1 * naiven (brute force) Algorithmus zum finden von Palindromen implementiert * externe inverteted suffix array Struktur implementiert ...
r5 - 15 Sep 2009 - 07:52 by fheeger
ThesisParallelismInSeqan
Parallelism In The SeqAn Library The purpose of this thesis is to allow "easy parallelism" in the SeqAn library. This will consist of identifying parts of the library ...
ThesisParallelismInSeqanPatterns
Parallelism In The SeqAn Library: Patterns for Parallelization A brief summary of patterns for parallelization, based on Massingill et al. 2000 . Finding Concurrency ...
ThesisParallelismInSeqanWeeklyReports
Parallelism In The SeqAn Library: #8220;Weekly #8221; Reports Weekly reports about ThesisParallelismInSeqan. General * 05/08 #8211;05/11: * Work on presentation ...
ThesisParallelismInSeqanWorkSchedule
Parallelism In The SeqAn Library: Schedule Tentative Schedule Tentative total: 25 weeks. Review of existing literature and other implementations (2 #8211;4 weeks ...
ThesisProposals
Thesis Proposals OUTDATED! Go to: https://kvv.imp.fu berlin.de/x/8RK4cp Here is the section for BSc and MSc students. At the beginning of the thesis the student and ...
ThesisSCFGs
Page ThesisSCFGs ((short description what this page is about)) (1) The software part and what has been done so far: parsing of scfg data from files transformation ...
ThesisScalingGenomeAlignment
Scaling genome alignment to hundreds of genomes Topic With the rapid development of next generation sequencing technologies more and more genomes are being sequenced ...
ThesisScoreMatrix
Substitution Matrix Generation Algorithms This Bachelor thesis gets you in touch with current research for string matching, modern implementation in C /SeqAn, sound ...
ThesisSeqAnBlast
BLAST Implementation in SeqAn Es soll ein BLASTX (Nukleotidsequenz 6 fach translatieren und gegen Proteindatenbank abgleichen) 'from scratch' für die SeqAn Bibliothek ...
r12 - 15 Sep 2012 - 08:31 by fsiemer
TutorS
List of current tutors Summer Semester 2015 LV (Title) Tutor's Name Tutor's Email Supervisor (Prof/WiMi) ... ...
r11 - 22 Feb 2016 - 10:41 by thwelln31416
UeZ
Page UeZ ((short description what this page is about)) Section 1 ((content)) Section 2 ((content)) Comments
NEW - 11 Jan 2013 - 14:18 by Krannich479
VariantDetectionAppliedPapers
Page VariantDetectionAppliedPapers Collection of applied variant detection papers, with comments. Applied Papers Genome wide mapping and assembly of structural variant ...
VariantDetectionPapers
Page VariantDetectionPapers Remarks to papers concerning variant detection in NGS data. Method Papers Simple variation VarScan: variant detection in massively parallel ...
VariantDetectionPapersSVformation
Page VariantDetectionPapersSVformation Collection of papers about classification of structural variants (SVs) and formation processes associated with different classes ...
VariantDetectionReviewPapers
Page VariantDetectionReviewPapers A collection of review papers concerning variant detection, not yet with comments. Reviews Genome structural variation discovery ...
ViralGenomes
Page ViralGenomes Non collinear alignments of viral genomes Introduction This is part of advanced algorithms in bioinformatics: genome comparison. I would like to ...
r5 - 10 Jun 2010 - 16:55 by homilius
ViralIntegration
The data for this project comes from the company febit. The goal is to: 1. Develop a local read mapper for color spaced reads. 2. To apply it to find viral integration ...
r12 - 18 Jul 2010 - 10:29 by cblasse
VocabularyAnneKatrin
Page VocabularyAnneKatrin Here I collect pieces of information and "vocabulary" that at some point seemed important. Mixture Models In statistics, a probability mixture ...
Vortrag
Page Vortrag Vortag Aufbau neu * 3min Read Mapping (Basti) * Grundlagen/Probleme (done) * 11min Projekt introduction (Basti)(done) * Motivation ...
WebHome
Return to ABI Homepage DEPRECATED! Go to our new wiki: https://wikis.fu berlin.de/display/abi/ Available Wiki Pages Table of Contents (Z A) Teaching ...
WebLeftBar
* ABI Library * Consultations Knut Reinert * Contact * Events, Conferences, Talks * Members * Projects * Publications * Teaching * Theses ...
WebNotify
* Main.WikiGuest example #64;your.company __ .WebChangesAlert, ., .UserRegistration
WebPreferences
ABI Web Preferences The following settings are web preferences of the ABI web. These preferences overwrite the site level preferences in . and , and can be ...
WebRss
" else="Wiki's ABI web"}% /ABI
WebStatistics
Statistics for ABI Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: ...
WeeklyReport
Page WeeklyReport Weekly reports about this master thesis: "Genomes per EMail efficient compression of biological sequences". . Week 1 (24.05.2010 30.05.2010 ...
WeeklyReportDFG
Weekly Report for the DFG project: Algorithm Engineering for High Throughput Sequencing Data Summarizes the weekly progress of the DFG project. Jul 2011 * 01. ...
WeeklyWorkProgressBScJournalingRawSequences
WeeklyWorkProgressBScJournalingRawSequences Weekly Progress of the BSc Thesis: Journaling Raw Sequences Kick of Meeting ((content)) Week 1 ((content)) Comments ...
WholeTranscriptomeAnalysis
MSc Thesis Whole transcriptome and miRNome analysis from next generation sequencing data Remark This thesis will be a joint project of the Algorithmische Bioinformatik ...
Worklog_Hauswedell
Page Worklog_Hauswedell Project Work log Hauswedell Friday, 25.06.2010: * second "real" meeting with Thieme to do planning and division of work * got access ...
Worklog_Thieme
Project Work log Thieme Friday, 25.06.2010: * second meeting with Hauswedell to do planning and division of work * adding source code to svn * try different ...
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